CRANberries

Fri, 19 Apr 2024

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

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

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

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

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

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Thu, 18 Apr 2024

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Wed, 17 Apr 2024

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

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

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

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

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

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

More information about DataPackageR at CRAN
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Tue, 16 Apr 2024

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Mon, 15 Apr 2024

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

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

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

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

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

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

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

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Sun, 14 Apr 2024

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

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

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Sat, 13 Apr 2024

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

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Fri, 12 Apr 2024

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

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

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

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

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

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

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

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

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

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

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Thu, 11 Apr 2024

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

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

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New package sgboost with initial version 0.1.0
Package: sgboost
Title: Sparse-Group Boosting
Version: 0.1.0
Description: Sparse-group boosting to be used in conjunction with the 'mboost' for modeling grouped data. Applicable to all sparse-group lasso type problems where within-group and between-group sparsity is desired. Interprets and visualizes individual variables and groups.
Imports: dplyr, mboost, stringr, rlang, tibble, ggplot2, ggforce
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/FabianObster/sgboost
BugReports: https://github.com/FabianObster/sgboost/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-10 20:03:03 UTC; fabia
Author: Fabian Obster [aut, cre, cph]
Maintainer: Fabian Obster <fabian.obster@unibw.de>
Repository: CRAN
Date/Publication: 2024-04-11 11:20:02 UTC

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

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

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Wed, 10 Apr 2024

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Tue, 09 Apr 2024

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

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

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New package complex with initial version 1.0.0
Package: complex
Title: Time Series Analysis and Forecasting Using Complex Variables
Version: 1.0.0
Date: 2024-04-09
URL: https://github.com/config-i1/complex
BugReports: https://github.com/config-i1/complex/issues
Language: en-GB
Description: Set of function implementing the instruments for complex-valued modelling, including time series analysis and forecasting. This is based on the monograph by Svetunkov Sergey and Svetunkov Ivan "Complex-valued Econometrics with Examples in R" which is in press by Springer (expected to be published in 2024).
License: LGPL-2.1
Depends: R (>= 3.5.0), greybox (>= 0.5.0), legion
Imports: stats, graphics, nloptr, mvtnorm, pracma
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, knitr, rmarkdown
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-04-09 11:29:51 UTC; config
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Repository: CRAN
Date/Publication: 2024-04-09 16:50:05 UTC

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New package stringx with initial version 0.2.8
Package: stringx
Title: Replacements for Base String Functions Powered by 'stringi'
Version: 0.2.8
Date: 2024-04-09
Description: English is the native language for only 5% of the World population. Also, only 17% of us can understand this text. Moreover, the Latin alphabet is the main one for merely 36% of the total. The early computer era, now a very long time ago, was dominated by the US. Due to the proliferation of the internet, smartphones, social media, and other technologies and communication platforms, this is no longer the case. This package replaces base R string functions (such as grep(), tolower(), sprintf(), and strptime()) with ones that fully support the Unicode standards related to natural language and date-time processing. It also fixes some long-standing inconsistencies, and introduces some new, useful features. Thanks to 'ICU' (International Components for Unicode) and 'stringi', they are fast, reliable, and portable across different platforms.
BugReports: https://github.com/gagolews/stringx/issues
URL: https://stringx.gagolewski.com/, https://github.com/gagolews/stringx
License: GPL (>= 2)
Depends: R (>= 4.1.0)
Imports: stringi (>= 1.7.2)
Suggests: realtest (>= 0.2.1)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-09 08:06:57 UTC; gagolews
Author: Marek Gagolewski [aut, cre, cph]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Repository: CRAN
Date/Publication: 2024-04-09 11:30:02 UTC

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New package leakyIV with initial version 0.0.1
Package: leakyIV
Title: Leaky Instrumental Variables
Version: 0.0.1
Date: 2024-04-09
Maintainer: David S. Watson <david.s.watson11@gmail.com>
Description: Instrumental variables (IVs) are a popular and powerful tool for estimating causal effects in the presence of unobserved confounding. However, classical methods rely on strong assumptions such as the exclusion criterion, which states that instrumental effects must be entirely mediated by treatments. In the so-called "leaky" IV setting, candidate instruments are allowed to have some direct influence on outcomes, rendering the average treatment effect (ATE) unidentifiable. But with limits on the amount of information leakage, we may still recover sharp bounds on the ATE, providing partial identification. This package implements methods for ATE bounding in the leaky IV setting with linear structural equations. For details, see Watson et al. (2024) <doi:10.48550/arXiv.2404.04446>.
License: GPL (>= 3)
URL: https://github.com/dswatson/leakyIV
BugReports: https://github.com/dswatson/leakyIV/issues
Imports: data.table, corpcor, glasso, Matrix, mvnfast, foreach
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-09 08:34:39 UTC; dswatson
Author: David S. Watson [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-09 09:20:03 UTC

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New package micronutr with initial version 0.1.1
Package: micronutr
Title: Determining Vitamin and Mineral Status of Populations
Version: 0.1.1
Description: Vitamin and mineral deficiencies continue to be a significant public health problem. This is particularly critical in developing countries where deficiencies to vitamin A, iron, iodine, and other micronutrients lead to adverse health consequences. Cross-sectional surveys are helpful in answering questions related to the magnitude and distribution of deficiencies of selected vitamins and minerals. This package provides tools for calculating and determining select vitamin and mineral deficiencies based on World Health Organization (WHO) guidelines found at <https://www.who.int/teams/nutrition-and-food-safety/databases/vitamin-and-mineral-nutrition-information-system>.
License: GPL (>= 3)
Depends: R (>= 2.10)
Suggests: covr, knitr, rmarkdown, spelling, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-GB
LazyData: true
URL: https://nutriverse.io/micronutr/, https://github.com/nutriverse/micronutr
BugReports: https://github.com/nutriverse/micronutr/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-08 20:59:55 UTC; ernestguevarra
Author: Ernest Guevarra [aut, cre, cph] , Nicholus Tint Zaw [aut, cph]
Maintainer: Ernest Guevarra <ernest@guevarra.io>
Repository: CRAN
Date/Publication: 2024-04-09 09:00:02 UTC

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New package kldest with initial version 1.0.0
Package: kldest
Title: Sample-Based Estimation of Kullback-Leibler Divergence
Version: 1.0.0
Maintainer: Niklas Hartung <niklas.hartung@gmail.com>
Description: Estimation algorithms for Kullback-Leibler divergence between two probability distributions, based on one or two samples, and including uncertainty quantification. Distributions can be uni- or multivariate and continuous, discrete or mixed.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, RANN
Suggests: knitr, rmarkdown, KernSmooth, testthat (>= 3.0.0)
URL: https://niklhart.github.io/kldest/
BugReports: https://github.com/niklhart/kldest/issues
NeedsCompilation: no
Packaged: 2024-04-08 13:15:50 UTC; niklashartung
Author: Niklas Hartung [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-09 08:20:02 UTC

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New package spaths with initial version 1.1.0
Package: spaths
Title: Shortest Paths Between Points in Grids
Version: 1.1.0
Description: Shortest paths between points in grids. Optional barriers and custom transition functions. Applications regarding planet Earth, as well as generally spheres and planes. Optimized for computational performance, customizability, and user friendliness. Graph-theoretical implementation tailored to gridded data. Currently focused on Dijkstra's (1959) <doi:10.1007/BF01386390> algorithm. Future updates broaden the scope to other least cost path algorithms and to centrality measures.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/ChristianDueben/spaths
BugReports: https://github.com/ChristianDueben/spaths/issues
Imports: base (>= 4.0.0), Rcpp (>= 1.0.9), data.table, parallel, stats, utils
LinkingTo: Rcpp
Suggests: terra, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-04-08 08:41:16 UTC; ac143977
Author: Christian Dueben [aut, cre]
Maintainer: Christian Dueben <christian.dueben@uni-hamburg.de>
Repository: CRAN
Date/Publication: 2024-04-09 07:50:02 UTC

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Mon, 08 Apr 2024

New package stcpR6 with initial version 0.9.6
Package: stcpR6
Title: Sequential Test and Change-Point Detection Algorithms Based on E-Values / E-Detectors
Version: 0.9.6
Description: Algorithms of nonparametric sequential test and online change-point detection for streams of univariate (sub-)Gaussian, binary, and bounded random variables, introduced in following publications - Shin et al. (2024) <doi:10.48550/arXiv.2203.03532>, Shin et al. (2021) <doi:10.48550/arXiv.2010.08082>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: methods, Rcpp (>= 1.0.12), R6
LinkingTo: Rcpp
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
URL: https://github.com/shinjaehyeok/stcpR6
BugReports: https://github.com/shinjaehyeok/stcpR6/issues
NeedsCompilation: yes
Packaged: 2024-04-08 04:32:28 UTC; shinj
Author: Jaehyeok Shin [aut, cre]
Maintainer: Jaehyeok Shin <shinjaehyeok@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-08 15:30:02 UTC

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New package mtanan with initial version 0.0.1
Package: mtanan
Title: Single Valued Neutrosophic Kruskal-Wallis and Mann Whitney Tests
Version: 0.0.1
Description: Dealing with neutrosophic data in single valued form using score, accuracy and certainty functions to calculate ranks of Single Valued Neutrosophic Set (SVNS), also to calculate the Mann-Whitney test, and making a post-hoc test after rejecting the null hypothesis using the Neutrosophic Statistics Kruskal-Wallis test. For more information see Miari, Mahmoud; Anan, Mohamad Taher; Zeina, Mohamed Bisher(2022) <https://digitalrepository.unm.edu/nss_journal/vol51/iss1/60/>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-07 10:23:41 UTC; HP
Author: Mohamad Taher Anan [aut, cre] , Mohamad Bisher Zeina [aut], Aya Khantomani [aut], Mahmoud Miari [aut]
Maintainer: Mohamad Taher Anan <mtanan200988@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-08 15:20:02 UTC

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New package MatchGATE with initial version 0.0.10
Package: MatchGATE
Title: Estimate Group Average Treatment Effects with Matching
Version: 0.0.10
Description: Two novel matching-based methods for estimating group average treatment effects (GATEs). The match_y1y0() and match_y1y0_bc() functions are used for imputing the potential outcomes based on matching and bias-corrected matching techniques, respectively. The EstGATE() function is employed to estimate the GATE after imputing the potential outcomes.
License: GPL-3
Encoding: UTF-8
Imports: locpol, stats
NeedsCompilation: no
Packaged: 2024-04-07 06:19:52 UTC; dell
Author: Zhaoqing Tian [aut, cre, com] , Peng Wu [aut, ths] , Yilin Chen [dtc]
Maintainer: Zhaoqing Tian <tzqluck@163.com>
Repository: CRAN
Date/Publication: 2024-04-08 15:10:05 UTC

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New package gtexture with initial version 1.0.0
Package: gtexture
Title: Generalized Application of Co-Occurrence Matrices and Haralick Texture
Version: 1.0.0
Description: Generalizes application of gray-level co-occurrence matrix (GLCM) metrics to objects outside of images. The current focus is to apply GLCM metrics to the study of biological networks and fitness landscapes that are used in studying evolutionary medicine and biology, particularly the evolution of cancer resistance. The package was developed as part of the author's publication in Physics in Medicine and Biology Barker-Clarke et al. (2023) <doi:10.1088/1361-6560/ace305>. A general reference to learn more about mathematical oncology can be found at Rockne et al. (2019) <doi:10.1088/1478-3975/ab1a09>.
License: MIT + file LICENSE
URL: <https://rbarkerclarke.github.io/gtexture/>
BugReports: https://github.com/rbarkerclarke/gtexture/issues
Imports: dlookr, dplyr (>= 1.0), fitscape (>= 0.1), igraph, magrittr (>= 2.0), rlang, tidyr
Suggests: stats, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-08 03:55:44 UTC; stephbc
Author: Rowan Barker-Clarke [aut, cre] , Raoul Wadhwa [aut] , Davis Weaver [aut], Jacob Scott [aut]
Maintainer: Rowan Barker-Clarke <rowanbarkerclarke@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-08 15:30:05 UTC

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New package gamma with initial version 1.0.5
Package: gamma
Title: Dose Rate Estimation from in-Situ Gamma-Ray Spectrometry Measurements
Version: 1.0.5
Description: Process in-situ Gamma-Ray Spectrometry for Luminescence Dating. This package allows to import, inspect and correct the energy shifts of Gamma-ray spectra. It provides methods for estimating the gamma dose rate by the use of a calibration curve as described in Mercier and Falguères (2007). The package only supports Canberra CNF and TKA files.
License: GPL-3
URL: https://crp2a.github.io/gamma/, https://github.com/crp2a/gamma
BugReports: https://github.com/crp2a/gamma/issues
Depends: R (>= 3.5)
Imports: ggplot2, graphics, IsoplotR, methods, rlang, rxylib, stats, tools, utils
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0), vdiffr (>= 1.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: false
NeedsCompilation: no
Packaged: 2024-04-08 15:32:23 UTC; nicolas
Author: Nicolas Frerebeau [aut] , Brice Lebrun [aut] , Guilhem Paradol [aut] , Magali Rizza [ctb] , Christelle Lahaye [ctb] , Archeosciences Bordeaux [cre], Universite Bordeaux Montaigne [cph, fnd], CNRS [fnd], LabEx Sciences archeologiques de Bordeaux [fnd] [...truncated...]
Maintainer: Archeosciences Bordeaux <services-archeosciences@u-bordeaux-montaigne.fr>
Repository: CRAN
Date/Publication: 2024-04-08 16:00:02 UTC

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New package validmind with initial version 0.1.1
Package: validmind
Title: Interface to the 'ValidMind' Platform
Version: 0.1.1
Maintainer: Andres Rodriguez <andres@validmind.ai>
Description: Deploy, execute, and analyze the results of models hosted on the 'ValidMind' platform <https://validmind.com>. This package interfaces with the 'Python' client library in order to allow advanced diagnostics and insight into trained models all from an 'R' environment.
License: AGPL-3
Encoding: UTF-8
URL: https://github.com/validmind/developer-framework
BugReports: https://github.com/validmind/developer-framework/issues
Imports: glue, reticulate, dplyr, plotly, htmltools, rmarkdown, DT, base64enc
NeedsCompilation: no
Packaged: 2024-04-05 19:11:49 UTC; erichare
Author: Andres Rodriguez [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-08 14:50:02 UTC

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New package rTwig with initial version 1.0.2
Package: rTwig
Title: Realistic Quantitative Structure Models
Version: 1.0.2
Description: Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM' and 'SimpleForest'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.
Encoding: UTF-8
Imports: igraph, R.matlab, tidytable, data.table, cobs, purrr, foreach, future, doFuture, progressr, rgl, colourvalues, Morpho, Rdpack, DescTools, kit, rmatio, Matrix (>= 1.6-3), randomcoloR
License: GPL (>= 3)
Depends: R (>= 3.5.0)
LazyData: true
Suggests: knitr, rmarkdown, ggplot2, ggpmisc, ggpubr, gt, yardstick, dplyr, tidyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-05 22:33:15 UTC; moral169
Author: Aidan Morales [aut, cre, cph], David W. MacFarlane [aut, cph]
Maintainer: Aidan Morales <moral169@msu.edu>
URL: https://aidanmorales.github.io/rTwig/, https://github.com/aidanmorales/rTwig
BugReports: https://github.com/aidanmorales/rTwig/issues
Repository: CRAN
Date/Publication: 2024-04-08 15:00:02 UTC

