Mon, 25 Oct 2021

New package uFTIR with initial version 0.1.4
Package: uFTIR
Title: Process and Analyze Agilent Cary 620 FTIR Microscope Images
Version: 0.1.4
Date: 2021-10-19
Maintainer: Fabio Corradini <fabio.corradini@inia.cl>
Description: A set of tools to read, process, and summarize Agilent Cary 620 uFTIR Microscope hyperspectral images primarily intended for microplastic analysis.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.4.0), parallel (>= 4.0.4)
Imports: Rcpp (>= 1.0.7), methods (>= 4.0.4), raster (>= 3.5.2), sp (>= 1.4.5)
Suggests: testthat (>= 3.1.0), rgeos (>= 0.5.8), signal (>= 0.7.7), rgdal (>= 1.5.27)
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2021-10-22 16:14:07 UTC; fabio
Author: Fabio Corradini [aut, cre] (<https://orcid.org/0000-0001-9696-7643>)
Repository: CRAN
Date/Publication: 2021-10-25 07:10:02 UTC

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New package simplermarkdown with initial version 0.0.2
Package: simplermarkdown
Title: Simple Engine for Generating Reports using R
Version: 0.0.2
Description: Runs R-code present in a pandoc markdown file and includes the resulting output in the resulting markdown file. This file can then be converted into any of the output formats supported by pandoc. The package can also be used as an engine for writing package vignettes.
BugReports: https://github.com/djvanderlaan/simplermarkdown/issues
URL: https://github.com/djvanderlaan/simplermarkdown
License: GPL (>= 3)
Encoding: UTF-8
Imports: rjson, tools
Suggests: MASS
VignetteBuilder: simplermarkdown
SystemRequirements: Pandoc (http://pandoc.org) needs to installed and available in the search path.
NeedsCompilation: no
Packaged: 2021-10-23 15:30:08 UTC; eoos
Author: Jan van der Laan [aut, cre] (<https://orcid.org/0000-0002-0693-1514>)
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Repository: CRAN
Date/Publication: 2021-10-25 07:50:02 UTC

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New package shinyGovstyle with initial version 0.0.6
Package: shinyGovstyle
Title: Custom Gov Style Inputs for Shiny
Version: 0.0.6
Description: Collection of 'shiny' application styling that are the based on the GOV.UK Design System. See <https://design-system.service.gov.uk/components/> for details.
Depends: R (>= 3.1.0)
License: GPL-3
Encoding: UTF-8
URL: https://github.com/moj-analytical-services/shinyGovstyle
BugReports: https://github.com/moj-analytical-services/shinyGovstyle/issues
Imports: shiny (>= 0.14), htmltools, shinyjs, jsonlite
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-10-21 17:18:13 UTC; rosswyatt
Author: Ross Wyatt [aut, cre]
Maintainer: Ross Wyatt <ross.wyatt@justice.gov.uk>
Repository: CRAN
Date/Publication: 2021-10-25 07:30:09 UTC

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New package rnpn with initial version 1.2.3
Package: rnpn
Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (<https://usanpn.org/>), which includes data on various life history events that occur at specific times.
Version: 1.2.3
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Imports: httr (>= 1.1.0), jsonlite (>= 0.9.19), data.table (>= 1.9.6), sp (>= 1.1-0), tibble, curl, raster, rgdal, plyr, XML, magrittr
Suggests: ggplot2, testthat, covr, knitr, markdown, rmarkdown, RColorBrewer, vcr
VignetteBuilder: knitr
URL: https://docs.ropensci.org/rnpn/ (website) https://github.com/ropensci/rnpn/ (devel)
NeedsCompilation: no
Packaged: 2021-10-22 21:07:54 UTC; usanpn
Author: Alyssa Rosemartin [aut, cre], Scott Chamberlain [aut], Lee Marsh [aut], Kevin Wong [aut]
Maintainer: Alyssa Rosemartin <alyssa@usanpn.org>
Repository: CRAN
Date/Publication: 2021-10-25 07:10:10 UTC

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New package gpx with initial version 1.0.0
Package: gpx
Title: Process GPX Files into R Data Structures
Version: 1.0.0
Description: Process open standard GPX files into data.frames for further use and analysis in R.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.0)
Imports: xml2, rvest, lubridate
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-10-23 11:39:19 UTC; mark
Author: Mark Ewing [aut, cre]
Maintainer: Mark Ewing <b.mark@ewingsonline.com>
Repository: CRAN
Date/Publication: 2021-10-25 07:40:02 UTC

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New package epidemia with initial version 1.0.0
Package: epidemia
Title: Modeling of Epidemics using Hierarchical Bayesian Models
Version: 1.0.0
Description: Flexibly specify and fit Bayesian statistical models for epidemics. 'epidemia' leverages Rs formula interface so that users can parameterize reproduction numbers and ascertainment rates in terms of predictors. Infections are propagated over time using self-exciting point processes. Multiple regions can be modeled simultaneously with multilevel models. The models and framework behind the package are described in Bhatt et al. (2021) <arXiv:2012.00394>. The design of the package has been inspired by, and has borrowed from, 'rstanarm' (Goodrich et al., 2020) <https://mc-stan.org/rstanarm/>. 'rstan' (Stan Development Team, 2020) <https://mc-stan.org/> is used as the back end for fitting models.
License: GPL-3
URL: https://github.com/ImperialCollegeLondon/epidemia/
Encoding: UTF-8
LazyData: true
Biarch: true
Depends: R (>= 3.5.0)
Imports: dplyr (>= 0.8.5), methods, Rcpp (>= 0.12.0), rstan (>= 2.18.1), rstantools (>= 2.0.0), magrittr, rstanarm, lme4, ggplot2, Matrix, scales, Rdpack, stats, zoo, tidyr, rlang, bayesplot, hrbrthemes
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
Suggests: testthat, knitr, gridExtra, bookdown, EpiEstim, lubridate, kableExtra, extrafont
RdMacros: Rdpack
NeedsCompilation: yes
Packaged: 2021-10-23 13:26:11 UTC; jamesscott
Author: James Scott [aut, cre] (<https://orcid.org/0000-0003-0106-5618>), Axel Gandy [aut] (<https://orcid.org/0000-0002-6777-0451>), Swapnil Mishra [aut] (<https://orcid.org/0000-0002-8759-5902>), Juliette Unwin [aut] (<https://orcid.org/0000-0002-9120-4003>), Seth Flaxman [aut] (<https://orcid.org/0000-0002-2477-4217>), Samir Bhatt [aut] (<https://orcid.org/0000-0002-0891-4611>), Jonathan Ish-Horowicz [ctb] (<https://orcid.org/0000-0002-5386-6620>), Leon Wu [ctb], Ben Goodrich [ctb], Jonah Gabry [ctb], Trustees of Columbia University [cph] (R/helpers.R), Paul-Christian Burkner [cph] (R/misc.R), Triad Sou [cph] (R/geom_stepribbon.R), Kengo Nagashima [cph] (R/geom_stepribbon.R)
Maintainer: James Scott <james.scott15@imperial.ac.uk>
Repository: CRAN
Date/Publication: 2021-10-25 07:50:05 UTC

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New package EDFtest with initial version 0.1.0
Package: EDFtest
Title: Goodness of Fit Based on Empirical Distribution Function
Version: 0.1.0
Date: 2021-10-22
Description: This repository contains software for the calculation of goodness-of-fit test statistics and their P-values. The three statistics computed are the Empirical Distribution function statistics called Cramer-von Mises, Anderson-Darling, and Watson statistics. The statistics and their P-values can be used to assess an assumed distribution.The following distributions are available: Uniform, Normal, Gamma, Logistic, Laplace, Weibull, Extreme Value, and Exponential.
License: MIT + file LICENSE
Encoding: UTF-8
BugReports: https://github.com/LiYao-sfu/EDFtest/issues
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown, stringi, testthat (>= 3.0.0)
Imports: CompQuadForm (>= 1.4.3), rmutil (>= 1.1.5), stats
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-24 03:08:14 UTC; liyao
Author: Li Yao [aut, cre], Richard Lockhart [aut]
Maintainer: Li Yao <yaoliy@sfu.ca>
Repository: CRAN
Date/Publication: 2021-10-25 07:20:14 UTC

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New package DominoPredictionLogging with initial version 0.1.0
Package: DominoPredictionLogging
Language: en-US
Title: Domino Prediction Logging
Version: 0.1.0
Date: 2021-10-20
Description: Instrument prediction code that lets you capture inputs to the model, predictions, prediction properties, and other metadata.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: covr, DT, lintr, testthat, spelling, rhub
URL: https://www.dominodatalab.com
Imports: rjson, methods, uuid, lgr
NeedsCompilation: no
Packaged: 2021-10-23 12:54:57 UTC; vivekanandatadala
Author: Vivekananda Tadala [aut, cre], Domino Data Lab Inc. [cph]
Maintainer: Vivekananda Tadala <vivekananda.tadala@dominodatalab.com>
Repository: CRAN
Date/Publication: 2021-10-25 07:50:13 UTC

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New package DMCfun with initial version 2.0.2
Package: DMCfun
Title: Diffusion Model of Conflict (DMC) in Reaction Time Tasks
Version: 2.0.2
Date: 2021-10-12
Description: DMC model simulation detailed in Ulrich, R., Schroeter, H., Leuthold, H., & Birngruber, T. (2015). Automatic and controlled stimulus processing in conflict tasks: Superimposed diffusion processes and delta functions. Cognitive Psychology, 78, 148-174. Ulrich et al. (2015) <doi:10.1016/j.cogpsych.2015.02.005>. Decision processes within choice reaction-time (CRT) tasks are often modelled using evidence accumulation models (EAMs), a variation of which is the Diffusion Decision Model (DDM, for a review, see Ratcliff & McKoon, 2008). Ulrich et al. (2015) introduced a Diffusion Model for Conflict tasks (DMC). The DMC model combines common features from within standard diffusion models with the addition of superimposed controlled and automatic activation. The DMC model is used to explain distributional reaction time (and error rate) patterns in common behavioural conflict-like tasks (e.g., Flanker task, Simon task). This R-package implements the DMC model and provides functionality to fit the model to observed data. Further details are provided in the following paper: Mackenzie, I. G., & Dudschig, C. (2021). DMCfun: An R package for fitting Diffusion Model of Conflict (DMC) to reaction time and error rate data. Methods in Psychology, 100074. <doi:10.1016/j.metip.2021.100074>.
URL: https://github.com/igmmgi/DMCfun, https://CRAN.R-project.org/package=DMCfun, https://www.sciencedirect.com/science/article/pii/S259026012100031X
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: DEoptim, Rcpp (>= 0.12.16), dplyr (>= 1.0.0), parallel, pbapply, shiny, tidyr
Suggests: testthat
LinkingTo: Rcpp, BH
LazyData: true
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2021-10-21 10:35:44 UTC; ian
Author: Ian G. Mackenzie [cre, aut], Carolin Dudschig [aut]
Maintainer: Ian G. Mackenzie <ian.mackenzie@uni-tuebingen.de>
Repository: CRAN
Date/Publication: 2021-10-25 07:30:14 UTC