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New package hdbayes with initial version 0.0.3
Package: hdbayes
Title: Bayesian Analysis of Generalized Linear Models with Historical Data
Version: 0.0.3
Description: User-friendly functions for leveraging (multiple) historical data set(s) for generalized linear models. Contains functions for sampling from the posterior distribution of a generalized linear model using the prior induced by the Bayesian hierarchical model, power prior by Ibrahim and Chen (2000) <doi:10.1214/ss/1009212673>, normalized power prior by Duan et al. (2006) <doi:10.1002/env.752>, normalized asymptotic power prior by Ibrahim et al. (2015) <doi:10.1002/sim.6728>, commensurate prior by Hobbs et al. (2011) <doi:10.1111/j.1541-0420.2011.01564.x>, robust meta-analytic-predictive prior by Schmidli et al. (2014) <doi:10.1111/biom.12242>, and the latent exchangeability prior (LEAP) by Alt et al. (2023) <arXiv:2303.05223>. The package compiles all the 'CmdStan' models once during installation using the 'instantiate' package.
License: MIT + file LICENSE
URL: https://github.com/ethan-alt/hdbayes
BugReports: https://github.com/ethan-alt/hdbayes/issues
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: instantiate (>= 0.1.0), callr, fs, formula.tools, stats, posterior, enrichwith, mclust, bridgesampling
Suggests: cmdstanr (>= 0.6.0), parallel
Additional_repositories: https://mc-stan.org/r-packages/
SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan)
LazyData: true
NeedsCompilation: yes
Packaged: 2024-04-05 20:39:28 UTC; xinxin
Author: Ethan M. Alt [aut, cre, cph] , Xinxin Chen [aut], Luiz M. Carvalho [aut], Joseph G. Ibrahim [aut], Xiuya Chang [ctb]
Maintainer: Ethan M. Alt <ethanalt@live.unc.edu>
Repository: CRAN
Date/Publication: 2024-04-08 14:50:08 UTC

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Sun, 07 Apr 2024

New package CodeDepends with initial version 0.6.6
Package: CodeDepends
Version: 0.6.6
Title: Analysis of R Code for Reproducible Research and Code Comprehension
Description: Tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.
Author: Duncan Temple Lang, Roger Peng, Deborah Nolan, Gabriel Becker
Maintainer: Gabriel Becker <gabembecker@gmail.com>
License: GPL
URL: https://github.com/duncantl/CodeDepends
BugReports: https://github.com/duncantl/CodeDepends/issues
Depends: methods
Imports: codetools, graph, XML, utils
Suggests: Rgraphviz, RUnit, knitr, highlight, RJSONIO, RCurl, Rcpp
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-07 21:08:18 UTC; gbecker
Repository: CRAN
Date/Publication: 2024-04-07 23:03:14 UTC

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Fri, 05 Apr 2024

New package fastdigest with initial version 0.6-4
Package: fastdigest
Version: 0.6-4
Title: Fast, Low Memory Footprint Digests of R Objects
Description: Provides an R interface to Bob Jenkin's streaming, non-cryptographic 'SpookyHash' hash algorithm for use in digest-based comparisons of R objects. 'fastdigest' plugs directly into R's internal serialization machinery, allowing digests of all R objects the serialize() function supports, including reference-style objects via custom hooks. Speed is high and scales linearly by object size; memory usage is constant and negligible.
Author: Gabriel Becker, based on SpookyHash algorithm and C++ code by Bob Jenkins
Suggests: RUnit
Maintainer: Gabriel Becker <gabembecker@gmail.com>
License: Artistic-2.0
NeedsCompilation: yes
Packaged: 2024-04-05 18:03:43 UTC; gbecker
Repository: CRAN
Date/Publication: 2024-04-05 23:42:59 UTC

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New package Thermistor with initial version 1.1.0
Package: Thermistor
Title: The Simulation of the Thermistor Network
Version: 1.1.0
Description: Given the circuit topology, simulating the Voltage vs. Temperature curve with a set of Resistors (R1, R2, R3 and R4) and Thermistors values (TH1 and TH2) for a given thermistor network shown in Seth DeLand (2024) "Optimal Component Selection Using the Mixed-Integer Genetic Algorithm" <https://ww2.mathworks.cn/matlabcentral/fileexchange/35810-optimal-component-selection-using-the-mixed-integer-genetic-algorithm> and the application in Mak and Wu (2019) <doi:10.1080/00401706.2019.1593246>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: ggplot2
Depends: R (>= 2.10)
Author: Yao Xiao [aut, cre] , Kang Fu [aut]
Maintainer: Yao Xiao <xystatistics@mails.ccnu.edu.cn>
NeedsCompilation: no
Packaged: 2024-04-05 10:01:19 UTC; xiaoyao
Repository: CRAN
Date/Publication: 2024-04-05 15:43:02 UTC

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New package SpaDES with initial version 2.0.10
Package: SpaDES
Title: Develop and Run Spatially Explicit Discrete Event Simulation Models
Description: Metapackage for implementing a variety of event-based models, with a focus on spatially explicit models. These include raster-based, event-based, and agent-based models. The core simulation components (provided by 'SpaDES.core') are built upon a discrete event simulation (DES; see Matloff (2011) ch 7.8.3 <https://nostarch.com/artofr.htm>) framework that facilitates modularity, and easily enables the user to include additional functionality by running user-built simulation modules (see also 'SpaDES.tools'). Included are numerous tools to visualize rasters and other maps (via 'quickPlot'), and caching methods for reproducible simulations (via 'reproducible'). Tools for running simulation experiments are provided by 'SpaDES.experiment'. Additional functionality is provided by the 'SpaDES.addins' and 'SpaDES.shiny' packages.
URL: https://spades.predictiveecology.org, https://github.com/PredictiveEcology/SpaDES
Date: 2024-04-04
Version: 2.0.10
Depends: R (>= 4.2)
Imports: methods, quickPlot (>= 1.0.2), reproducible (>= 2.0.10), SpaDES.core (>= 2.0.3), SpaDES.tools (>= 2.0.5), utils
Suggests: covr, knitr, rmarkdown, testthat
Encoding: UTF-8
Language: en-CA
License: GPL-3
VignetteBuilder: knitr, rmarkdown
BugReports: https://github.com/PredictiveEcology/SpaDES/issues
ByteCompile: yes
NeedsCompilation: no
Packaged: 2024-04-04 19:17:15 UTC; achubaty
Author: Alex M Chubaty [aut, cre] , Eliot J B McIntire [aut] , Yong Luo [ctb], Steve Cumming [ctb], His Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Repository: CRAN
Date/Publication: 2024-04-05 15:43:05 UTC

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New package Qindex.data with initial version 0.1.0
Package: Qindex.data
Title: Data for Package 'Qindex'
Version: 0.1.0
Date: 2024-04-05
Description: Example data used in package 'Qindex'.
LazyData: true
LazyDataCompression: xz
Encoding: UTF-8
License: GPL-2
Depends: R (>= 4.3),
Language: en-US
Suggests: knitr
NeedsCompilation: no
Packaged: 2024-04-05 14:05:18 UTC; tingtingzhan
Author: Tingting Zhan [aut, cre, cph] , Misung Yi [aut, cph] , Inna Chervoneva [aut, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-05 15:53:12 UTC

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New package childfree with initial version 0.0.1
Package: childfree
Title: Access and Harmonize Childfree Demographic Data
Version: 0.0.1
Description: Reads demographic data from a variety of public data sources, extracting and harmonizing variables useful for the study of childfree individuals. The identification of childfree individuals and those with other family statuses uses Neal & Neal's (2024) "A Framework for Studying Adults who Neither have Nor Want Children" <doi:10.1177/10664807231198869>; A pre-print is available at <doi:10.31234/osf.io/fa89m>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 2.10)
Imports: rio, utils,
Suggests: knitr,
VignetteBuilder: knitr
URL: https://www.zacharyneal.com/childfree, https://www.jennawneal.com/childfree-adults, https://github.com/zpneal/childfree
BugReports: https://github.com/zpneal/childfree/issues
NeedsCompilation: no
Packaged: 2024-04-05 12:36:32 UTC; zacharyneal
Author: Zachary Neal [aut, cre] , Jennifer Watling Neal [aut]
Maintainer: Zachary Neal <zpneal@msu.edu>
Repository: CRAN
Date/Publication: 2024-04-05 15:53:03 UTC

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New package BayesianMCPMod with initial version 1.0.1
Package: BayesianMCPMod
Title: Simulate, Evaluate, and Analyze Dose Finding Trials with Bayesian MCPMod
Version: 1.0.1
Description: Bayesian MCPMod (Fleischer et al. (2022) <doi:10.1002/pst.2193>) is an innovative method that improves the traditional MCPMod by systematically incorporating historical data, such as previous placebo group data. This R package offers functions for simulating, analyzing, and evaluating Bayesian MCPMod trials with normally distributed endpoints. It enables the assessment of trial designs incorporating historical data across various true dose-response relationships and sample sizes. Robust mixture prior distributions, such as those derived with the Meta-Analytic-Predictive approach (Schmidli et al. (2014) <doi:10.1111/biom.12242>), can be specified for each dose group. Resulting mixture posterior distributions are used in the Bayesian Multiple Comparison Procedure and modeling steps. The modeling step also includes a weighted model averaging approach (Pinheiro et al. (2014) <doi:10.1002/sim.6052>). Estimated dose-response relationships can be bootstrapped and visualiz [...truncated...]
License: Apache License (>= 2)
URL: https://github.com/Boehringer-Ingelheim/BayesianMCPMod
BugReports: https://github.com/Boehringer-Ingelheim/BayesianMCPMod/issues
Depends: R (>= 4.2)
Imports: checkmate, DoseFinding (>= 1.1-1), ggplot2, nloptr, RBesT, stats
Suggests: clinDR, dplyr, knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-04-03 21:04:14 UTC; wojcie
Author: Boehringer Ingelheim Pharma GmbH & Co. KG [cph, fnd], Stephan Wojciekowski [aut, cre], Lars Andersen [aut], Steven Brooks [ctb], Sebastian Bossert [aut]
Maintainer: Stephan Wojciekowski <stephan.wojciekowski@boehringer-ingelheim.com>
Repository: CRAN
Date/Publication: 2024-04-05 13:53:00 UTC

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New package RealVAMS with initial version 0.4-6
Package: RealVAMS
Title: Multivariate VAM Fitting
Version: 0.4-6
Date: 2024-04-05
Description: Fits a multivariate value-added model (VAM), see Broatch, Green, and Karl (2018) <doi:10.32614/RJ-2018-033> and Broatch and Lohr (2012) <doi:10.3102/1076998610396900>, with normally distributed test scores and a binary outcome indicator. A pseudo-likelihood approach, Wolfinger (1993) <doi:10.1080/00949659308811554>, is used for the estimation of this joint generalized linear mixed model. The inner loop of the pseudo-likelihood routine (estimation of a linear mixed model) occurs in the framework of the EM algorithm presented by Karl, Yang, and Lohr (2013) <DOI:10.1016/j.csda.2012.10.004>. This material is based upon work supported by the National Science Foundation under grants DRL-1336027 and DRL-1336265.
License: GPL-2
Depends: R (>= 3.0.0), Matrix
Imports: numDeriv, Rcpp (>= 0.11.2), methods, stats, utils, grDevices, graphics
LazyData: yes
ByteCompile: yes
NeedsCompilation: yes
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2024-04-05 08:12:50 UTC; andre
Author: Andrew Karl [cre, aut] , Jennifer Broatch [aut], Jennifer Green [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Repository: CRAN
Date/Publication: 2024-04-05 09:13:06 UTC

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New package fableCount with initial version 0.1.0
Package: fableCount
Title: INGARCH and GLARMA Models for Count Time Series in Fable Framework
Description: Provides a tidy R interface for count time series analysis. It includes implementation of the INGARCH (Integer Generalized Autoregressive Conditional Heteroskedasticity) model from the 'tscount' package and the GLARMA (Generalized Linear Autoregressive Moving Averages) model from the 'glarma' package. Additionally, it offers automated parameter selection algorithms based on the minimization of a penalized likelihood.
Version: 0.1.0
Depends: R (>= 4.0.0), fabletools (>= 0.3.0), tscount (>= 1.4.3), glarma (>= 1.6.0), fable (>= 0.3.4)
Imports: stats, dplyr (>= 1.0.0), tsibble (>= 0.9.0), tibble, tidyr, distributional, lubridate, stringr, tsibbledata
Suggests: Rcpp, utils, rlang, covr, feasts, forecast, knitr, rmarkdown, testthat
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-04 20:52:53 UTC; GUSTAVO PC
Author: Gustavo Almeida [aut, cre] , Marcel Vieira [aut] , Conselho Nacional de Desenvolvimento Cientifico e Tecnologico - CNPq [fnd], JFSalvando Todos - Plataforma de Analises Estatisticas [fnd, cph]
Maintainer: Gustavo Almeida <gustavoalmeidasilva@ice.ufjf.br>
Repository: CRAN
Date/Publication: 2024-04-05 09:13:03 UTC

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New package GPvam with initial version 3.1-0
Package: GPvam
Title: Maximum Likelihood Estimation of Multiple Membership Mixed Models Used in Value-Added Modeling
Version: 3.1-0
Date: 2024-04-05
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>, is used to estimate the generalized, variable, and complete persistence models, Mariano et al. (2010) <doi:10.3102/1076998609346967>. These are multiple-membership linear mixed models with teachers modeled as "G-side" effects and students modeled with either "G-side" or "R-side" effects.
Depends: R (>= 3.2.0), Matrix
Imports: numDeriv, Rcpp (>= 0.11.2), graphics, grDevices, methods, stats, utils
LinkingTo: Rcpp, RcppArmadillo
ByteCompile: yes
NeedsCompilation: yes
LazyData: yes
License: GPL-2
Packaged: 2024-04-05 07:52:53 UTC; andre
Author: Andrew Karl [cre, aut] , Yan Yang [aut], Sharon Lohr [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Repository: CRAN
Date/Publication: 2024-04-05 08:23:00 UTC

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New package GEmetrics with initial version 1.0.0
Package: GEmetrics
Title: Best Linear Unbiased Prediction of Genotype-by-Environment Metrics
Version: 1.0.0
Description: Provides functions to calculate the best linear unbiased prediction of genotype-by-environment metrics: ecovalence, environmental variance, Finlay and Wilkinson regression and Lin and Binns superiority measure, based on a multi-environment genomic prediction model.
License: GPL (>= 3)
Encoding: UTF-8
Imports: stats, BGLR
Depends: R (>= 3.6.0)
NeedsCompilation: no
Packaged: 2024-04-05 06:55:27 UTC; rio
Author: Simon Rio [aut, cre] , Humberto Fanelli Carvalho [aut] , Julio Isidro y Sanchez [aut]
Maintainer: Simon Rio <simon.rio@cirad.fr>
Repository: CRAN
Date/Publication: 2024-04-05 08:32:58 UTC

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Thu, 04 Apr 2024

New package CDVI with initial version 0.1.0
Package: CDVI
Title: Cuddy-Della Valle Index for Capturing the Instability in Time Series Data
Version: 0.1.0
Author: Dr. S. Vishnu Shankar [aut, cre], Dr. Ranjit Kumar Paul [aut], Dr. Md Yeasin [aut], Dr. Himadri Shekhar Roy [aut]
Maintainer: Dr. S. Vishnu Shankar <S.vishnushankar55@gmail.com>
Description: Cuddy-Della valle index gives the degree of instability present in the data by accommodating the effect of a trend. The adjusted R squared value of the best fitted model is chosen. The index is obtained by multiplying the coefficient of variation with square root of one minus the adjusted R-squared value. This package has been developed using concept of Shankar et al. (2022)<doi:10.3389/fsufs.2023.1208898>.
License: GPL-3
Encoding: UTF-8
Imports: stats, base
NeedsCompilation: no
Packaged: 2024-04-04 14:23:28 UTC; JARVIS
Repository: CRAN
Date/Publication: 2024-04-04 18:03:00 UTC

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New package CARMS with initial version 1.0.1
Package: CARMS
Version: 1.0.1
Date: 2024-4-4
Title: Continuous Time Markov Rate Modeling for Reliability Analysis
Description: Emulation of an application originally created by Paul Pukite. Computer Aided Rate Modeling and Simulation. Jan Pukite and Paul Pukite, (1998, ISBN 978-0-7803-3482), William J. Stewart, (1994, ISBN: 0-691-03699-3).
License: GPL (>= 3)
Copyright: copyright (c) OpenReliability.org 2024
URL: http://www.openreliability.org
LazyLoad: yes
Imports: Rcpp, methods, diagram
Author: David Silkworth [aut], Paul Pukite [aut], Jacob Ormerod [cre], OpenReliability.org [cph]
Maintainer: Jacob Ormerod <jake@openreliability.org>
NeedsCompilation: yes
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2024-04-04 15:28:47 UTC; djs
Repository: CRAN
Date/Publication: 2024-04-04 18:03:03 UTC