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New package collateral with initial version 0.5.2
Package: collateral
Title: Quickly Evaluate Captured Side Effects
Version: 0.5.2
Description: Map functions while capturing results, errors, warnings, messages and other output tidily, then filter and summarise data frames or lists on the basis of those side effects.
URL: https://collateral.jamesgoldie.dev, https://github.com/jimjam-slam/collateral
Language: en-AU
Depends: R (>= 3.1.0)
Imports: purrr, crayon, methods, pillar
License: MIT + file LICENSE
Encoding: UTF-8
BugReports: https://github.com/jimjam-slam/collateral/issues
Suggests: dplyr, tibble, tidyr, furrr, ggplot2, knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-24 05:58:40 UTC; rensa
Author: James Goldie [aut, cre] (<https://orcid.org/0000-0002-5024-6207>), Jean-Francois Zinque [ctb], Mikhail Balyasin [ctb]
Maintainer: James Goldie <me@jamesgoldie.dev>
Repository: CRAN
Date/Publication: 2021-10-25 07:50:09 UTC

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New package tidysmd with initial version 0.1.0
Package: tidysmd
Title: Tidy Standardized Mean Differences
Version: 0.1.0
Description: Tidy standardized mean differences ('SMDs'). 'tidysmd' uses the 'smd' package to calculate standardized mean differences for variables in a data frame, returning the results in a tidy format.
License: MIT + file LICENSE
URL: https://github.com/malcolmbarrett/tidysmd, https://malcolmbarrett.github.io/tidysmd/
BugReports: https://github.com/malcolmbarrett/tidysmd/issues
Depends: R (>= 2.10)
Imports: dplyr, ellipsis, glue, purrr, rlang, smd, stats, tidyr, tidyselect
Suggests: spelling, covr, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
Language: en-US
NeedsCompilation: no
Packaged: 2021-10-22 13:45:22 UTC; malcolmbarrett
Author: Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-25 07:00:02 UTC

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New package stepjglm with initial version 0.0.1
Package: stepjglm
Title: Variable Selection for Joint Modeling of Mean and Dispersion
Version: 0.0.1
Description: A Package for selecting variables for the joint modeling of mean and dispersion (including models for mixture experiments) based on hypothesis testing and the quality of model's fit. In each iteration of the selection process, a criterion for checking the goodness of fit is used as a filter for choosing the terms that will be evaluated by a hypothesis test. Pinto & Pereira (2021) <arXiv:2109.07978>.
Author: Leandro A. Pereira [aut, cre], Edmilson R. Pinto [aut]
Maintainer: Leandro A. Pereira <leandro.ap@ufu.br>
License: GPL-3
Depends: R (>= 3.5.0), stats
LazyData: true
Imports: rsq
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-10-22 18:16:33 UTC; lealv
Repository: CRAN
Date/Publication: 2021-10-25 06:50:02 UTC

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New package RepertoiR with initial version 0.0.1
Package: RepertoiR
Title: Repertoire Graphical Visualization
Version: 0.0.1
Description: Visualization platform for T cell receptor repertoire analysis output results. It includes comparison of sequence frequency among samples, network of similar sequences and convergent recombination source between species. Currently repertoire analysis is in early stage of development and requires new approaches for repertoire data examination and assessment as we intend to develop. No publication is available yet (will be available in the near future), Efroni (2021) <https:>.
License: MIT + file LICENSE
URL: https://github.com/systemsbiomed/RepertoiR
BugReports: https://github.com/systemsbiomed/RepertoiR/issues
Imports: circlize, grDevices, igraph, reshape2, stringdist, stringi, stringr
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-10-22 09:16:57 UTC; User
Author: Ido Hasson [aut, cre] (<https://orcid.org/0000-0001-8382-5638>), Sol Efroni [aut], Hagit Philip [aut], Alona Zilberberg [aut]
Maintainer: Ido Hasson <idoh@systemsbiomed.org>
Repository: CRAN
Date/Publication: 2021-10-25 07:00:21 UTC

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New package meteospain with initial version 0.0.2
Package: meteospain
Title: Access to Spanish Meteorological Stations Services
Version: 0.0.2
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG, Meteoclimatic...).
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: ggforce, ggplot2, keyring, knitr, rmarkdown, testthat (>= 3.0.0)
Imports: assertthat, crayon, dplyr, glue, httr, jsonlite, lubridate, magrittr, purrr, rlang, sf, stringr, tidyr, units, xml2, vctrs
Config/testthat/parallel: true
VignetteBuilder: knitr
URL: https://emf-creaf.github.io/meteospain/, https://github.com/emf-creaf/meteospain
BugReports: https://github.com/emf-creaf/meteospain/issues
NeedsCompilation: no
Packaged: 2021-10-22 11:42:33 UTC; malditobarbudo
Author: Victor Granda [aut, cre] (<https://orcid.org/0000-0002-0469-1991>), Miquel de Caceres [ctb] (<https://orcid.org/0000-0001-7132-2080>), Aitor Ameztegui [ctb] (<https://orcid.org/0000-0003-2006-1559>)
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-25 07:00:05 UTC