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New package YatchewTest with initial version 1.0.0
Package: YatchewTest
Title: Yatchew (1997), De Chaisemartin, D'Haultfoeuille & Gurgand (2024) Linearity Test
Version: 1.0.0
Maintainer: Diego Ciccia <diego.ciccia@sciencespo.fr>
Description: Test of linearity originally proposed by Yatchew (1997) <doi:10.1016/S0165-1765(97)00218-8> and improved by de Chaisemartin, D'Haultfoeuille and Gurgand (2024) <doi:10.2139/ssrn.4284811> to be robust under heteroskedasticity.
License: MIT + file LICENSE
Imports: Rcpp, ggplot2
LinkingTo: Rcpp
Author: Diego Ciccia [aut, cre], Felix Knau [aut], Doulo Sow [aut], Clement de Chaisemartin [aut], Xavier D'Haultfoeuille [aut]
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-04-04 07:52:16 UTC; 39380
Repository: CRAN
Date/Publication: 2024-04-04 17:23:02 UTC

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New package testex with initial version 0.1.0
Package: testex
Title: Add Tests to Examples
Version: 0.1.0
Description: Add tests in-line in examples. Provides standalone functions for facilitating easier test writing in Rd files. However, a more familiar interface is provided using 'roxygen2' tags. Tools are also provided for facilitating package configuration and use with 'testthat'.
URL: https://github.com/dgkf/testex, https://dgkf.github.io/testex/
License: MIT + file LICENSE
Depends: R (>= 3.2.0)
Imports: utils
Suggests: testthat, withr, callr, roxygen2, spelling, knitr, rmarkdown
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-03 17:31:15 UTC; root
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-04 17:00:02 UTC

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New package plsmmLasso with initial version 1.0.0
Package: plsmmLasso
Title: Variable Selection and Inference for Partial Semiparametric Linear Mixed-Effects Model
Version: 1.0.0
Description: Implements a partial linear semiparametric mixed-effects model (PLSMM) featuring a random intercept and applies a lasso penalty to both the fixed effects and the coefficients associated with the nonlinear function. The model also accommodates interactions between the nonlinear function and a grouping variable, allowing for the capture of group-specific nonlinearities. Nonlinear functions are modeled using a set of bases functions. Estimation is conducted using a penalized Expectation-Maximization algorithm, and the package offers flexibility in choosing between various information criteria for model selection. Post-selection inference is carried out using a debiasing method, while inference on the nonlinear functions employs a bootstrap approach.
License: GPL (>= 3)
Imports: dplyr, ggplot2, glmnet, hdi, MASS, mvtnorm, rlang, scalreg, stats
Encoding: UTF-8
URL: https://github.com/Sami-Leon/plsmmLasso
BugReports: https://github.com/Sami-Leon/plsmmLasso/issues
NeedsCompilation: no
Packaged: 2024-04-04 14:04:45 UTC; sami
Author: Sami Leon [aut, cre, cph] , Tong Tong Wu [ths]
Maintainer: Sami Leon <samileon@hotmail.fr>
Repository: CRAN
Date/Publication: 2024-04-04 17:52:59 UTC

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New package mlr3fda with initial version 0.1.0
Package: mlr3fda
Title: Extending 'mlr3' to Functional Data Analysis
Version: 0.1.0
Description: Extends the 'mlr3' ecosystem to functional analysis by adding support for irregular and regular functional data as defined in the 'tf' package. The package provides 'PipeOps' for preprocessing functional columns and for extracting scalar features, thereby allowing standard machine learning algorithms to be applied afterwards. Available operations include simple functional features such as the mean or maximum, smoothing, interpolation, flattening, and functional 'PCA'.
License: LGPL-3
URL: https://mlr3fda.mlr-org.com, https://github.com/mlr-org/mlr3fda
BugReports: https://github.com/mlr-org/mlr3fda/issues
Depends: mlr3 (>= 0.14.0), R (>= 3.1.0)
Imports: checkmate, data.table, lgr, mlr3misc (>= 0.14.0), mlr3pipelines, paradox, R6, tf
Suggests: rpart, testthat (>= 3.0.0), zoo
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-04-04 07:55:52 UTC; sebi
Author: Sebastian Fischer [aut, cre] , Maximilian Muecke [aut] , Fabian Scheipl [ctb] , Bernd Bischl [ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-04 17:22:59 UTC

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New package LSDirf with initial version 0.1.3
Package: LSDirf
Title: Impulse-Response Function Analysis for Agent-Based Models
Version: 0.1.3
Date: 2024-4-4
Description: Performing impulse-response function (IRF) analysis of relevant variables of agent-based simulation models, in particular for models described in 'LSD' format. Based on the data produced by the simulation model, it performs both linear and state-dependent IRF analysis, providing the tools required by the Counterfactual Monte Carlo (CMC) methodology (Amendola and Pereira (2024) <doi:10.2139/ssrn.4740360>), including state identification and sensitivity. CMC proposes retrieving the causal effect of shocks by exploiting the opportunity to directly observe the counterfactual in a fully controlled experimental setup. 'LSD' (Laboratory for Simulation Development) is free software available at <https://www.labsimdev.org/>).
Depends: R (>= 4.0.0)
Imports: stats, utils, grDevices, graphics, boot, digest, gplots, abind, partykit, randomForest
Suggests: LSDinterface, LSDsensitivity
License: GPL-3
Language: en-US
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-04 13:43:12 UTC; Marcelo
Author: Marcelo C. Pereira [aut, cre] , Marco Amendola [aut]
Maintainer: Marcelo C. Pereira <mcper@unicamp.br>
Repository: CRAN
Date/Publication: 2024-04-04 17:53:02 UTC

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New package pipenostics with initial version 0.2.0
Package: pipenostics
Title: Diagnostics, Reliability and Predictive Maintenance of Pipeline Systems
Version: 0.2.0
Description: Functions representing some useful empirical and data-driven models of heat loss, corrosion diagnostics, reliability and predictive maintenance of pipeline systems. The package is an option for technical engineering departments of heat generating and heat transfer companies that use or plan to use regulatory calculations in their activities. Methods are described in Timashev et al. (2016) <doi:10.1007/978-3-319-25307-7>, A.C.Reddy (2017) <doi:10.1016/j.matpr.2017.07.081>, Minenergo (2008) <https://docs.cntd.ru/document/902148459>, Minenergo (2005) <https://docs.cntd.ru/document/1200035568>, Xing LU. (2014) <doi:10.1080/23744731.2016.1258371>.
URL: https://omega1x.github.io/pipenostics/
BugReports: https://github.com/omega1x/pipenostics/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: checkmate, iapws
Suggests: testthat (>= 3.0.0), covr
NeedsCompilation: no
Packaged: 2024-04-02 13:43:18 UTC; devpro
Author: Yuri Possokhov [aut, cre]
Maintainer: Yuri Possokhov <omega1x@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-04 15:33:04 UTC

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New package InsuSensCalc with initial version 0.0.1
Package: InsuSensCalc
Title: Insulin Sensitivity Indices Calculator
Version: 0.0.1
Maintainer: Sufyan Suleman <sufyansuleman@hotmail.com>
Description: It facilitates the calculation of 40 different insulin sensitivity indices based on fasting, oral glucose tolerance test (OGTT), lipid (adipose), and tracer (palmitate and glycerol rate) and dxa (fat mass) measurement values. It enables easy and accurate assessment of insulin sensitivity, critical for understanding and managing metabolic disorders like diabetes and obesity. Indices calculated are described in Gastaldelli (2022). <doi:10.1002/oby.23503> and Lorenzo (2010). <doi:10.1210/jc.2010-1144>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, tibble, magrittr, tidyr
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
URL: https://github.com/sufyansuleman/InsuSensCalc
BugReports: https://github.com/sufyansuleman/InsuSensCalc/issues
NeedsCompilation: no
Packaged: 2024-04-03 21:03:08 UTC; rnh585
Author: Sufyan Suleman [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-04 12:03:01 UTC

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New package DPTM with initial version 1.3.8
Package: DPTM
Title: Dynamic Panel Multiple Threshold Model with Fixed Effects
Version: 1.3.8
Date: 2024-03-28
Description: Compute the fixed effects dynamic panel threshold model suggested by Ramírez-Rondán (2020) <doi:10.1080/07474938.2019.1624401>, and dynamic panel linear model suggested by Hsiao et al. (2002) <doi:10.1016/S0304-4076(01)00143-9>, where maximum likelihood type estimators are used. Multiple threshold estimation based on Markov Chain Monte Carlo (MCMC) is allowed, and model selection of linear model, threshold model and multiple threshold model is also allowed.
License: GPL (>= 3)
URL: https://github.com/HujieBai/DPTM
Encoding: UTF-8
Imports: Rcpp (>= 1.0.12),BayesianTools, purrr, MASS,stats,coda,parabar
LinkingTo: Rcpp,RcppEigen
Depends: R (>= 4.3.0)
LazyData: true
NeedsCompilation: yes
Packaged: 2024-04-04 03:22:13 UTC; 11514
Author: Bai Hujie [aut, cre, cph]
Maintainer: Bai Hujie <hujiebai@163.com>
Repository: CRAN
Date/Publication: 2024-04-04 12:13:01 UTC

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New package nonprobsvy with initial version 0.1.0
Package: nonprobsvy
Title: Inference Based on Non-Probability Samples
Version: 0.1.0
Description: Statistical inference with non-probability samples when auxiliary information from external sources such as probability samples or population totals or means is available. Details can be found in: Wu et al. (2020) <doi:10.1080/01621459.2019.1677241>, Kim et al. (2021) <doi:10.1111/rssa.12696>, Wu et al. (2023) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2022002/article/00002-eng.htm>, Kim et al. (2021) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2021001/article/00004-eng.htm>, Kim et al. (2020) <doi:10.1111/rssb.12354>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/ncn-foreigners/nonprobsvy, https://ncn-foreigners.github.io/nonprobsvy/
BugReports: https://github.com/ncn-foreigners/nonprobsvy/issues
Suggests: tinytest, covr, sampling, spelling
Depends: R (>= 4.0.0), survey
Imports: maxLik, stats, Matrix, MASS, ncvreg, mathjaxr, RANN, Rcpp (>= 1.0.12), nleqslv, doParallel, foreach, parallel
LinkingTo: Rcpp, RcppArmadillo
Language: en-US
NeedsCompilation: yes
Packaged: 2024-04-03 15:34:22 UTC; berenz
Author: Lukasz Chrostowski [aut, cre], Maciej Beresewicz [aut, ctb] , Piotr Chlebicki [ctb]
Maintainer: Lukasz Chrostowski <lukchr@st.amu.edu.pl>
Repository: CRAN
Date/Publication: 2024-04-04 11:23:03 UTC

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Wed, 03 Apr 2024

New package rdracor with initial version 1.0.3
Package: rdracor
Title: Access to the 'DraCor' API
Description: Provide an interface for 'Drama Corpora Project' ('DraCor') API: <https://dracor.org/documentation/api>.
Version: 1.0.3
License: GPL (>= 3)
Encoding: UTF-8
Imports: jsonlite (>= 1.6), utils, data.table (>= 1.12.2), xml2 (>= 1.2.2), igraph (>= 1.2.4.1), httr (>= 1.4.1), tibble (>= 3.1.8), purrr (>= 0.3.5), stringr (>= 1.4.1), tidyr (>= 1.2.1), Rdpack (>= 2.4)
Suggests: testthat (>= 2.1.0)
URL: https://github.com/dracor-org/rdracor
BugReports: https://github.com/dracor-org/rdracor/issues
NeedsCompilation: no
Packaged: 2024-04-03 15:55:47 UTC; ivan
Author: Ivan Pozdniakov [aut, cre]
Maintainer: Ivan Pozdniakov <bucherr@yandex.ru>
Repository: CRAN
Date/Publication: 2024-04-03 23:40:06 UTC

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New package FamEvent with initial version 3.1
Package: FamEvent
Title: Family Age-at-Onset Data Simulation and Penetrance Estimation
Version: 3.1
Date: 2024-04-03
Author: Yun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent Briollais
Maintainer: Yun-Hee Choi <yun-hee.choi@schulich.uwo.ca>
Description: Simulates age-at-onset traits associated with a segregating major gene in family data obtained from population-based, clinic-based, or multi-stage designs. Appropriate ascertainment correction is utilized to estimate age-dependent penetrance functions either parametrically from the fitted model or nonparametrically from the data. The Expectation and Maximization algorithm can infer missing genotypes and carrier probabilities estimated from family's genotype and phenotype information or from a fitted model. Plot functions include pedigrees of simulated families and predicted penetrance curves based on specified parameter values. For more information see Choi, Y.-H., Briollais, L., He, W. and Kopciuk, K. (2021) FamEvent: An R Package for Generating and Modeling Time-to-Event Data in Family Designs, Journal of Statistical Software 97 (7), 1-30.
License: GPL (>= 2.0)
NeedsCompilation: no
LazyData: true
Depends: R (>= 3.3.0), survival
Imports: MASS, stats, kinship2, truncnorm, eha, pracma, cmprsk, matrixcalc
Repository: CRAN
Packaged: 2024-04-03 17:58:44 UTC; yun-heechoi
Date/Publication: 2024-04-03 23:33:10 UTC

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New package CoreMicrobiomeR with initial version 0.1.0
Package: CoreMicrobiomeR
Title: Identification of Core Microbiome
Version: 0.1.0
Imports: fastmatch, vegan, SRS, edgeR, ggplot2, ggrepel, stats, plotly, reshape2
Maintainer: Mohammad Samir Farooqi <samirfarooqi8@gmail.com>
Description: The Core Microbiome refers to the group of microorganisms that are consistently present in a particular environment, habitat, or host species. These microorganisms play a crucial role in the functioning and stability of that ecosystem. Identifying these microorganisms can contribute to the emerging field of personalized medicine. The 'CoreMicrobiomeR' is designed to facilitate the identification, statistical testing, and visualization of this group of microorganisms.This package offers three key functions to analyze and visualize microbial community data. This package has been developed based on the research papers published by Pereira et al.(2018) <doi:10.1186/s12864-018-4637-6> and Beule L, Karlovsky P. (2020) <doi:10.7717/peerj.9593>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Author: Sorna A M [aut], Mohammad Samir Farooqi [aut, cre], Dwijesh Chandra Mishra [aut], Krishna Kumar Chaturvedi [aut], Anu Sharma [aut], Prawin Arya [aut], Sudhir Srivastava [aut], Sharanbasappa [aut], Girish Kumar Jha [aut], Kabilan S [ctb]
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-04-03 05:57:33 UTC; kabil
Repository: CRAN
Date/Publication: 2024-04-03 20:03:02 UTC

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New package coglasso with initial version 1.0.2
Package: coglasso
Title: Collaborative Graphical Lasso - Multi-Omics Network Reconstruction
Version: 1.0.2
Description: Reconstruct networks from multi-omics data sets with the collaborative graphical lasso (coglasso) algorithm described in Albanese, A., Kohlen, W., and Behrouzi, P. (2024) <arXiv:2403.18602>. Build multiple networks using the coglasso() function, select the best one with stars_coglasso().
URL: https://github.com/DrQuestion/coglasso, https://drquestion.github.io/coglasso/
BugReports: https://github.com/DrQuestion/coglasso/issues
License: GPL (>= 2)
Imports: Matrix, Rcpp (>= 1.0.11), stats, utils
LinkingTo: Rcpp, RcppEigen
Depends: R (>= 2.10)
LazyData: true
Encoding: UTF-8
Suggests: igraph, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-04-03 10:39:10 UTC; aless
Author: Alessio Albanese [aut, cre, cph] , Pariya Behrouzi [aut]
Maintainer: Alessio Albanese <alessio.albanese@wur.nl>
Repository: CRAN
Date/Publication: 2024-04-03 20:02:59 UTC

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New package TimeVizPro with initial version 1.0
Package: TimeVizPro
Title: Dynamic Data Explorer: Visualize and Forecast with 'TimeVizPro'
Version: 1.0
Date: 2024-03-11
Description: Unless the power of time-series data visualization with ease using our package. Designed with simplicity in mind, it offers three key features through the 'shiny' package. The first output shows time-series charts with forecast, allowing users to visualize trends and changes effortlessly. The second one presents averages per country presented in tables with accompanying sparklines, providing a quick and attractive overview of the data. The last one displayed a customizable world map colored based on user-defined variables for any chosen number of countries, offering an advanced visual approach to understanding geographical data distribution. This package operates with just a few simple arguments, enabling users to conduct sophisticated analyses without the need for complex programming skills. Transform your time- series data analysis experience with our user-friendly tool.
Depends: R (>= 4.0.0), shiny, countrycode
Imports: sparkline, ggplot2, ggiraph, dplyr
Suggests: openxlsx, htmltools, htmlwidgets, DT
License: GPL-3
Author: Hossein Hassani [aut], Fernando Cantu Bazaldua [aut], Leila Marvian Mashhad [aut, cre]
Maintainer: Leila Marvian Mashhad <Leila.marveian@gmail.com>
NeedsCompilation: no
Packaged: 2024-04-02 16:44:58 UTC; ne_da
Repository: CRAN
Date/Publication: 2024-04-03 19:43:07 UTC

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New package scimo with initial version 0.0.1
Package: scimo
Title: Extra Recipes Steps for Dealing with Omics Data
Version: 0.0.1
Description: Omics data (e.g. transcriptomics, proteomics, metagenomics...) offer a detailed and multi-dimensional perspective on the molecular components and interactions within complex biological (eco)systems. Analyzing these data requires adapted procedures, which are implemented as steps according to the 'recipes' package.
License: GPL (>= 3)
URL: https://github.com/abichat/scimo
BugReports: https://github.com/abichat/scimo/issues
Depends: R (>= 2.10), recipes
Imports: dplyr, generics, magrittr, rlang, stats, tibble, tidyr
Suggests: ggplot2, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: false
NeedsCompilation: no
Packaged: 2024-04-02 17:20:13 UTC; antoinebichat
Author: Antoine BICHAT [aut, cre] , Julie AUBERT [ctb]
Maintainer: Antoine BICHAT <antoine.bichat@proton.me>
Repository: CRAN
Date/Publication: 2024-04-03 19:40:02 UTC

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New package psborrow2 with initial version 0.0.3.2
Package: psborrow2
Title: Bayesian Dynamic Borrowing Analysis and Simulation
Version: 0.0.3.2
Description: Bayesian dynamic borrowing is an approach to incorporating external data to supplement a randomized, controlled trial analysis in which external data are incorporated in a dynamic way (e.g., based on similarity of outcomes); see Viele 2013 <doi:10.1002/pst.1589> for an overview. This package implements the hierarchical commensurate prior approach to dynamic borrowing as described in Hobbes 2011 <doi:10.1111/j.1541-0420.2011.01564.x>. There are three main functionalities. First, 'psborrow2' provides a user-friendly interface for applying dynamic borrowing on the study results handles the Markov Chain Monte Carlo sampling on behalf of the user. Second, 'psborrow2' provides a simulation framework to compare different borrowing parameters (e.g. full borrowing, no borrowing, dynamic borrowing) and other trial and borrowing characteristics (e.g. sample size, covariates) in a unified way. Third, 'psborrow2' provides a set of functions to generate data for simulation studies, and a [...truncated...]
URL: https://github.com/Genentech/psborrow2, https://genentech.github.io/psborrow2/index.html
BugReports: https://github.com/Genentech/psborrow2/issues
License: Apache License 2.0
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: checkmate, glue, methods, graphics, posterior, generics, Matrix, mvtnorm, future, simsurv
Suggests: cmdstanr, survival, flexsurv, testthat (>= 3.0), usethis (>= 2.1.5), vdiffr, tibble, xml2, knitr, rmarkdown, bayesplot, matrixcalc, WeightIt, MatchIt, BayesPPD, ggsurvfit, gbm, ggplot2, cobalt, table1, gt, gtsummary
Additional_repositories: https://mc-stan.org/r-packages/
Language: en-US
SystemRequirements: cmdstan
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-02 15:30:54 UTC; secrestm
Author: Matt Secrest [aut, cre] , Isaac Gravestock [aut], Craig Gower-Page [ctb], Genentech, Inc. [cph, fnd]
Maintainer: Matt Secrest <secrestm@gene.com>
Repository: CRAN
Date/Publication: 2024-04-03 19:30:02 UTC

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New package midi with initial version 0.1.0
Package: midi
Title: Microstructure Information from Diffusion Imaging
Version: 0.1.0
Description: An implementation of a taxonomy of models of restricted diffusion in biological tissues parametrized by the tissue geometry (axis, diameter, density, etc.). This is primarily used in the context of diffusion magnetic resonance (MR) imaging to model the MR signal attenuation in the presence of diffusion gradients. The goal is to provide tools to simulate the MR signal attenuation predicted by these models under different experimental conditions. The package feeds a companion 'shiny' app available at <https://midi-pastrami.apps.math.cnrs.fr> that serves as a graphical interface to the models and tools provided by the package. Models currently available are the ones in Neuman (1974) <doi:10.1063/1.1680931>, Van Gelderen et al. (1994) <doi:10.1006/jmrb.1994.1038>, Stanisz et al. (1997) <doi:10.1002/mrm.1910370115>, Soderman & Jonsson (1995) <doi:10.1006/jmra.1995.0014> and Callaghan (1995) <doi:10.1006/jmra.1995.1055>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5)
URL: https://github.com/lmjl-alea/midi, https://lmjl-alea.github.io/midi/
BugReports: https://github.com/lmjl-alea/midi/issues
Imports: cli, ggplot2, plotly, purrr, R6, rlang, withr
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-04-02 16:24:18 UTC; stamm-a
Author: Aymeric Stamm [aut, cre]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Repository: CRAN
Date/Publication: 2024-04-03 19:43:03 UTC

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New package fase with initial version 1.0.1
Package: fase
Title: Functional Adjacency Spectral Embedding
Version: 1.0.1
Description: Latent process embedding for functional network data with the Functional Adjacency Spectral Embedding. Fits smooth latent processes based on cubic spline bases. Also generates functional network data from three models, and evaluates a network generalized cross-validation criterion for dimension selection. For more information, see MacDonald, Zhu and Levina (2022+) <arXiv:2210.07491>.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/peterwmacd/fase
BugReports: https://github.com/peterwmacd/fase/issues
Imports: RSpectra (>= 0.16.1), rTensor (>= 1.4.8), splines2 (>= 0.4.7)
NeedsCompilation: no
Packaged: 2024-03-06 20:14:00 UTC; petermacdonald
Author: Peter W. MacDonald [aut, cre, cph]
Maintainer: Peter W. MacDonald <pwmacdon@umich.edu>
Repository: CRAN
Date/Publication: 2024-04-03 19:33:05 UTC

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New package EngrEcon with initial version 1.0.0
Package: EngrEcon
Title: Engineering Economics Analysis for Engineering Projects Cost Analysis
Version: 1.0.0
Maintainer: Liya Abera <liya.eshetu.abera@gmail.com>
Description: Computing economic analysis in civil infrastructure and ecosystem restoration projects is a typical activity. This package contains Standard cost engineering and engineering economics methods that are applied to convert between present, future, and annualized costs. Newnan D. (2020) <ISBN 9780190931919> “Engineering Economic Analysis”.
License: GPL-3
URL: GitHub (<https://github.com/USACE-WRISES>)
Encoding: UTF-8
Depends: R (>= 4.1.0)
NeedsCompilation: no
Packaged: 2024-04-02 22:07:22 UTC; SHARIFUL ISLAM
Author: Liya Abera [aut, cre] , S. Kyle McKay [aut]
Repository: CRAN
Date/Publication: 2024-04-03 19:53:00 UTC

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New package BioTIMEr with initial version 0.2.2
Package: BioTIMEr
Title: Tools to Use and Explore the 'BioTIME' Database
Version: 0.2.2
Maintainer: Alban Sagouis <alban.sagouis@idiv.de>
License: MIT + file LICENSE
URL: https://github.com/bioTIMEHub/BioTIMEr
BugReports: https://github.com/bioTIMEHub/BioTIMEr/issues
Description: The 'BioTIME' database was first published in 2018 and inspired ideas, questions, project and research article. To make it even more accessible, an R package was created. The 'BioTIMEr' package provides tools designed to interact with the 'BioTIME' database. The functions provided include the 'BioTIME' recommended methods for preparing (gridding and rarefaction) time series data, a selection of standard biodiversity metrics (including species richness, numerical abundance and exponential Shannon) alongside examples on how to display change over time. It also includes a sample subset of both the query and meta data, the full versions of which are freely available on the 'BioTIME' website <https://biotime.st-andrews.ac.uk/home.php>.
Depends: R (>= 3.5.0)
Imports: dplyr, tidyr, ggplot2, vegan, dggridR, checkmate
Suggests: maps, knitr, rmarkdown, formatR, testthat (>= 3.0.0), vdiffr
Language: en-GB
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-02 21:33:16 UTC; rstudio
Author: Alban Sagouis [aut, cre] , Faye Moyes [aut] , Ines S. Martins [aut, rev] , Shane A. Blowes [ctb] , Viviana Brambilla [ctb] , Cher F. Y. Chow [ctb] , Ada Fontrodona-Eslava [ctb] , Laura Antao [ctb, rev] , Jonathan M. Chase [fnd] , Maria Dornelas [fnd, [...truncated...]
Repository: CRAN
Date/Publication: 2024-04-03 19:53:03 UTC

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Tue, 02 Apr 2024

New package ulid with initial version 0.3.1
Package: ulid
Title: Generate Universally Unique 'Lexicographically' 'Sortable' Identifiers
Version: 0.3.1
Date: 2024-04-02
Description: Universally unique identifiers ('UUIDs') can be sub-optimal for many uses-cases because they are not the most character efficient way of encoding 128 bits of randomness; v1/v2 versions are impractical in many environments, as they require access to a unique, stable MAC address; v3/v5 versions require a unique seed and produce randomly distributed IDs, which can cause fragmentation in many data structures; v4 provides no other information than randomness which can cause fragmentation in many data structures. Providing an alternative, 'ULIDs' (<https://github.com/ulid/spec>) have 128-bit compatibility with 'UUID', 1.21e+24 unique 'ULIDs' per millisecond, support standard (text) sorting, canonically encoded as a 26 character string, as opposed to the 36 character 'UUID', use 'base32' encoding for better efficiency and readability (5 bits per character), are case insensitive, have no special characters (i.e. are 'URL' safe) and have a monotonic sort order (correctly detects and handl [...truncated...]
URL: https://github.com/eddelbuettel/ulid
BugReports: https://github.com/eddelbuettel/ulid/issues
NeedsCompilation: yes
Encoding: UTF-8
License: MIT + file LICENSE
Suggests: tinytest
Imports: Rcpp
LinkingTo: Rcpp
Packaged: 2024-04-02 11:58:33 UTC; edd
Author: Bob Rudis [aut] , Suyash Verma [aut] , Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Repository: CRAN
Date/Publication: 2024-04-02 13:40:02 UTC

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New package rtpcr with initial version 1.0.0
Package: rtpcr
Title: qPCR Data Analysis
Version: 1.0.0
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation and statistical analysis of real-time PCR data based on one reference gene. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor) or analysis of variance (for cases where more than two levels or factors exist) to calculate the fold change or relative expression. The functions also provide standard deviations and confidence limits for means, apply statistical mean comparisons, and present letter mean grouping. To facilitate using 'rtpcr', different datasets have been employed in the examples and the outputs are [...truncated...]
License: GPL-3
Imports: agricolae, ggplot2, lme4, reshape2, tidyr, dplyr, grid
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2024-04-02 10:53:33 UTC; GM
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Repository: CRAN
Date/Publication: 2024-04-02 13:32:03 UTC

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New package rQSAR with initial version 1.0.0
Package: rQSAR
Title: QSAR Modeling with Multiple Algorithms: MLR, PLS, and Random Forest
Version: 1.0.0
Description: Quantitative Structure-Activity Relationship (QSAR) modeling is a valuable tool in computational chemistry and drug design, where it aims to predict the activity or property of chemical compounds based on their molecular structure. In this vignette, we present the 'rQSAR' package, which provides functions for variable selection and QSAR modeling using Multiple Linear Regression (MLR), Partial Least Squares (PLS), and Random Forest algorithms.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.6.0), dplyr, corrplot, tibble, gridExtra
Imports: utils, rcdk (>= 3.8.1), ggplot2, caret, pls,randomForest, leaps, stats
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-02 08:26:12 UTC; USER
Author: Oche Ambrose George [aut, cre]
Maintainer: Oche Ambrose George <ocheab1@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-02 13:22:04 UTC
Suggests: rmarkdown,knitr

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New package RQdeltaCT with initial version 1.2.1
Package: RQdeltaCT
Title: Relative Quantification of Gene Expression using Delta Ct Methods
Version: 1.2.1
Description: The commonly used methods for relative quantification of gene expression are the delta Ct family methods (encompassing 2^-Ct, 2^-dCt, and 2^-ddCt methods), originally proposed by Kenneth J. Livak and Thomas D. Schmittgen (2001) <doi:10.1006/meth.2001.1262>. These methods were designed to analyse gene expression data (Ct values) obtained from qPCR (quantitative Polymerase Chain Reaction) experiments. The main idea is to normalise gene expression values using endogenous control gene, present gene expression levels in linear form by using the 2^-(value)^ transformation, and calculate differences in gene expression levels between groups of samples (or technical replicates of a single sample). The 'RQdeltaCT' package offers functions that encompass all of these steps for comparison of either independent groups of samples or groups with paired samples, together with importing qPCR datasets, performing multi-step quality control of data, enabling numerous data visualisations, enrichment [...truncated...]
URL: <https://github.com/Donadelnal/RQdeltaCT>
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: tidyverse, dplyr, ggplot2, magrittr, tidyr, tidyselect, coin, ctrlGene, ggsignif, Hmisc, corrplot, ggpmisc, pROC, oddsratio, stats, graphics, grDevices, utils, pheatmap, GGally
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-02 10:52:47 UTC; Admin
Author: Daniel Zalewski [aut, cre]
Maintainer: Daniel Zalewski <daniel.piotr.zalewski@gmail.com>
Repository: CRAN
Date/Publication: 2024-04-02 13:32:07 UTC

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New package plusCode2 with initial version 0.1.0
Package: plusCode2
Title: Coordinates to 'Plus Code' Conversion Tool
Version: 0.1.0
Date: 2024-04-02
Description: Generates 'Plus Code' of geometric objects or data frames that contain them, giving the possibility to specify the precision of the area. The main feature of the package comes from the open-source code developed by 'Google Inc.' present in the repository <https://github.com/google/open-location-code/blob/main/java/src/main/java/com/google/openlocationcode/OpenLocationCode.java>. For details about 'Plus Code', visit <https://maps.google.com/pluscodes/> or <https://github.com/google/open-location-code>.
License: MIT + file LICENSE
URL: https://github.com/Armando-d/plusCode2
Encoding: UTF-8
Depends: R (>= 4.3)
Imports: sf
NeedsCompilation: no
Packaged: 2024-04-02 08:26:49 UTC; armando.daniello
Author: Armando d'Aniello [aut, cre, cph], Google Inc. [cph]
Maintainer: Armando d'Aniello <armando.daniello@istat.it>
Repository: CRAN
Date/Publication: 2024-04-02 13:12:03 UTC

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New package pkgGraphR with initial version 0.2.0
Package: pkgGraphR
Title: Graph the Relationship Between Functions in an R Package
Version: 0.2.0
Maintainer: David Oliver <doliv071@gmail.com>
BugReports: https://gitlab.com/doliv071/pkggraphr/-/issues
URL: https://gitlab.com/doliv071/pkggraphr
Description: It is often useful when developing an R package to track the relationship between functions in order to appropriately test and track changes. This package generates a graph of the relationship between all R functions in a package. It can also be used on any directory containing .R files which can be very useful for 'shiny' apps or other non-package workflows.
License: GPL (>= 3)
Encoding: UTF-8
Imports: DiagrammeR, dplyr, purrr, stats, utils
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-01 17:15:14 UTC; oliverd
Author: David Oliver [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-04-02 13:02:04 UTC