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New package FORTLS with initial version 1.0.4
Package: FORTLS
Title: Automatic Processing of TLS Point Cloud Data for Forestry Purposes
Version: 1.0.4
Date: 2021-10-22
Author: Juan Alberto Molina-Valero [aut, cph, cre], María José Ginzo Villamayor [aut, com], Manuel Antonio Novo Pérez [aut, com], Adela Martínez-Calvo [aut, com], Juan Gabriel Álvarez-González [aut, ths], Fernando Montes [aut], César Pérez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <juanalberto.molina.valero@usc.es>
Description: Process automation of Terrestrial Laser Scanner (TLS) point cloud data derived from single scans. 'FORTLS' enables (i) detection of trees and estimation of diameter at breast height (dbh), (ii) estimation of some stand variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories (FIs) at stand level and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2020, <doi:10.3390/IECF2020-08066>).
URL: https://github.com/Molina-Valero/FORTLS
BugReports: https://github.com/Molina-Valero/FORTLS/issues
License: GPL-3
Depends: R (>= 3.5.0)
Imports: dbscan, Distance, ggvoronoi, htmlwidgets, lidR, moments, plotly, progress, Rcpp(>= 1.0.7), raster, RCSF, scales, sp, tidyr, vroom
Suggests: testthat
LinkingTo: Rcpp, RcppEigen
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2021-10-22 14:48:00 UTC; Juan
Repository: CRAN
Date/Publication: 2021-10-25 07:00:23 UTC

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New package conText with initial version 1.0.0
Package: conText
Version: 1.0.0
Title: 'a la Carte' on Text (ConText) Embedding Regression
Description: A fast, flexible and transparent framework to estimate context-specific word and short document embeddings using the 'a la carte' embeddings approach developed by Khodak et al. (2018) <arXiv:1805.05388> and evaluate hypotheses about covariate effects on embeddings using the regression framework developed by Rodriguez et al. (2021)<https://github.com/prodriguezsosa/EmbeddingRegression>.
License: GPL-3
Depends: R (>= 3.6.0)
Imports: dplyr, Matrix (>= 1.3-2), quanteda (>= 3.0.0), text2vec (>= 0.6), reshape2 (>= 1.4.4), fastDummies (>= 1.6.3), stringr (>= 1.4.0), ggplot2, methods
URL: https://github.com/prodriguezsosa/EmbeddingRegression
BugReports: https://github.com/prodriguezsosa/ConText/issues
Maintainer: Pedro L. Rodriguez <pedro.rodriguez@Vanderbilt.Edu>
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Language: en-US
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2021-10-22 15:45:18 UTC; pedrorodriguez
Author: Pedro L. Rodriguez [aut, cre, cph] (<https://orcid.org/0000-0003-4762-4550>), Arthur Spirling [aut] (<https://orcid.org/0000-0001-9959-1805>), Brandon Stewart [aut] (<https://orcid.org/0000-0002-7657-3089>), Christopher Barrie [ctb] (<https://orcid.org/0000-0002-9156-990X>)
Repository: CRAN
Date/Publication: 2021-10-25 07:00:16 UTC

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Sun, 24 Oct 2021

New package osmdata with initial version 0.1.8
Package: osmdata
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Version: 0.1.8
Maintainer: Mark Padgham <mark.padgham@email.com>
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (<https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.
License: GPL-3
URL: https://docs.ropensci.org/osmdata/ (website) https://github.com/ropensci/osmdata/ (devel)
BugReports: https://github.com/ropensci/osmdata/issues
Depends: R (>= 3.2.4)
Imports: curl, httr, jsonlite, lubridate, magrittr, methods, Rcpp (>= 0.12.4), rvest, sp, tibble, utils, xml2
Suggests: knitr, markdown, raster, rmarkdown, sf, testthat
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
SystemRequirements: C++11
X-schema.org-applicationCategory: Data Access
Packaged: 2021-10-17 10:38:42 UTC; smexus
Author: Mark Padgham [aut, cre], Bob Rudis [aut], Robin Lovelace [aut], Maëlle Salmon [aut], Andrew Smith [ctb], James Smith [ctb], Andrea Gilardi [ctb], Enrico Spinielli [ctb], Anthony North [ctb], Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Finkelstein Noam [ctb, cph] (Author of included stub.R code), Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Repository: CRAN
Date/Publication: 2021-10-17 12:20:02 UTC

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New package covid19br with initial version 0.1.3
Package: covid19br
Title: Brazilian COVID-19 Pandemic Data
Version: 0.1.3
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at country, region, state, and city-levels. The package also downloads the world-level COVID-19 data from the John Hopkins University's repository.
URL: https://fndemarqui.github.io/covid19br/
BugReports: https://github.com/fndemarqui/covid19br/issues
Encoding: UTF-8
License: AGPL (>= 3)
Depends: R (>= 3.5.0)
Imports: data.table, dplyr, rlang, sf, tidyr
Suggests: ggrepel, kableExtra, knitr, leaflet, pracma, plotly, rmarkdown, testthat, tidyverse
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-17 16:55:28 UTC; fndemarqui
Author: Fabio Demarqui [aut, cre], Cristiano Santos [aut], Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Repository: CRAN
Date/Publication: 2021-10-17 17:50:02 UTC

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Fri, 22 Oct 2021

New package SSNbayes with initial version 0.0.1
Package: SSNbayes
Title: Bayesian Spatio-Temporal Analysis in Stream Networks
Version: 0.0.1
Depends: R (>= 3.5.0)
Imports: plyr, dplyr, rstan, SSN
Description: Fits Bayesian spatio-temporal models and makes predictions on stream networks using the approach by Santos-Fernandez, Edgar, et al. (2021)."Bayesian spatio-temporal models for stream networks" <arXiv:2103.03538>. In these models, spatial dependence is captured using stream distance and flow connectivity, while temporal autocorrelation is modelled using vector autoregression methods.
License: GPL-2
Encoding: UTF-8
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
URL: https://github.com/EdgarSantos-Fernandez/SSNbayes
BugReports: https://github.com/EdgarSantos-Fernandez/SSNbayes/issues
NeedsCompilation: no
Packaged: 2021-10-21 23:14:26 UTC; santosfe
Author: Edgar Santos-Fernandez [aut, cre, cph]
Maintainer: Edgar Santos-Fernandez <santosfe@qut.edu.au>
Repository: CRAN
Date/Publication: 2021-10-22 07:50:02 UTC