More information about pkgGraphR at CRAN
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New package confintROB with initial version 1.0
Package: confintROB
Title: Bootstrap Confidence Intervals for Robust and Classical Linear Mixed Model Estimators
Version: 1.0
Date: 2024-04-02
Maintainer: Fabio Mason <fabio.mason@unige.ch>
Encoding: UTF-8
Description: The main function calculates confidence intervals (CI) for Mixed Models, utilizing both classical estimators from the lmer() function in the 'lme4' package and robust estimators from the rlmer() function in the 'robustlmm' package, as well as the varComprob() function in the 'robustvarComp' package. Three methods are available: the classical Wald method, the wild bootstrap, and the parametric bootstrap. Bootstrap methods offer flexibility in obtaining lower and upper bounds through percentile or BCa methods. More details are given in \n Mason, F., Cantoni, E., & Ghisletta, P. (2021) <doi:10.5964/meth.6607> and \n Mason, F., Cantoni, E., & Ghisletta, P. (2024) <doi:10.1037/met0000643>.
License: GPL-2
NeedsCompilation: no
Depends: R (>= 3.5.0)
Imports: foreach, lme4, MASS, mvtnorm, tidyr, methods
Suggests: robustlmm (>= 3.1-1), robustvarComp (>= 0.1-7), lmerTest (>= 3.1-3), xtable, ggplot2, parallel, doParallel
LazyData: true
Packaged: 2024-04-02 11:47:45 UTC; mason
Author: Fabio Mason [aut, cre], Manuel Koller [aut], Eva Cantoni [ctb, ths], Paolo Ghisletta [ths]
Repository: CRAN
Date/Publication: 2024-04-02 13:42:06 UTC

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New package UpAndDownPlots with initial version 0.5.0
Package: UpAndDownPlots
Title: Displays Percentage and Absolute Changes
Version: 0.5.0
Description: Displays percentage changes by height and absolute changes by area for up to three nested or non-nested levels. The plots visualise changes in indices and markets, showing how the changes for sectors or for individual components contribute to the overall change. Data can be classified by up to three levels of grouping variables in a layered, hierarchical plot. Each level can be ordered in several ways including by baseline, by percentage change, and by absolute change. The vignettes give examples.
Depends: R (>= 3.5.0)
Imports: tidyverse, ggplot2, dplyr, tidyr, forcats, gridExtra, ggthemes
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, colorspace
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-01 12:39:42 UTC; antonyunwin2
Author: Antony Unwin [aut, cre, cph], Bill Venables [ctb]
Maintainer: Antony Unwin <unwin@math.uni-augsburg.de>
Repository: CRAN
Date/Publication: 2024-04-02 12:42:08 UTC

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New package surveygraph with initial version 0.1.1
Package: surveygraph
Title: Network Representations of Attitudes
Version: 0.1.1
Author: Samuel Unicomb [aut, cre], Alejandro Dinkelberg [aut], Padraig MacCarron [aut], David O'Sullivan [aut], Paul Maher [aut], Mike Quayle [aut]
Maintainer: Samuel Unicomb <samuelunicomb@gmail.com>
Description: A tool for computing network representations of attitudes, extracted from tabular data such as sociological surveys. By treating a survey as a bipartite network, we measure the similarity between respondents and survey items to produce network edges. We do this in both a respondent network, as well as a survey item network. Used in combination with graph visualisation libraries, this technique helps practitioners in the social sciences identify network structure that may be present within a survey.
Depends: R (>= 2.15.1)
URL: https://surveygraph.ie/
BugReports: https://github.com/surveygraph/surveygraphr/issues
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: covr, ggplot2, igraph, knitr, rmarkdown, testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-04-01 16:03:45 UTC; samuelunicomb
Repository: CRAN
Date/Publication: 2024-04-02 12:10:02 UTC

More information about surveygraph at CRAN
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New package knnmi with initial version 1.0
Package: knnmi
Title: k-Nearest Neighbor Mutual Information Estimator
Version: 1.0
Description: This is a 'C++' mutual information (MI) library based on the k-nearest neighbor (KNN) algorithm. There are three functions provided for computing MI for continuous values, mixed continuous and discrete values, and conditional MI for continuous values. They are based on algorithms by A. Kraskov, et. al. (2004) <doi:10.1103/PhysRevE.69.066138>, BC Ross (2014)<doi:10.1371/journal.pone.0087357>, and A. Tsimpiris (2012) <doi:10.1016/j.eswa.2012.05.014>, respectively.
License: GPL (>= 3)
Depends: R (>= 4.1.0)
Suggests: spelling, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
Language: en-US
NeedsCompilation: yes
Packaged: 2024-03-29 17:51:49 UTC; bgregor
Author: Brian Gregor [aut, cre] , Katia Bulekova [aut] , Reina Chau [aut] , Stefano Monti [aut] , Benoit Jacob [cph] , Gael Guennebaud [cph] , Jose Luis Blanco [cph] , Pranjal Kumar Rai [cph]
Maintainer: Brian Gregor <bgregor@bu.edu>
Repository: CRAN
Date/Publication: 2024-04-02 12:32:06 UTC

More information about knnmi at CRAN
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New package cnmap with initial version 0.1.0
Package: cnmap
Title: China Map Data from AutoNavi Map
Version: 0.1.0
Maintainer: Panfeng Zhang <zhangpanfeng@jlnu.edu.cn>
Description: According to the code or the name of the administrative division at the county level and above provided by the Ministry of Civil Affairs of the People's Republic of China in 2022 (<https://www.mca.gov.cn/mzsj/xzqh/2022/202201xzqh.html>), get the map file online from the website of AutoNavi Map (<http://datav.aliyun.com/portal/school/atlas/area_selector>).
URL: https://github.com/PanfengZhang/cnmap
BugReports: https://github.com/PanfengZhang/cnmap/issues
Depends: R (>= 4.3.0)
Imports: sf, terra
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-04-01 12:58:51 UTC; zhang
Author: Panfeng Zhang [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-02 12:42:06 UTC

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Mon, 01 Apr 2024

New package hcci with initial version 1.1.0
Package: hcci
Title: Interval Estimation of Linear Models with Heteroskedasticity
Version: 1.1.0
Maintainer: Pedro Rafael Diniz Marinho <pedro.rafael.marinho@gmail.com>
Description: Calculates the interval estimates for the parameters of linear models with heteroscedastic regression using bootstrap - (Wild Bootstrap) and double bootstrap-t (Wild Bootstrap). It is also possible to calculate confidence intervals using the percentile bootstrap and percentile bootstrap double. The package can calculate consistent estimates of the covariance matrix of the parameters of linear regression models with heteroscedasticity of unknown form. The package also provides a function to consistently calculate the covariance matrix of the parameters of linear models with heteroscedasticity of unknown form. The bootstrap methods exported by the package are based on the master's thesis of the first author, available at <https://raw.githubusercontent.com/prdm0/hcci/master/references/dissertacao_mestrado.pdf>. The hcci package in previous versions was cited in the book VINOD, Hrishikesh D. Hands-on Intermediate Econometrics Using R: Templates for Learning Quantitative Methods and R [...truncated...]
Author: Pedro Rafael Diniz Marinho [aut, cre], Francisco Cribari Neto [aut, ctb]
License: GPL (>= 3)
URL: https://github.com/prdm0/hcci
BugReports: https://github.com/prdm0/hcci/issues
NeedsCompilation: no
Packaged: 2024-04-01 13:23:03 UTC; prdm0
Repository: CRAN
Date/Publication: 2024-04-01 15:50:02 UTC

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New package SCCS with initial version 1.7
Package: SCCS
Title: The Self-Controlled Case Series Method
Version: 1.7
Date: 2024-04-01
Author: Yonas Ghebremichael Weldeselassie, Heather Whitaker, Paddy Farrington
Maintainer: "Yonas Ghebremichael Weldeselassie" <yonas.weldeselassie@open.ac.uk>
Description: Various self-controlled case series models used to investigate associations between time-varying exposures such as vaccines or other drugs or non drug exposures and an adverse event can be fitted. Detailed information on the self-controlled case series method and its extensions with more examples can be found in Farrington, P., Whitaker, H., and Ghebremichael Weldeselassie, Y. (2018, ISBN: 978-1-4987-8159-6. Self-controlled Case Series studies: A modelling Guide with R. Boca Raton: Chapman & Hall/CRC Press) and <https://sccs-studies.info/index.html>.
License: GPL (>= 2)
Depends: R (>= 2.14.0)
Imports: survival, splines, corpcor, fda, R.methodsS3, gnm
LazyData: yes
Packaged: 2024-04-01 08:43:38 UTC; yw399
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2024-04-01 12:10:11 UTC

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New package refseqR with initial version 1.0.1
Package: refseqR
Title: Common Computational Operations Working with RefSeq Entries (GenBank)
Version: 1.0.1
Maintainer: Jose V. Die <jose.die@uco.es>
Description: Fetches NCBI data (RefSeq <https://www.ncbi.nlm.nih.gov/refseq/> database) and provides an environment to extract information at the level of gene, mRNA or protein accessions.
License: MIT + file LICENSE
URL: https://github.com/jdieramon/refseqR
BugReports: https://github.com/jdieramon/refseqR/issues
Encoding: UTF-8
Imports: IRanges, rentrez, tibble, Biostrings
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-30 14:22:02 UTC; jdieramon
Author: Jose V. Die [aut, cre] , Lluis Revilla Sancho [ctb]
Repository: CRAN
Date/Publication: 2024-04-01 12:00:02 UTC

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New package mefdind with initial version 0.1
Package: mefdind
Title: Imports Data from MoE Spain
Version: 0.1
Description: Imports indicator data provided by the Ministry of Education (MoE),Spain. The data is stored at <https://www.educacionyfp.gob.es/servicios-al-ciudadano/estadisticas/no-universitaria.html> Includes functions for reading, downloading, and selecting data for main series. This package is not sponsored or supported by the MoE Spain. Importa datos con indicadores del Ministerio de Educación y Formación Profesional (MEFD) de Españá. Los datos están en <https://www.educacionyfp.gob.es/servicios-al-ciudadano/estadisticas/no-universitaria.html> Contiene funciones para leer, descargar, y seleccionar bases de datos de series principales. Este paquete no es patrocinado o respaldado por el MEFD.
License: GPL-2
Language: es
URL: https://eldafani.github.io/mefdind/, https://github.com/eldafani/mefdind
BugReports: https://github.com/eldafani/mefdind/issues
Imports: rvest, stringr, utils
Encoding: UTF-8
Depends: R (>= 3.5.0)
LazyData: yes
NeedsCompilation: no
Repository: CRAN
Packaged: 2024-03-29 21:35:44 UTC; eldani
Author: Daniel Caro [aut, cre, cph]
Maintainer: Daniel Caro <dcarov@gmail.com>
Date/Publication: 2024-04-01 11:00:02 UTC

More information about mefdind at CRAN
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New package ERDbuilder with initial version 1.0.0
Package: ERDbuilder
Title: Entity Relationship Diagrams Builder
Version: 1.0.0
Description: Build entity relationship diagrams (ERD) to specify the nature of the relationship between tables in a database.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/gbasulto/ERDbuilder, https://gbasulto.github.io/ERDbuilder/
BugReports: https://github.com/gbasulto/ERDbuilder/issues
Imports: DiagrammeR, dplyr
Suggests: knitr, rmarkdown, gt, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-29 21:53:38 UTC; basulto
Author: Jonathan Wood [aut] , Guillermo Basulto-Elias [aut, cre]
Maintainer: Guillermo Basulto-Elias <basulto@iastate.edu>
Repository: CRAN
Date/Publication: 2024-04-01 11:00:04 UTC

More information about ERDbuilder at CRAN
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New package funModeling with initial version 1.9.5
Package: funModeling
Title: Exploratory Data Analysis and Data Preparation Tool-Box
Description: Around 10% of almost any predictive modeling project is spent in predictive modeling, 'funModeling' and the book Data Science Live Book (<https://livebook.datascienceheroes.com/>) are intended to cover remaining 90%: data preparation, profiling, selecting best variables 'dataViz', assessing model performance and other functions.
Version: 1.9.5
Date: 2024-03-30
Maintainer: Pablo Casas <pcasas.biz@gmail.com>
License: GPL-2
BugReports: https://github.com/pablo14/funModeling/issues
URL: https://livebook.datascienceheroes.com
LazyData: true
Encoding: UTF-8
Imports: ROCR, ggplot2, gridExtra, pander, reshape2, scales, dplyr, lazyeval, utils, RColorBrewer, moments, entropy, cli, stringr
Depends: R (>= 3.4.0), Hmisc (>= 3.17.1)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-30 17:57:38 UTC; jausis
Author: Pablo Casas [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-01 08:00:05 UTC

More information about funModeling at CRAN
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Fri, 29 Mar 2024

New package trainsplit with initial version 1.0
Package: trainsplit
Title: Split a Dataframe, Tibble, or Data.table into Training and Test Sets
Version: 1.0
Description: Split a dataframe, tibble, or data.table into a list containing training and test sets. Can specify either number or percentage of observations to go into the training set.
URL: https://github.com/eastnile/trainsplit
Encoding: UTF-8
Imports: data.table
Suggests: tibble, dplyr
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2024-03-28 23:45:20 UTC; Zhaochen He
Author: Zhaochen He [aut, cre]
Maintainer: Zhaochen He <eastnileuc@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-29 21:10:02 UTC

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New package tracenma with initial version 0.1.0
Package: tracenma
Title: Database for Developing Transitivity Methodology in Network Meta-Analysis
Version: 0.1.0
Date: 2024-03-27
Maintainer: Loukia Spineli <Spineli.Loukia@mh-hannover.de>
Description: Functions to access the database of 217 data-frames with aggregate study-level characteristics (that may act as effect modifiers) extracted from published systematic reviews with network meta-analysis. The database shall only be used for developing and appraising the methodology to assess the transitivity assumption quantitatively.
License: GPL (>= 3)
URL: https://CRAN.R-project.org/package=tracenma, https://github.com/LoukiaSpin/tracenma, https://loukiaspin.github.io/tracenma/
BugReports: https://github.com/LoukiaSpin/tracenma/issues
Depends: R (>= 4.0.0)
Suggests: netmeta, nmadb, rmarkdown
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-03-29 16:16:52 UTC; Loukia
Author: Loukia Spineli [aut, cre]
Repository: CRAN
Date/Publication: 2024-03-29 21:40:02 UTC

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New package CGR with initial version 0.1.0
Package: CGR
Title: Compound Growth Rate for Capturing the Growth Rate Over the Period
Version: 0.1.0
Author: Dr. S. Vishnu Shankar [aut, cre], Dr. Ranjit Kumar Paul [aut], Dr. Himadri Shekhar Roy [aut], Dr. Md Yeasin [aut]
Maintainer: Dr. S. Vishnu Shankar <S.vishnushankar55@gmail.com>
Description: The compound growth rate indicates the percentage change of a specific variable over a defined period. It is calculated using non-linear models, particularly the exponential model. To estimate the compound growth rates, the growth model is first converted to semilog form and then analyzed using Ordinary Least Squares (OLS) regression. This package has been developed using concept of Shankar et al. (2022)<doi:10.3389/fsufs.2023.1208898>.
License: GPL-3
Encoding: UTF-8
Imports: stats, base
NeedsCompilation: no
Packaged: 2024-03-29 12:53:39 UTC; Admin
Repository: CRAN
Date/Publication: 2024-03-29 21:30:02 UTC

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New package perplexR with initial version 0.0.3
Package: perplexR
Title: A Coding Assistant using Perplexity's Large Language Models
Version: 0.0.3
Maintainer: Gabriel Kaiser <quantresearch.gk@gmail.com>
Description: A coding assistant using Perplexity's Large Language Models <https://www.perplexity.ai/> API. A set of functions and 'RStudio' add-ins that aim to help R developers.
License: GPL (>= 3)
URL: https://github.com/GabrielKaiserQFin/perplexR
BugReports: https://github.com/GabrielKaiserQFin/perplexR/issues
Imports: clipr, httr, jsonlite, miniUI, rstudioapi, shiny, utils
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-03-28 09:58:24 UTC; Gabriel
Author: Gabriel Kaiser [aut, cre]
Repository: CRAN
Date/Publication: 2024-03-29 20:50:02 UTC

More information about perplexR at CRAN
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New package ccdR with initial version 1.0.0
Package: ccdR
Title: Utilities for Interacting with the 'CCTE' APIs
Version: 1.0.0
Description: Access chemical, hazard, and bioactivity data from the Center for Computational Toxicology and Exposure ('CCTE') APIs <https://api-ccte.epa.gov/docs/>. 'ccdR' was developed to streamline the process of accessing the information available through the 'CCTE' APIs without requiring prior knowledge of how to use APIs. All data is also available on the CompTox Chemical Dashboard ('CCD') <https://comptox.epa.gov/dashboard/>.
License: GPL (>= 3)
Imports: cli, data.table, httr, jsonlite, purrr, rlang, stringr, tidyr, tibble, urltools
Encoding: UTF-8
LazyData: true
Suggests: countcolors, devtools, ggplot2, gridExtra, httptest, knitr, prettydoc, rmarkdown, testthat (>= 3.0.0), XML
URL: https://github.com/USEPA/ccdR
BugReports: https://github.com/USEPA/ccdR/issues
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-03-28 12:48:38 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: 2024-03-29 20:50:07 UTC

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New package bdsvd with initial version 0.1-0
Package: bdsvd
Title: Block Structure Detection Using Singular Vectors
Version: 0.1-0
Maintainer: Jan O. Bauer <j.bauer@vu.nl>
Description: Performs block diagonal covariance matrix detection using singular vectors (BD-SVD), which can be extended to hierarchical variable clustering (HC-SVD). The methods are described in Bauer (202Xa) <arXiv:2211.16155> and Bauer (202Xb) <arXiv:2308.06820>.
License: GPL (>= 2)
Imports: irlba, methods, stats
Encoding: UTF-8
Suggests: cvCovEst, mvtnorm, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-03-28 16:11:34 UTC; jan
Author: Jan O. Bauer [aut, cre] , Ron Holzapfel [aut]
Repository: CRAN
Date/Publication: 2024-03-29 21:00:05 UTC

More information about bdsvd at CRAN
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New package ReporterScore with initial version 0.1.4
Package: ReporterScore
Title: Generalized Reporter Score-Based Enrichment Analysis for Omics Data
Version: 0.1.4
Description: Inspired by the classic 'RSA', we developed the improved 'Generalized Reporter Score-based Analysis (GRSA)' method, implemented in the R package 'ReporterScore', along with comprehensive visualization methods and pathway databases. 'GRSA' is a threshold-free method that works well with all types of biomedical features, such as genes, chemical compounds, and microbial species. Importantly, the 'GRSA' supports multi-group and longitudinal experimental designs, because of the included multi-group-compatible statistical methods.
License: GPL-3
Encoding: UTF-8
Imports: magrittr, dplyr, stats, ggplot2 (>= 3.2.0), pcutils (>= 0.2.5), utils, scales, ggnewscale, ggrepel, reshape2, stringr, foreach
Suggests: knitr, rmarkdown, plyr, e1071, factoextra, snow, doSNOW, pheatmap, readr, R.utils, KEGGREST, clusterProfiler, enrichplot, pathview, GSA, vegan, MetaNet, igraph, ggraph, PADOG, safe, rSEA, GSVA
Depends: R (>= 4.2.0)
VignetteBuilder: knitr
BugReports: https://github.com/Asa12138/ReporterScore/issues
URL: https://github.com/Asa12138/ReporterScore
NeedsCompilation: no
Packaged: 2024-03-26 14:10:05 UTC; asa
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Repository: CRAN
Date/Publication: 2024-03-29 16:30:09 UTC

More information about ReporterScore at CRAN
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New package jcolors with initial version 0.0.5
Package: jcolors
Title: Colors Palettes for R and 'ggplot2', Additional Themes for 'ggplot2'
Version: 0.0.5
Description: Contains a selection of color palettes and 'ggplot2' themes designed by the package author.
URL: https://jaredhuling.org/jcolors/
BugReports: https://github.com/jaredhuling/jcolors/issues
License: GPL-2
Encoding: UTF-8
Depends: R (>= 3.2.0)
Imports: grDevices, scales, ggplot2 (>= 3.0.0)
Suggests: knitr, rmarkdown, gridExtra
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-28 16:53:28 UTC; huling
Author: Jared Huling [aut, cre]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-29 16:00:06 UTC

More information about jcolors at CRAN
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Thu, 28 Mar 2024

New package SurviMChd with initial version 0.1.2
Title: High Dimensional Survival Data Analysis with Markov Chain Monte Carlo
Package: SurviMChd
Version: 0.1.2
Date: 2024-03-26
Depends: R (>= 3.5.0)
Imports: rjags,R2jags,dplyr
LazyData: Yes
LazyDataCompression: xz
ByteCompile: Yes
Description: High dimensional survival data analysis with Markov Chain Monte Carlo(MCMC). Currently supports frailty data analysis. Allows for Weibull and Exponential distribution. Includes function for interval censored data.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Maintainer: Atanu Bhattacharjee <atanustat@gmail.com>
Packaged: 2024-03-27 21:47:34 UTC; Atanu Bhattacharjee
Author: Atanu Bhattacharjee [aut, cre, ctb], Akash Pawar [aut, ctb]
Repository: CRAN
Date/Publication: 2024-03-28 16:30:05 UTC

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New package sdrt with initial version 1.0.0
Package: sdrt
Title: Estimating the Sufficient Dimension Reduction Subspaces in Time Series
Version: 1.0.0
Maintainer: Tharindu P. De Alwis <talwis@wpi.edu>
Depends: R(>= 3.5.0), stats
Imports: psych, tseries, pracma
Description: The sdrt() function is designed for estimating subspaces for Sufficient Dimension Reduction (SDR) in time series, with a specific focus on the Time Series Central Mean subspace (TS-CMS). The package employs the Fourier transformation method proposed by Samadi and De Alwis (2023) <doi:10.48550/arXiv.2312.02110> and the Nadaraya-Watson kernel smoother method proposed by Park et al. (2009) <doi:10.1198/jcgs.2009.08076> for estimating the TS-CMS. The package provides tools for estimating distances between subspaces and includes functions for selecting model parameters using the Fourier transformation method.
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-03-27 16:56:57 UTC; talwis
Author: Tharindu P. De Alwis [aut, cre] , S. Yaser Samadi [ctb, aut]
Repository: CRAN
Date/Publication: 2024-03-28 16:30:02 UTC

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New package ILSM with initial version 1.0.1
Package: ILSM
Title: Analyze Inter-Layer Structure of Multilayer Ecological Network
Version: 1.0.1
Description: In view of the analysis of the structural characteristics of the multilayer network has been complete, however, there is still a lack of a unified operation that can quickly obtain the corresponding characteristics of the multilayer network. To solve this insufficiency, 'ILSM' was designed for supporting calculating such metrics of multilayer network by functions of this R package.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, Matrix, igraph
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-28 03:33:55 UTC; Admin
Author: WeiCheng Sun [aut, cre], Chuan Yan [aut], Yangyang Zhao [aut]
Maintainer: WeiCheng Sun <sunwch2023@lzu.edu.cn>
Repository: CRAN
Date/Publication: 2024-03-28 16:30:07 UTC

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New package multivarious with initial version 0.2.0
Package: multivarious
Title: Extensible Data Structures for Multivariate Analysis
Version: 0.2.0
Description: Provides a set of basic and extensible data structures and functions for multivariate analysis, including dimensionality reduction techniques, projection methods, and preprocessing functions. The aim of this package is to offer a flexible and user-friendly framework for multivariate analysis that can be easily extended for custom requirements and specific data analysis tasks.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: rlang, chk, glmnet, corpcor, Matrix, purrr, rsvd, svd, pls, irlba, RSpectra, proxy, matrixStats, fitdistrplus
Suggests: covr, randomForest, testthat, magrittr, knitr, rmarkdown, MASS
URL: https://bbuchsbaum.github.io/multivarious/
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-27 13:14:27 UTC; bbuchsbaum
Author: Bradley Buchsbaum [aut, cre]
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-28 16:00:02 UTC

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New package gamstransfer with initial version 3.0.1
Package: gamstransfer
Title: A Data Interface Between 'GAMS' and R
Version: 3.0.1
Date: 2024-03-26
Maintainer: Atharv Bhosekar <abhosekar@gams.com>
Description: Read, analyze, modify, and write 'GAMS' (General Algebraic Modeling System) data. The main focus of 'gamstransfer' is the highly efficient transfer of data with 'GAMS' <https://www.gams.com/>, while keeping these operations as simple as possible for the user. The transfer of data usually takes place via an intermediate GDX (GAMS Data Exchange) file. Additionally, 'gamstransfer' provides utility functions to get an overview of 'GAMS' data and to check its validity.
License: MIT + file LICENSE
Imports: Rcpp (>= 1.0.6), R6 (>= 2.5.1), R.utils (>= 2.11.0), collections(>= 0.3.6)
LinkingTo: Rcpp
Suggests: testthat (>= 3.0.0)
URL: https://github.com/GAMS-dev/transfer-r/tree/main/gamstransfer
BugReports: https://github.com/GAMS-dev/transfer-r/issues
SystemRequirements: C++17
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-03-27 11:24:25 UTC; abhosekar
Author: Atharv Bhosekar [aut, cre], GAMS Development Corp. [cph, fnd], GAMS Software GmbH [cph, fnd]
Repository: CRAN
Date/Publication: 2024-03-28 16:00:10 UTC

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New package CompExpDes with initial version 1.0.0
Package: CompExpDes
Title: Computer Experiment Designs
Version: 1.0.0
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Description: In computer experiments space-filling designs are having great impact. Most popularly used space-filling designs are Uniform designs (UDs), Latin hypercube designs (LHDs) etc. For further references one can see Mckay (1979) <DOI:10.1080/00401706.1979.10489755> and Fang (1980) <https://cir.nii.ac.jp/crid/1570291225616774784>. In this package, we have provided algorithms for generate efficient LHDs and UDs. Here, generated LHDs are efficient as they possess lower value of Maxpro measure, Phi_p value and Maximum Absolute Correlation (MAC) value. On the other hand, the produced UDs are having good space-filling property as they attained the lower bound of Discrete Discrepancy measure.
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-03-27 09:28:06 UTC; Ashutosh
Author: Ashutosh Dalal [aut, cre], Cini Varghese [aut, ctb], Rajender Parsad [aut, ctb], Mohd Harun [aut, ctb]
Repository: CRAN
Date/Publication: 2024-03-28 15:50:15 UTC

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New package PAFit with initial version 1.2.10
Package: PAFit
Title: Generative Mechanism Estimation in Temporal Complex Networks
Version: 1.2.10
Date: 2024-03-28
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongphamthe@gmail.com>
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>. Thong Pham et al. (2020) <doi:10.18637/jss.v092.i03>. Thong Pham et al. (2021) <doi:10.1093/comnet/cnab024>.
URL: https://github.com/thongphamthe/PAFit
BugReports: https://github.com/thongphamthe/PAFit/issues
License: GPL-3
Depends: R(>= 2.10.0)
Imports: Rcpp (>= 0.11.3) , grDevices, graphics, stats, RColorBrewer, VGAM, MASS, magicaxis, networkDynamic, network, plyr, igraph, mapproj, knitr, methods, ggplot2
LinkingTo: Rcpp
LazyData: True
Encoding: UTF-8
NeedsCompilation: yes
Suggests: R.rsp
VignetteBuilder: R.rsp
Packaged: 2024-03-27 17:02:13 UTC; thong
Repository: CRAN
Date/Publication: 2024-03-28 10:30:02 UTC

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Wed, 27 Mar 2024

New package random.cdisc.data with initial version 0.3.15
Package: random.cdisc.data
Title: Create Random ADaM Datasets
Version: 0.3.15
Date: 2024-03-26
Description: A set of functions to create random Analysis Data Model (ADaM) datasets and cached dataset. ADaM dataset specifications are described by the Clinical Data Interchange Standards Consortium (CDISC) Analysis Data Model Team.
License: Apache License 2.0
Depends: R (>= 3.6)
Imports: checkmate (>= 2.1.0), dplyr (>= 1.1.2), lifecycle (>= 1.0.3), lubridate (>= 1.7.10), magrittr (>= 1.5), rlang (>= 1.1.0), stringr (>= 1.4.1), tibble (>= 3.2.1), tidyr (>= 1.1.4), yaml (>= 2.1.19)
Suggests: diffdf, knitr (>= 1.42), rmarkdown (>= 2.19), testthat (>= 3.0.4), withr (>= 2.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-03-27 01:26:32 UTC; rstudio
Author: Pawel Rucki [aut], Nick Paszty [aut], Jana Stoilova [aut], Joe Zhu [aut, cre], Davide Garolini [aut], Emily de la Rua [aut], Christopher DiPietrantonio [aut], Adrian Waddell [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Repository: CRAN
Date/Publication: 2024-03-27 18:40:02 UTC

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New package HTSeed with initial version 0.1.0
Package: HTSeed
Title: Fitting of Hydrotime Model for Seed Germination Time Course
Description: The seed germination process starts with water uptake by the seed and ends with the protrusion of radicle and plumule under varying temperatures and soil water potential. Hydrotime is a way to describe the relationship between water potential and seed germination rates at germination percentages. One important quantity before applying hydrotime modeling of germination percentages is to consider the proportion of viable seeds that could germinate under saturated conditions. This package can be used to apply correction factors at various water potentials before estimating parameters like stress tolerance, and uniformity of the hydrotime model. Three different distributions namely, Gaussian, Logistic, and Extreme value distributions have been considered to fit the model to the seed germination time course. Details can be found in Bradford (2002) <https://www.jstor.org/stable/4046371>, and Bradford and Still(2004) <https://www.jstor.org/stable/23433495>.
Author: Dr. Himadri Ghosh [aut, cre], Dr. Ritwika Das [aut], Dr. Debopam Rakshit [aut]
Maintainer: Dr. Himadri Ghosh <hghosh@gmail.com>
Version: 0.1.0
Encoding: UTF-8
License: GPL-3
Imports: dplyr
NeedsCompilation: no
Packaged: 2024-03-27 06:52:38 UTC; Debopam
Repository: CRAN
Date/Publication: 2024-03-27 18:40:07 UTC

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New package vcfppR with initial version 0.4.3
Package: vcfppR
Title: Rapid Manipulation of the Variant Call Format (VCF)
Version: 0.4.3
Copyright: See the file COPYRIGHTS for various htslib copyright details
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Encoding: UTF-8
Depends: R (>= 3.6.0)
Suggests: testthat (>= 3.0.0)
SystemRequirements: libcurl: libcurl-devel (rpm) or libcurl4-openssl-dev (deb), GNU make.
Imports: Rcpp, methods, stats, utils
LinkingTo: Rcpp
URL: https://github.com/Zilong-Li/vcfppR
BugReports: https://github.com/Zilong-Li/vcfppR/issues
License: MIT + file LICENSE
NeedsCompilation: yes
Packaged: 2024-03-26 20:18:48 UTC; rlk420
Author: Zilong Li [aut, cre] , Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies, Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-27 17:30:02 UTC

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New package plantphysioR with initial version 1.0.0
Package: plantphysioR
Title: Fundamental Formulas for Plant Physiology
Version: 1.0.0
Description: Functions tailored for scientific and student communities involved in plant science research. Functionalities encompass estimation chlorophyll content according to Arnon (1949) <doi:10.1104/pp.24.1.1>, determination water potential of Polyethylene glycol(PEG)6000 as in Michel and Kaufmann (1973) <doi:10.1104/pp.51.5.914> and functions related to estimation of yield related indices like Abiotic tolerance index as given by Moosavi et al.(2008)<doi:10.22059/JDESERT.2008.27115>, Geometric mean productivity (GMP) by Fernandez (1992) <ISBN:92-9058-081-X>, Golden Mean by Moradi et al.(2012)<doi:10.14207/ejsd.2012.v1n3p543>, HAM by Schneider et al.(1997)<doi:10.2135/cropsci1997.0011183X003700010007x>,MPI and TOL by Hossain etal., (1990)<doi:10.2135/cropsci1990.0011183X003000030030x>, RDI by Fischer et al. (1979)<doi:10.1071/AR9791001>,SSI by Fisher et al.(1978)<doi:10.1071/AR9780897>, STI by Fernandez (1993)<doi:10.22001/wvc.72511>,Y [...truncated...]
License: GPL (>= 3)
URL: https://github.com/rameshram96/plantphysioR
BugReports: https://github.com/rameshram96/plantphysioR/issues
Depends: R (>= 2.10)
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-03-27 05:49:50 UTC; Ramesh_PhD
Author: Ramesh Ramasamy [aut, cre]
Maintainer: Ramesh Ramasamy <ramesh.rahu96@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-27 10:10:03 UTC