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New package ggfacto with initial version 0.2.2
Package: ggfacto
Title: Graphs for Correspondence Analysis
Version: 0.2.2
Description: Readable, complete and pretty graphs for correspondence analysis made with 'FactoMineR'. They can be rendered as interactive 'HTML' plots, showing useful informations at mouse hover. The interest is not mainly visual but statistical: it helps the reader to keep in mind the data contained in the cross-table or Burt table while reading the correspondence analysis, thus preventing over-interpretation. Graphs are made with 'ggplot2', which means that you can use the + syntax to manually add as many graphical pieces you want, or change theme elements.
URL: https://github.com/BriceNocenti/ggfacto
BugReports: https://github.com/BriceNocenti/ggfacto/issues
License: GPL (>= 3)
Encoding: UTF-8
Imports: magrittr (>= 1.5.0), FactoMineR (>= 2.0.0), ggiraph (>= 0.7.0), ggplot2 (>= 3.0.0), widgetframe (>= 0.3.0), dplyr (>= 1.0.0), forcats (>= 0.5.0), purrr (>= 0.3.0), rlang (>= 0.4.0), stringi (>= 1.4.6), stringr (>= 1.4.0), tibble (>= 3.0.0), tidyr (>= 1.0.0), tidyselect (>= 1.1.0), vctrs (>= 0.3.0), ggrepel (>= 0.9.0), gridExtra (>= 2.0), tabxplor (>= 1.0.0), stats (>= 4.0.0), grDevices (>= 4.0.0), htmlwidgets (>= 1.4.0), kableExtra (>= 1.3.0)
Suggests: finalfit (>= 1.0.0)
NeedsCompilation: no
Packaged: 2021-10-21 18:15:38 UTC; Brice
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-22 07:40:02 UTC

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New package garma with initial version 0.9.10
Package: garma
Title: Fitting and Forecasting Gegenbauer ARMA Time Series Models
Version: 0.9.10
Date: 2021-10-21
Maintainer: Richard Hunt <maint@huntemail.id.au>
Description: Methods for estimating univariate long memory-seasonal/cyclical Gegenbauer time series processes. See for example (2018) <doi:10.1214/18-STS649>. Refer to the vignette for details of fitting these processes.
License: GPL-3
URL: https://github.com/rlph50/garma
Encoding: UTF-8
Depends: forecast, ggplot2
Imports: Rsolnp, pracma, signal, zoo, lubridate, crayon, utils, nloptr, BB, GA, dfoptim, pso, FKF, tswge
Suggests: longmemo, yardstick, tidyverse, testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-21 21:12:24 UTC; richard
Author: Richard Hunt [aut, cre]
Repository: CRAN
Date/Publication: 2021-10-22 07:40:06 UTC

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New package BrailleR with initial version 0.32.1
Package: BrailleR
Title: Improved Access for Blind Users
Version: 0.32.1
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Description: Blind users do not have access to the graphical output from R without printing the content of graphics windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.
License: GPL-2
Depends: R (>= 3.4.0)
Imports: devtools, dplyr, extrafont, ggplot2, grid, gridGraphics, gridSVG, hunspell, knitr, magrittr, mathjaxr, moments, nortest, reticulate, rlang, rmarkdown, roloc, rolocISCCNBS, utils, whisker, XML, xtable
Suggests: ggfortify, installr, markdown, spelling
SystemRequirements: Python 3 and wxPython 4.0
VignetteBuilder: knitr
URL: https://github.com/ajrgodfrey/BrailleR
BugReports: https://github.com/ajrgodfrey/BrailleR/issues
RdMacros: mathjaxr
Language: en-US
NeedsCompilation: no
Packaged: 2021-10-22 00:24:00 UTC; ajgodfre
Author: A. Jonathan R. Godfrey [aut, cre], Debra Warren [aut], Donal Fitzpatrick [ctb], Duncan Murdoch [ctb], Greg Snow [ctb], Henrik Bengtsson [ctb], James Curtis [ctb], JooYoung Seo [ctb], Marshall Flax [ctb], Paul Murrell [aut], Sophie Banks [ctb], Timothy Bilton [aut], Tony Hirst [ctb], Tsan-Kuang Lee [ctb], Volker Sorge [aut], Yihui Xie [ctb]
Repository: CRAN
Date/Publication: 2021-10-22 08:00:06 UTC

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Thu, 21 Oct 2021

New package rcbayes with initial version 0.1.0
Package: rcbayes
Title: Estimate Rogers-Castro Migration Age Schedules with Bayesian Models
Version: 0.1.0
Description: A collection of functions to estimate Rogers-Castro migration age schedules using 'Stan'. This model which describes the fundamental relationship between migration and age in the form of a flexible multi-exponential migration model was most notably proposed in Rogers and Castro (1978) <doi:10.1068/a100475>.
License: MIT + file LICENSE
Encoding: UTF-8
Biarch: true
Depends: R (>= 3.4.0)
Imports: methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.1.1), Rdpack, dplyr, rlang, stats, tibble, tidybayes, magrittr, shiny, shinythemes
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests: knitr, rmarkdown, ggplot2
SystemRequirements: GNU make
VignetteBuilder: knitr
RdMacros: Rdpack
NeedsCompilation: yes
Packaged: 2021-10-21 02:40:57 UTC; jessieyeung
Author: Jessie Yeung [aut, cre], Monica Alexander [aut] (<https://orcid.org/0000-0002-8135-3435>)
Maintainer: Jessie Yeung <jessieyeung1@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-21 17:10:02 UTC

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New package jenga with initial version 1.0.0
Package: jenga
Title: Fast Extrapolation of Time Features using K-Nearest Neighbors
Version: 1.0.0
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Description: Fast extrapolation of univariate and multivariate time features using K-Nearest Neighbors. The compact set of hyper-parameters is tuned via grid or random search.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6)
Imports: purrr, abind, ggplot2, readr, stringr, lubridate, narray, imputeTS, scales, tictoc, modeest, moments, philentropy
URL: https://rpubs.com/giancarlo_vercellino/jenga
NeedsCompilation: no
Packaged: 2021-10-21 12:38:26 UTC; gvercellino
Repository: CRAN
Date/Publication: 2021-10-21 17:40:02 UTC

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New package GCPBayes with initial version 3.1.0
Package: GCPBayes
Title: Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure
Version: 3.1.0
Author: Taban Baghfalaki
Maintainer: Taban Baghfalaki <t.baghfalaki@gmail.com>
Description: Run a Gibbs sampler for a multivariate Bayesian sparse group selection model with Dirac, continuous and hierarchical spike prior for detecting pleiotropy on the traits. This package is designed for summary statistics containing estimated regression coefficients and its estimated covariance matrix. The methodology is available from: Baghfalaki, T., Sugier, P. E., Truong, T., Pettitt, A. N., Mengersen, K., & Liquet, B. (2021) <doi:10.1002/sim.8855>.
License: GPL (>= 2.0)
Encoding: UTF-8
Imports: MASS, arm, mvtnorm, invgamma, gdata, truncnorm, postpack, wiqid, usethis, Rcpp
LazyData: true
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2021-09-29 10:00:12 UTC; t_baghfalaki
Repository: CRAN
Date/Publication: 2021-10-21 17:30:02 UTC

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New package fdaMocca with initial version 0.1-0
Encoding: UTF-8
Package: fdaMocca
Version: 0.1-0
Author: Natalya Pya Arnqvist[aut, cre], Per Arnqvist [aut, cre], Sara Sjöstedt de Luna [aut]
Maintainer: Natalya Pya Arnqvist <nat.pya@gmail.com>
Title: Model-Based Clustering for Functional Data with Covariates
Date: 2021-10-21
Description: Routines for model-based functional cluster analysis for functional data with optional covariates. The idea is to cluster functional subjects (often called functional objects) into homogenous groups by using spline smoothers (for functional data) together with scalar covariates. The spline coefficients and the covariates are modelled as a multivariate Gaussian mixture model, where the number of mixtures corresponds to the number of clusters. The parameters of the model are estimated by maximizing the observed mixture likelihood via an EM algorithm (Arnqvist and Sjöstedt de Luna, 2019) <arXiv:1904.10265>. The clustering method is used to analyze annual lake sediment from lake Kassjön (Northern Sweden) which cover more than 6400 years and can be seen as historical records of weather and climate.
Depends: R (>= 3.6.0)
Imports: stats, graphics, Matrix, parallel, foreach, doParallel, mvtnorm, fda, grDevices
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2021-10-21 12:24:46 UTC; natalya
Repository: CRAN
Date/Publication: 2021-10-21 17:40:04 UTC

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New package CoordinateCleaner with initial version 2.0-20
Package: CoordinateCleaner
Title: Automated Cleaning of Occurrence Records from Biological Collections
Version: 2.0-20
Description: Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.
Language: en-gb
Encoding: UTF-8
License: GPL-3
URL: https://ropensci.github.io/CoordinateCleaner/
BugReports: https://github.com/ropensci/CoordinateCleaner/issues
Depends: R (>= 3.5.0)
Imports: dplyr, geosphere, ggplot2, graphics, grDevices, methods, raster, rgbif, rgeos, rgdal, rnaturalearth, stats, sp, tidyselect, utils
LazyData: true
Suggests: covr, countrycode, knitr, maps, magrittr, paleobioDB, rmarkdown, rnaturalearthdata, testthat, viridis
SystemRequirements: GDAL (>= 2.0.1)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-20 18:24:55 UTC; az64mycy
Author: Alexander Zizka [aut, cre], Daniele Silvestro [ctb], Tobias Andermann [ctb], Josue Azevedo [ctb], Camila Duarte Ritter [ctb], Daniel Edler [ctb], Harith Farooq [ctb], Andrei Herdean [ctb], Maria Ariza [ctb], Ruud Scharn [ctb], Sten Svanteson [ctb], Niklas Wengstrom [ctb], Vera Zizka [ctb], Alexandre Antonelli [ctb], Irene Steves [rev] (Irene reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>), Francisco Rodriguez-Sanchez [rev] (Francisco reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>)
Maintainer: Alexander Zizka <zizka.alexander@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-21 17:10:05 UTC

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New package scatterPlotMatrix with initial version 0.1.0
Package: scatterPlotMatrix
Title: 'Htmlwidget' for a Scatter Plot Matrix & Multiple Scatter Plot
Version: 0.1.0
Description: Create a scatter plot matrix, using 'htmlwidgets' package and 'd3.js'.
URL: https://ifpen.gitlabfr.com/detocs/scatterplotmatrix
BugReports: https://ifpen.gitlabfr.com/detocs/scatterplotmatrix/-/issues
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Imports: htmlwidgets
Suggests: testthat, shiny, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-20 17:07:25 UTC; chazalviel
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), David Chazalviel [aut, cre], Harry Stevens [cph] (d3-regression library in htmlwidgets/lib, https://github.com/HarryStevens/d3-regression)
Maintainer: David Chazalviel <david.chazalviel@club-internet.fr>
Repository: CRAN
Date/Publication: 2021-10-21 17:00:02 UTC