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New package Oncofilterfast with initial version 1.0.0
Package: Oncofilterfast
Title: Aids in the Analysis of Genes Influencing Cancer Survival
Version: 1.0.0
Maintainer: Pheonix Chen <shuaiyuchen4@gmail.com>
Description: Aids in the analysis of genes influencing cancer survival by including a principal function, calculator(), which calculates the P-value for each provided gene under the optimal cutoff in cancer survival studies. Grounded in methodologies from significant works, this package references Therneau's 'survival' package (Therneau, 2024; <https://CRAN.R-project.org/package=survival>) and the survival analysis extensions by Therneau and Grambsch (2000, ISBN 0-387-98784-3). It also integrates the 'survminer' package by Kassambara et al. (2021; <https://CRAN.R-project.org/package=survminer>), enhancing survival curve visualizations with 'ggplot2'.
License: Apache License 2.0
Encoding: UTF-8
Depends: survival, survminer
NeedsCompilation: no
Packaged: 2024-03-27 04:20:49 UTC; 86157
Author: Pheonix Chen [aut, cre]
Repository: CRAN
Date/Publication: 2024-03-27 10:10:06 UTC

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New package KEPTED with initial version 0.1.0
Package: KEPTED
Title: Kernel-Embedding-of-Probability Test for Elliptical Distribution
URL: https://github.com/tyy20/KEPTED
BugReports: https://github.com/tyy20/KEPTED/issues
Version: 0.1.0
Maintainer: Yin Tang <yqt5219@psu.edu>
Description: Provides an implementation of a kernel-embedding of probability test for elliptical distribution. This is an asymptotic test for elliptical distribution under general alternatives, and the location and shape parameters are assumed to be unknown. Some side-products are posted, including the transformation between rectangular and polar coordinates and two product-type kernel functions. See Tang and Li (2024) <arXiv:2306.10594> for details.
Encoding: UTF-8
License: BSD_3_clause + file LICENSE
Imports: expm, CompQuadForm, cubature, stats
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-26 21:21:10 UTC; yintang
Author: Yin Tang [aut, cre], Bing Li [cph, aut]
Repository: CRAN
Date/Publication: 2024-03-27 09:50:02 UTC

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New package hydroDCindex with initial version 1.0.0
Package: hydroDCindex
Title: Duration Curve Hydrological Model Indexes
Version: 1.0.0
Date: 2024-03-15
Description: Compute duration curves of daily flow series, both real and modeled, to be compared through indexes of flow duration curves. The package functions include comparative plots and goodness of fit tests. Flow duration curve indexes are based on: Yilmaz et al., (2008) <DOI:10.1029/2007WR006716>.
License: GPL-3
LazyData: true
Encoding: UTF-8
Imports: stats
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-03-26 23:23:39 UTC; CLAA300697
Author: Alonso Arriagada [aut, cre]
Maintainer: Alonso Arriagada <alonso.arriagada@usach.cl>
Repository: CRAN
Date/Publication: 2024-03-27 10:00:02 UTC

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New package daltoolboxdp with initial version 1.0.767
Package: daltoolboxdp
Title: Data Pre-Processing Extensions
Version: 1.0.767
Description: An important aspect of data analytics is related to data management support for artificial intelligence. It is related to preparing data correctly. This package provides extensions to support data preparation in terms of both data sampling and data engineering. Overall, the package provides researchers with a comprehensive set of functionalities for data science based on experiment lines, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_20>.
License: MIT + file LICENSE
URL: https://github.com/cefet-rj-dal/daltoolboxdp
Encoding: UTF-8
Imports: daltoolbox, leaps, FSelector, doBy, glmnet, smotefamily
NeedsCompilation: no
Packaged: 2024-03-26 18:50:34 UTC; gpca
Author: Eduardo Ogasawara [aut, ths, cre] , Federal Center for Technological Education of Rio de Janeiro [cph]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Repository: CRAN
Date/Publication: 2024-03-27 09:40:02 UTC

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New package CvmortalityMult with initial version 0.0.1
Package: CvmortalityMult
Title: Cross-Validation for Multi-Population Mortality Models
Version: 0.0.1
Date: 2024-03-20
Description: Implementation of cross-validation method for testing the forecasting accuracy of several multi-population mortality models. The family of multi-population includes several multi-population mortality models proposed through the actuarial and demography literature. The package includes functions for fitting and forecast the mortality rates of several populations. Additionally, we include functions for testing the forecasting accuracy of different multi-population models. References. Atance, D., Debon, A., and Navarro, E. (2020) <doi:10.3390/math8091550>. Bergmeir, C. & Benitez, J.M. (2012) <doi:10.1016/j.ins.2011.12.028>. Debon, A., Montes, F., & Martinez-Ruiz, F. (2011) <doi:10.1007/s13385-011-0043-z>. Lee, R.D. & Carter, L.R. (1992) <doi:10.1080/01621459.1992.10475265>. Russolillo, M., Giordano, G., & Haberman, S. (2011) <doi:10.1080/03461231003611933>. Santolino, M. (2023) <doi:10.3390/risks11100170>.
License: MIT + file LICENSE
URL: https://github.com/davidAtance/CvmortalityMult
BugReports: https://github.com/davidAtance/CvmortalityMult/issues
LazyLoad: yes
LazyData: true
Depends: R (>= 3.50)
Imports: StMoMo, forecast, gnm, tmap, sf
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-03-26 19:43:40 UTC; david
Author: David Atance [aut, cre] , Ana Debon [aut]
Maintainer: David Atance <david.atance@uah.es>
Repository: CRAN
Date/Publication: 2024-03-27 09:40:05 UTC

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New package mpitbR with initial version 1.0.0
Package: mpitbR
Title: Calculate Alkire-Foster Multidimensional Poverty Measures
Version: 1.0.0
Maintainer: Ignacio Girela <ignacio.girela@unc.edu.ar>
Description: Estimate Multidimensional Poverty Indices disaggregated by population subgroups based on the Alkire and Foster method (2011) <doi:10.1016/j.jpubeco.2010.11.006>. This includes the calculation of standard errors and confidence intervals. Other partial indices such as incidence, intensity and indicator-specific measures as well as intertemporal changes analysis can also be estimated. The standard errors and confidence intervals are calculated considering the complex survey design.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: purrr, stats, survey
Depends: R (>= 2.10)
Suggests: parallel
URL: https://github.com/girelaignacio/mpitbR
BugReports: https://github.com/girelaignacio/mpitbR/issues
NeedsCompilation: no
Packaged: 2024-03-26 16:44:15 UTC; girel
Author: Ignacio Girela [aut, cre, cph] , CONICET [fnd]
Repository: CRAN
Date/Publication: 2024-03-27 08:50:02 UTC

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Tue, 26 Mar 2024

New package httk with initial version 2.3.1
Package: httk
Version: 2.3.1
Date: 2024-03-18
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals and species using chemical-specific in vitro data and physiological information. These tools allow incorporation of chemical toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE") into bioinformatics, as described by Pearce et al. (2017) (<doi:10.18637/jss.v079.i04>). Chemical-specific in vitro data characterizing toxicokinetics have been obtained from relatively high-throughput experiments. The chemical-independent ("generic") physiologically-based ("PBTK") and empirical (for example, one compartment) "TK" models included here can be parameterized with in vitro data or in silico predictions which are provided for thousands of chemicals, multiple exposure routes, and various species. High throughput toxicokinetics ("HTTK") is the combination of in vitro data and generic models. We establish the expected accuracy of HTTK for chemicals without in vivo data through statistical evaluation of HTTK predicti [...truncated...]
Depends: R (>= 2.10)
Imports: deSolve, msm, data.table, survey, mvtnorm, truncnorm, stats, graphics, utils, magrittr, purrr, methods, Rdpack, ggplot2
Suggests: knitr, rmarkdown, R.rsp, gplots, scales, EnvStats, MASS, RColorBrewer, stringr, reshape, viridis, gmodels, colorspace, cowplot, ggrepel, dplyr, forcats, smatr, gridExtra, readxl, ks
License: GPL-3
LazyData: true
LazyDataCompression: xz
Encoding: UTF-8
VignetteBuilder: knitr, R.rsp
URL: https://www.epa.gov/chemical-research/rapid-chemical-exposure-and-dose-research
BugReports: https://github.com/USEPA/CompTox-ExpoCast-httk
NeedsCompilation: yes
Packaged: 2024-03-21 18:56:25 UTC; jwambaug
Author: John Wambaugh [aut, cre] , Sarah Davidson-Fritz [aut] , Robert Pearce [aut] , Caroline Ring [aut] , Greg Honda [aut] , Mark Sfeir [aut], Matt Linakis [aut] , Dustin Kapraun [aut] , Nathan Pollesch [ctb] , Miyuki Breen [ctb] , Shannon Bell [ctb] , Xia [...truncated...]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Copyright: This package is primarily developed by employees of the U.S. Federal government as part of their official duties and is therefore public domain.
Repository: CRAN
Date/Publication: 2024-03-27 00:00:02 UTC

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New package vcPB with initial version 1.1.1
Package: vcPB
Title: Longitudinal PB Varying-Coefficient Groupwise Disparity Model
Version: 1.1.1
Description: Estimating the disparity between two groups based on the extended model of the Peters-Belson (PB) method. Our model is the first work on the longitudinal data, and also can set a varying variable to find the complicated association between other variables and the varying variable. Our work is an extension of the Peters-Belson method which was originally published in Peters (1941)<doi:10.1080/00220671.1941.10881036> and Belson (1956)<doi:10.2307/2985420>.
Depends: KernSmooth, rlist, lme4, methods
License: GPL-3
Encoding: UTF-8
URL: https://github.com/SangkyuStat/vcPB, https://sangkyustat.github.io/vcPB/
BugReports: https://github.com/SangkyuStat/vcPB/issues
NeedsCompilation: no
Packaged: 2024-03-26 15:11:49 UTC; lees57
Author: Sang Kyu Lee [aut, cre], Seonjin Kim [aut], Hyokyoung Hong [aut], Mi-Ok Kim [aut]
Maintainer: Sang Kyu Lee <lsk0816@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-26 17:00:02 UTC

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New package swaRmverse with initial version 0.1.0
Package: swaRmverse
Title: Swarm Space Creation
Version: 0.1.0
Date: 2024-02-29
Maintainer: Marina Papadopoulou <m.papadopoulou.rug@gmail.com>
Description: Provides a pipeline for the comparative analysis of collective movement data (e.g. fish schools, bird flocks, baboon troops) by processing 2-dimensional positional data (x,y,t) from GPS trackers or computer vision tracking systems, discretizing events of collective motion, calculating a set of established metrics that characterize each event, and placing the events in a multi-dimensional swarm space constructed from these metrics. The swarm space concept, the metrics and data sets included are described in: Papadopoulou Marina, Furtbauer Ines, O'Bryan Lisa R., Garnier Simon, Georgopoulou Dimitra G., Bracken Anna M., Christensen Charlotte and King Andrew J. (2023) <doi:10.1098/rstb.2022.0068>.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://marinapapa.github.io/swaRmverse/, https://github.com/marinapapa/swaRmverse
BugReports: https://github.com/marinapapa/swaRmverse/issues
Depends: R (>= 3.5)
Imports: parallel, pbapply, Rtsne, trackdf, swaRm, geosphere
Suggests: knitr, rmarkdown, ggplot2, testthat (>= 3.0.0), covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-26 11:17:18 UTC; 2GSWARM
Author: Marina Papadopoulou [aut, cre] , Simon Garnier [ctb, cph]
Repository: CRAN
Date/Publication: 2024-03-26 17:00:05 UTC

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New package sbrl with initial version 1.3
Package: sbrl
Title: Scalable Bayesian Rule Lists Model
Version: 1.3
Date: 2024-03-21
Author: Hongyu Yang [aut, cre], Morris Chen [ctb], Cynthia Rudin [aut, ctb], Margo Seltzer [aut, ctb], The President and Fellows of Harvard College [cph]
Maintainer: Hongyu Yang <edwardyhy1@gmail.com>
Description: An efficient implementation of Scalable Bayesian Rule Lists Algorithm, a competitor algorithm for decision tree algorithms; see Hongyu Yang, Cynthia Rudin, Margo Seltzer (2017) <https://proceedings.mlr.press/v70/yang17h.html>. It builds from pre-mined association rules and have a logical structure identical to a decision list or one-sided decision tree. Fully optimized over rule lists, this algorithm strikes practical balance between accuracy, interpretability, and computational speed.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.4), arules, methods
RcppModules: sbrl
LinkingTo: Rcpp
NeedsCompilation: yes
LazyData: yes
SystemRequirements: gmp (>= 4.2.0), gsl
Packaged: 2024-03-26 06:42:39 UTC; hongyuy
Repository: CRAN
Date/Publication: 2024-03-26 16:50:02 UTC

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New package pmxcv with initial version 0.0.1.0
Package: pmxcv
Title: Integration-Based Coefficients of Variance
Version: 0.0.1.0
Description: Estimate coefficient of variance percent (CV%) for any arbitrary distribution, including some built-in estimates for commonly-used transformations in pharmacometrics. Methods are described in various sources, but applied here as summarized in: Prybylski, (2024) <doi:10.1007/s40262-023-01343-2>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-03-26 12:47:11 UTC; PRYBYJ
Author: John Prybylski [aut, cre]
Maintainer: John Prybylski <john.prybylski@pfizer.com>
Repository: CRAN
Date/Publication: 2024-03-26 17:00:09 UTC

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New package flexOR with initial version 0.9.6
Encoding: UTF-8
Package: flexOR
Version: 0.9.6
Date: 2024-03-25
Title: Flexible Odds Ratio Curves
Maintainer: Marta Azevedo <marta.vasconcelos4@gmail.com>
Depends: R (>= 3.1.0)
Imports: gam, graphics, grDevices, mgcv, stats
Suggests: knitr, mlbench, R.rsp, rmarkdown, plotly
Description: Provides flexible hazard ratio curves that enable modeling non-linear relationships between continuous predictors and survival outcomes. This package facilitates a deeper understanding of the impact of each continuous predictor on the outcome by presenting results in terms of odds ratio (OR) curves based on splines. These curves allow for comparison against a specified reference value, aiding in the interpretation of the predictor's effect.
License: GPL-3
URL: https://github.com/martaaaa/flexOR
BugReports: https://github.com/martaaaa/flexOR/issues
LazyLoad: yes
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2024-03-26 09:43:31 UTC; marta
Author: Marta Azevedo [aut, cre] , Luis Meira-Machado [aut] , Artur Araujo [aut]
Repository: CRAN
Date/Publication: 2024-03-26 16:50:05 UTC

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New package REMLA with initial version 1.0
Package: REMLA
Title: Robust Expectation-Maximization Estimation for Latent Variable Models
Version: 1.0
Date: 2024-03-11
Description: Traditional latent variable models assume that the population is homogeneous, meaning that all individuals in the population are assumed to have the same latent structure. However, this assumption is often violated in practice given that individuals may differ in their age, gender, socioeconomic status, and other factors that can affect their latent structure. The robust expectation maximization (REM) algorithm is a statistical method for estimating the parameters of a latent variable model in the presence of population heterogeneity as recommended by Nieser & Cochran (2023) <doi:10.1037/met0000413>. The REM algorithm is based on the expectation-maximization (EM) algorithm, but it allows for the case when all the data are generated by the assumed data generating model.
License: GPL (>= 3)
URL: https://github.com/knieser/REM
Imports: GPArotation, stats, geex
Encoding: UTF-8
Suggests: knitr, lavaan, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-25 19:37:38 UTC; bryanortiz
Author: Bryan Ortiz-Torres [aut, cre], Kenneth Nieser [aut]
Maintainer: Bryan Ortiz-Torres <bortiztorres@wisc.edu>
Repository: CRAN
Date/Publication: 2024-03-26 09:20:02 UTC