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New package supernova with initial version 2.4.4
Package: supernova
Title: Judd, McClelland, & Ryan Formatting for ANOVA Output
Version: 2.4.4
Date: 2021-10-20
Encoding: UTF-8
LazyData: yes
Description: Produces ANOVA tables in the format used by Judd, McClelland, and Ryan (2017, ISBN: 978-1138819832) in their introductory textbook, Data Analysis. This includes proportional reduction in error and formatting to improve ease the transition between the book and R.
License: GPL-3
Depends: R (>= 3.4.0)
Suggests: car, covr, lintr, lme4, testthat (>= 2.1.0), vdiffr, tidyr
Imports: ggplot2, tibble, cli, magrittr, purrr, rlang, stringr, vctrs, pillar (>= 1.5.0), methods, backports
URL: https://github.com/UCLATALL/supernova
BugReports: https://github.com/UCLATALL/supernova/issues
NeedsCompilation: no
Packaged: 2021-10-20 17:07:39 UTC; Adam
Author: Adam Blake [cre, aut] (<https://orcid.org/0000-0001-7881-8652>), Jeff Chrabaszcz [aut], Ji Son [aut] (<https://orcid.org/0000-0002-4258-4791>), Jim Stigler [aut] (<https://orcid.org/0000-0001-6107-7827>)
Maintainer: Adam Blake <adamblake@g.ucla.edu>
Repository: CRAN
Date/Publication: 2021-10-21 15:50:02 UTC

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New package shinyr with initial version 0.3.0
Package: shinyr
Title: Data Insights Through Inbuilt R Shiny App
Version: 0.3.0
Description: It builds dynamic R shiny based dashboards to analyze any CSV files. It provides simple dashboard design to subset the data, perform exploratory data analysis and preliminary machine learning (supervised and unsupervised). It also provides filters based on columns of interest.
Depends: R (>= 3.1.0),
Imports: dplyr, shiny, shinydashboard, tm, wordcloud, corrplot, randomForest, RColorBrewer, caret, nnet, plotly, e1071, knitr
Maintainer: Jayachandra N <itsjay510@gmail.com>
License: GPL-3
Encoding: UTF-8
Suggests: testthat
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2021-10-20 10:50:11 UTC; JJJN
Author: Jayachandra N [aut, cre], Pushker Ravindra [aut]
Repository: CRAN
Date/Publication: 2021-10-21 15:30:02 UTC

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New package repairData with initial version 0.1.0
Package: repairData
Title: Open Repair Alliance Datasets 2021
Version: 0.1.0
Description: The complete data set of open repair data, full compliant with the Open Repair Data Standards (ORDS). It combines the datasets contributed by partner organizations of the Open Repair Alliance (ORA). Last updated: 2021-02-22. The package also contains via quests enriched datasets on batteries, printer, mobiles, and tablets.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
URL: https://github.com/petzi53/repairData
BugReports: https://github.com/petzi53/repairData/issues
NeedsCompilation: no
Packaged: 2021-10-20 09:15:29 UTC; petzi
Author: Peter Baumgartner [aut, cre] (<https://orcid.org/0000-0003-4526-8791>)
Maintainer: Peter Baumgartner <petzi53@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-21 15:20:02 UTC

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New package pixelclasser with initial version 1.0.0
Package: pixelclasser
Title: Classifies Image Pixels by Colour
Version: 1.0.0
Description: Contains functions to classify the pixels of an image file by its colour. It implements a simple form of the techniques known as Support Vector Machine adapted to this particular problem.
Encoding: UTF-8
License: GPL-3
LazyData: false
Imports: graphics, grDevices, jpeg, tiff,
Suggests: knitr, rmarkdown, testthat, covr
VignetteBuilder: knitr, rmarkdown
URL: https://github.com/ropensci/pixelclasser
BugReports: https://github.com/ropensci/pixelclasser
Language: en-GB
NeedsCompilation: no
Packaged: 2021-10-20 15:08:15 UTC; mnium
Author: Carlos Real [aut, cre] (<https://orcid.org/0000-0002-5433-6728>), Quentin Read [rev]
Maintainer: Carlos Real <carlos.real@usc.es>
Repository: CRAN
Date/Publication: 2021-10-21 15:40:02 UTC

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New package opGMMassessment with initial version 0.1.0
Package: opGMMassessment
Title: Optimized Automated Gaussian Mixture Assessment
Version: 0.1.0
Author: Jorn Lotsch [aut,cre] (<https://orcid.org/0000-0002-5818-6958>), Sebastian Malkusch [aut] (<https://orcid.org/0000-0001-6766-140X>)
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Description: Necessary functions for optimized automated evaluation of the number and parameters of Gaussian mixtures in one-dimensional data. Various methods are available for parameter estimation and for determining the number of modes in the mixture.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: AdaptGauss, DataVisualizations, DistributionOptimization, cluster, mixtools, grDevices, methods, foreach, stats, utils, rlang, ggplot2, parallel, caTools, dplyr, mclust, mixAK, multimode, NbClust, ClusterR, doParallel
NeedsCompilation: no
Packaged: 2021-10-20 12:01:08 UTC; joern
Repository: CRAN
Date/Publication: 2021-10-21 15:30:05 UTC