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New package glmMisrep with initial version 0.1.0
Package: glmMisrep
Title: Generalized Linear Models Adjusting for Misrepresentation
Version: 0.1.0
Depends: R (>= 3.5.0)
Description: Fit Generalized Linear Models to continuous and count outcomes, as well as estimate the prevalence of misrepresentation of an important binary predictor. Misrepresentation typically arises when there is an incentive for the binary factor to be misclassified in one direction (e.g., in insurance settings where policy holders may purposely deny a risk status in order to lower the insurance premium). This is accomplished by treating a subset of the response variable as resulting from a mixture distribution. Model parameters are estimated via the Expectation Maximization algorithm and standard errors of the estimates are obtained from closed forms of the Observed Fisher Information. For an introduction to the models and the misrepresentation framework, see Xia et. al., (2023) <https://variancejournal.org/article/73151-maximum-likelihood-approaches-to-misrepresentation-models-in-glm-ratemaking-model-comparisons>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: MASS, poisson.glm.mix, stats
NeedsCompilation: no
Packaged: 2024-03-25 14:33:06 UTC; patri
Author: Patrick Rafael [cre, aut], Xia Michelle [aut], Rexford Akakpo [aut]
Maintainer: Patrick Rafael <pbr2608@vt.edu>
Repository: CRAN
Date/Publication: 2024-03-26 09:00:02 UTC

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New package fabPrediction with initial version 1.0.4
Package: fabPrediction
Title: Compute FAB (Frequentist and Bayes) Conformal Prediction Intervals
Version: 1.0.4
Description: Computes and plots prediction intervals for numerical data or prediction sets for categorical data using prior information. Empirical Bayes procedures to estimate the prior information from multi-group data are included. See, e.g.,Bersson and Hoff (2022) <arXiv:2204.08122> "Optimal Conformal Prediction for Small Areas".
License: GPL-3
Encoding: UTF-8
Imports: sae (>= 1.3), parallel, stats, graphics
Suggests: knitr, devtools
NeedsCompilation: yes
ByteCompile: yes
VignetteBuilder: knitr
URL: https://github.com/betsybersson/fabPrediction
BugReports: https://github.com/betsybersson/fabPrediction/issues
Packaged: 2024-03-25 13:51:40 UTC; betsybersson
Author: Elizabeth Bersson [aut, cre, cph]
Maintainer: Elizabeth Bersson <elizabeth.bersson@duke.edu>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-03-26 09:00:05 UTC

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New package o2geosocial with initial version 1.1.2
Package: o2geosocial
Title: Reconstruction of Transmission Chains from Surveillance Data
Version: 1.1.2
URL: https://github.com/alxsrobert/o2geosocial
Encoding: UTF-8
Maintainer: Alexis Robert <alexis.robert@lshtm.ac.uk>
Description: Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. (2020) <doi:10.1098/rsif.2020.0084>).
License: MIT + file LICENSE
Imports: Rcpp, methods, stats, grDevices, geosphere, ggplot2, visNetwork, data.table, outbreaker2
LazyData: true
Depends: R(>= 3.5.0)
LinkingTo: Rcpp
Suggests: testthat, tigris, sf, knitr, socialmixr, rmarkdown
VignetteBuilder: knitr
BugReports: https://github.com/alxsrobert/o2geosocial/issues
NeedsCompilation: yes
Packaged: 2024-03-22 08:04:43 UTC; eidearob
Author: Alexis Robert [aut, cre, cph] , Sebastian Funk [aut] , Adam J Kucharski [aut] , Thibaut Jombart [ctb]
Repository: CRAN
Date/Publication: 2024-03-26 06:40:12 UTC

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New package AccelStab with initial version 2.0.1
Package: AccelStab
Title: Accelerated Stability Kinetic Modelling
Version: 2.0.1
Description: Estimate the Šesták–Berggren kinetic model (degradation model) from experimental data. A A closed-form (analytic) solution to the degradation model is implemented as a non-linear fit, allowing for the extrapolation of the degradation of a drug product - both in time and temperature. Parametric bootstrap, with kinetic parameters drawn from the multivariate t-distribution, and analytical formulae (the delta method) are available options to calculate the confidence and prediction intervals. The results (modelling, extrapolations and statistical intervals) can be visualised with multiple plots. The examples illustrate the accelerated stability modelling in drugs and vaccines development.
License: AGPL (>= 3)
Encoding: UTF-8
Imports: dplyr, ggplot2, minpack.lm, mvtnorm, stats, scales
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, lifecycle
Depends: R (>= 4.1.0)
LazyData: true
Language: en-GB
URL: https://github.com/AccelStab/AccelStab
BugReports: https://github.com/AccelStab/AccelStab/issues
NeedsCompilation: no
Packaged: 2024-03-20 10:49:01 UTC; benwe
Author: Bernard G Franq [aut, cph], Ben Wells [cre], Alex Ball [ctb]
Maintainer: Ben Wells <benwells@bayezian.com>
Repository: CRAN
Date/Publication: 2024-03-26 06:42:58 UTC

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Mon, 25 Mar 2024

New package qtlpoly with initial version 0.2.4
Package: qtlpoly
Title: Random-Effect Multiple QTL Mapping in Autopolyploids
Version: 0.2.4
Maintainer: Gabriel de Siqueira Gesteira <gdesiqu@ncsu.edu>
Description: Performs random-effect multiple interval mapping (REMIM) in full-sib families of autopolyploid species based on restricted maximum likelihood (REML) estimation and score statistics, as described in Pereira et al. (2020) <doi:10.1534/genetics.120.303080>.
License: GPL-3
URL: https://gabrielgesteira.github.io/QTLpoly/
BugReports: https://github.com/gabrielgesteira/QTLpoly/issues
Encoding: UTF-8
LazyData: TRUE
LazyDataCompression: xz
Depends: R (>= 4.0)
Imports: ggplot2 (>= 3.1), abind (>= 1.4), MASS (>= 7.3), gtools (>= 3.9.2), CompQuadForm, Matrix, RLRsim, mvtnorm, nlme, quadprog, parallel, doParallel, foreach, stats, methods, mappoly, Rcpp (>= 0.12.19)
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Suggests: rmarkdown, devtools, knitr
NeedsCompilation: yes
Packaged: 2024-03-20 18:48:26 UTC; gdesiqu
Author: Guilherme da Silva Pereira [aut] , Marcelo Mollinari [ctb] , Gabriel de Siqueira Gesteira [ctb, cre] , Zhao-Bang Zeng [ctb] , Long Qu [ctb] , Giovanny Covarrubias-Pazaran [ctb]
Repository: CRAN
Date/Publication: 2024-03-25 20:50:06 UTC

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New package MetaNet with initial version 0.1.2
Package: MetaNet
Title: Network Analysis for Omics Data
Version: 0.1.2
Description: Comprehensive network analysis package. Calculate correlation network fastly, accelerate lots of analysis by parallel computing. Support for multi-omics data, search sub-nets fluently. Handle bigger data, more than 10,000 nodes in each omics. Offer various layout method for multi-omics network and some interfaces to other software ('Gephi', 'Cytoscape', 'ggplot2'), easy to visualize. Provide comprehensive topology indexes calculation, including ecological network stability.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.1.0), igraph (>= 1.3.5)
LazyData: true
Imports: graphics, dplyr, ggplot2 (>= 3.2.0), ggnewscale, ggrepel, RColorBrewer, grDevices, magrittr, reshape2, stats, tibble, utils, pcutils (>= 0.2.5), rlang
Suggests: pheatmap, vegan, stringr, foreach, doSNOW, snow, knitr, rmarkdown, prettydoc, Hmisc, gifski, ggraph, networkD3, ggpmisc, ggtree, treeio, circlize, ggpubr
VignetteBuilder: knitr
BugReports: https://github.com/Asa12138/MetaNet/issues
URL: https://github.com/Asa12138/MetaNet
ByteCompile: true
NeedsCompilation: no
Packaged: 2024-03-21 16:16:27 UTC; asa
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Repository: CRAN
Date/Publication: 2024-03-25 20:40:07 UTC

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New package gamlss.ggplots with initial version 2.1-12
Package: gamlss.ggplots
Title: Plotting Functions for Generalized Additive Model for Location Scale and Shape
Version: 2.1-12
Date: 2024-04-21
Description: Functions for plotting Generalized Additive Models for Location Scale and Shape from the 'gamlss' package, Stasinopoulos and Rigby (2007) <doi:10.18637/jss.v023.i07>, using the graphical methods from 'ggplot2'.
License: GPL-2 | GPL-3
URL: https://www.gamlss.com/
BugReports: https://github.com/gamlss-dev/gamlss.ggplots/issues
Depends: R (>= 3.5.0), gamlss.dist, gamlss (>= 4.3.3), gamlss.foreach
Imports: methods, ggridges, ellipse, gamlss.inf, foreach, mgcv, ggplot2, yaImpute
Suggests: glmnet, reshape2, igraph, networkD3, grid, gridExtra
LazyLoad: yes
NeedsCompilation: no
Packaged: 2024-03-21 20:35:39 UTC; dimitriosstasinopoulos
Author: Mikis Stasinopoulos [aut, cre, cph] , Robert Rigby [aut] , Fernanda De Bastiani [aut] , Julian Merder [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>
Repository: CRAN
Date/Publication: 2024-03-25 20:40:02 UTC

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New package Dtableone with initial version 1.1.0
Package: Dtableone
Title: Tabular Comparison of Paired Diagnostic Tests
Version: 1.1.0
Description: Offers statistical methods to compare diagnostic performance between two binary diagnostic tests on the same subject in clinical studies. Includes functions for generating formatted tables to display diagnostic outcomes, facilitating a clear and comprehensive comparison directly through the R console. Inspired by and extending the functionalities of the 'DTComPair', 'tableone', and 'gtsummary' packages.
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.3.0)
Imports: dplyr, epiR (>= 2.0.61), irr (>= 0.84.1), pROC (>= 1.18.5)
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-03-25 04:55:08 UTC; mrcc
Author: Youngmi Park [aut, cre], Soyeon Ahn [aut], Seong Jun Byun [aut]
Maintainer: Youngmi Park <02141@snubh.org>
Repository: CRAN
Date/Publication: 2024-03-25 20:20:02 UTC

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New package PolyTree with initial version 0.0.1
Package: PolyTree
Title: Estimate Causal Polytree from Data
Version: 0.0.1
Maintainer: Sourav Chatterjee <souravc@stanford.edu>
Description: Given a data matrix with rows representing data vectors and columns representing variables, produces a directed polytree for the underlying causal structure. Based on the algorithm developed in Chatterjee and Vidyasagar (2022) <arxiv:2209.07028>. The method is fully nonparametric, making no use of linearity assumptions, and especially useful when the number of variables is large.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: FOCI, igraph
NeedsCompilation: no
Packaged: 2024-03-24 02:47:21 UTC; sourav
Author: Sourav Chatterjee [aut, cre]
Repository: CRAN
Date/Publication: 2024-03-25 19:10:12 UTC

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New package ieugwasr with initial version 0.2.0
Package: ieugwasr
Title: Interface to the 'OpenGWAS' Database API
Version: 0.2.0
Description: Interface to the 'OpenGWAS' database API <https://gwas-api.mrcieu.ac.uk/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.
License: MIT + file LICENSE
URL: https://github.com/MRCIEU/ieugwasr, https://mrcieu.github.io/ieugwasr/
BugReports: https://github.com/MRCIEU/ieugwasr/issues
Depends: R (>= 4.0)
Imports: dplyr, googleAuthR, httr, jsonlite, magrittr, rlang, stats
Suggests: knitr, microbenchmark, pander, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-03-23 19:43:35 UTC; gh13047
Author: Gibran Hemani [aut, cre, cph] , Ben Elsworth [aut] , Tom Palmer [aut] , Rita Rasteiro [aut]
Maintainer: Gibran Hemani <g.hemani@bristol.ac.uk>
Repository: CRAN
Date/Publication: 2024-03-25 19:10:02 UTC

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New package fmx with initial version 0.1.0
Package: fmx
Title: Finite Mixture Parametrization
Version: 0.1.0
Date: 2024-03-23
Description: A parametrization framework for finite mixture distribution using S4 objects. Density, cumulative density, quantile and simulation functions are defined. Currently normal, Tukey g-&-h, skew-normal and skew-t distributions are well tested. The gamma, negative binomial distributions are being tested.
License: GPL-2
Imports: methods, goftest, sn, TukeyGH77, VGAM
Encoding: UTF-8
Language: en-US
Depends: R (>= 4.3.0)
Suggests: fitdistrplus, ggplot2, mixtools, mixsmsn, scales
NeedsCompilation: no
Packaged: 2024-03-23 14:06:03 UTC; tingtingzhan
Author: Tingting Zhan [aut, cre, cph], Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-25 19:00:02 UTC

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New package changeS with initial version 1.0.1
Package: changeS
Title: S-Curve Fit for Changepoint Analysis
Version: 1.0.1
Maintainer: Norm Matloff <nsmatloff@ucdavis.edu>
Description: Estimation of changepoints using an "S-curve" approximation. Formation of confidence intervals for changepoint locations and magnitudes. Both abrupt and gradual changes can be modeled.
Depends: R (>= 3.5.0), nls.multstart, ggplot2, stringr
Suggests: knitr,rmarkdown
VignetteBuilder: knitr
License: GPL (>= 2)
URL: https://github.com/matloff/changeS
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-03-23 19:46:31 UTC; normanmatloff
Author: Lan Jiang [aut], Collin Kennedy [aut], Norm Matloff [aut, cre]
Repository: CRAN
Date/Publication: 2024-03-25 19:10:06 UTC

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New package biopixR with initial version 0.2.4
Package: biopixR
Title: Extracting Insights from Biological Images
Version: 0.2.4
Description: Combines the 'magick' and 'imager' packages to streamline image analysis, focusing on feature extraction and quantification from biological images, especially microparticles. By providing high throughput pipelines and clustering capabilities, 'biopixR' facilitates efficient insight generation for researchers (Schneider J. et al. (2019) <doi:10.21037/jlpm.2019.04.05>).
License: LGPL (>= 3)
VignetteBuilder: knitr
BuildVignettes: true
Depends: R (>= 4.2.0), data.table, imager, magick, tcltk, foreach
Suggests: knitr, rmarkdown, doParallel, kohonen
Encoding: UTF-8
LazyData: true
LazyLoad: yes
NeedsCompilation: no
Language: en-US
URL: https://github.com/Brauckhoff/biopixR
BugReports: https://github.com/Brauckhoff/biopixR/issues
Packaged: 2024-03-24 08:25:58 UTC; brauctim
Author: Tim Brauckhoff [aut, cre] , Stefan Roediger [ctb] , Coline Kieffer [ctb]
Maintainer: Tim Brauckhoff <Tim.Brauckhoff@b-tu.de>
Repository: CRAN
Date/Publication: 2024-03-25 19:10:09 UTC

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New package TCPMOR with initial version 1.0
Package: TCPMOR
Title: Two Cut-Points with Maximum Odds Ratio
Version: 1.0
Description: Enables the computation of the 'two cut-points with maximum odds ratio (OR) value method' for data analysis, particularly suited for binary classification tasks. Users can identify optimal cut-points in a continuous variable by maximizing the odds ratio while maintaining an equal risk level, useful for tasks such as medical diagnostics, risk assessment, or predictive modeling.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: SemiPar, stats
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-03-23 11:44:41 UTC; 14715
Author: Xianying He [aut], Shuo Yang [aut, cre], Yi Fei [ctb], Jinxin Zhang [aut]
Maintainer: Shuo Yang <yangsh223@mail2.sysu.edu.cn>
Repository: CRAN
Date/Publication: 2024-03-25 18:50:02 UTC

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