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Wed, 20 Oct 2021

New package supercompress with initial version 1.0
Package: supercompress
Title: Supervised Compression of Big Data
Version: 1.0
Imports: FNN, stats
Description: A supervised compression method that incorporates the response for reducing big data to a carefully selected subset. Please see Joseph and Mak (2021) <doi:10.1002/sam.11508>. This research is supported by a U.S. National Science Foundation (NSF) grant CMMI-1921646.
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-10-19 18:57:05 UTC; billhuang
Author: Chaofan Huang [aut, cre], V. Roshan Joseph [aut]
Maintainer: Chaofan Huang <chaofan.huang@gatech.edu>
Repository: CRAN
Date/Publication: 2021-10-20 12:00:01 UTC

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New package catSplit with initial version 0.1.0
Package: catSplit
Title: Encode Categorical Variables with Split Information from CART
Version: 0.1.0
Description: Use primary and surrogate split information from CART (Classification and Regression Trees - Breiman L (1984)) as the vector representation for a categorical variable. Outputs binary columns for each categorical variable making use of target information.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: rpart, caret, dplyr, stats, utils, data.table, stringr, OpenML, farff
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-10-19 18:41:06 UTC; SORU
Author: Mine Gazioglu [aut, cre], Mustafa Baydogan [ctb]
Maintainer: Mine Gazioglu <mine.gazioglu40@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-20 11:50:02 UTC

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New package SenTinMixt with initial version 1.0.0
Package: SenTinMixt
Title: Parsimonious Mixtures of MSEN and MTIN Distributions
Version: 1.0.0
Description: Implements parsimonious mixtures of MSEN and MTIN distributions via expectation- maximization based algorithms for model-based clustering. For each mixture component, parsimony is reached via the eigen-decomposition of the scale matrices and by imposing a constraint on the tailedness parameter. This produces a family of 28 parsimonious mixture models for each distribution.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: doSNOW, foreach, snow, TSdist, tidyr, data.table, expint, zipfR, mclust, rlist, withr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-10-19 14:37:09 UTC; Daniele
Author: Salvatore D. Tomarchio [aut, cre], Bagnato Luca [aut], Antonio Punzo [aut]
Maintainer: Salvatore D. Tomarchio <daniele.tomarchio@unict.it>
Repository: CRAN
Date/Publication: 2021-10-20 06:50:02 UTC

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New package proxirr with initial version 0.1
Package: proxirr
Title: Alpha and Beta Proximity to Irreplaceability
Date: 2021-10-13
Version: 0.1
Description: Functions to measure Alpha and Beta Proximity to Irreplaceability. The methods for Alpha and Beta irreplaceability were first described in: Baisero D., Schuster R. & Plumptre A.J. Redefining and Mapping Global Irreplaceability. Conservation Biology 2021;1-11. <doi:10.1111/cobi.13806>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: tinytest
NeedsCompilation: no
Packaged: 2021-10-19 14:12:04 UTC; redlist
Author: Daniele Baisero [aut, cre, cph] (<https://orcid.org/0000-0002-1266-7174>)
Maintainer: Daniele Baisero <daniele.baisero@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-20 06:40:02 UTC

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New package MixtureMissing with initial version 1.0.0
Package: MixtureMissing
Title: Robust Model-Based Clustering for Data Sets with Missing Values at Random
Version: 1.0.0
Description: Implementation of robust model based cluster analysis with missing data. The models used are: Multivariate Contaminated Normal Mixtures (MCNM), Multivariate Student's t Mixtures (MtM), and Multivariate Normal Mixtures (MNM) for data sets with missing values at random. "Cluster analysis and outlier detection with missing data" Hung Tong, Cristina Tortora (2020) <arXiv:2012.05394>.
Imports: ContaminatedMixt (>= 1.3.4.1), mvtnorm (>= 1.1-2), mnormt (>= 2.0.2), cluster (>= 2.1.2), rootSolve (>= 1.8.2.2), ggplot2 (>= 3.3.5), GGally (>= 2.0.0)
Suggests: mice (>= 3.10.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Repository: CRAN
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2021-10-18 23:10:07 UTC; hungt
Author: Hung Tong [aut, cre], Cristina Tortora [aut, ths, dgs]
Maintainer: Hung Tong <hungtongmx@gmail.com>
Date/Publication: 2021-10-20 06:40:05 UTC

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Tue, 19 Oct 2021

New package R2BayesX with initial version 1.1-1.1
Package: R2BayesX
Version: 1.1-1.1
Date: 2017-12-05
Title: Estimate Structured Additive Regression Models with 'BayesX'
Description: An R interface to estimate structured additive regression (STAR) models with 'BayesX'.
Depends: R (>= 2.13.0), BayesXsrc, colorspace, mgcv
Suggests: akima, coda, maps, maptools, MBA, parallel, shapefiles, sp, spdep, splines, rgdal, spData, rgeos
Imports: methods
License: GPL-2 | GPL-3
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2021-10-19 11:35:09 UTC; hornik
Author: Nikolaus Umlauf [aut, cre], Thomas Kneib [aut], Stefan Lang [aut], Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Repository: CRAN
Date/Publication: 2021-10-19 12:06:37 UTC

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New package BayesXsrc with initial version 3.0-1.1
Package: BayesXsrc
Version: 3.0-1.1
Date: 2018-04-13
Title: R Package Distribution of the BayesX C++ Sources
Description: BayesX performs Bayesian inference in structured additive regression (STAR) models. The R package BayesXsrc provides the BayesX command line tool for easy installation. A convenient R interface is provided in package R2BayesX.
Depends: R (>= 2.8.0)
Suggests: R2BayesX
SystemRequirements: GNU make
License: GPL-2 | GPL-3
URL: http://www.BayesX.org/
NeedsCompilation: yes
Packaged: 2021-10-18 17:26:24 UTC; hornik
Author: Nikolaus Umlauf [aut, cre], Daniel Adler [aut], Thomas Kneib [aut], Stefan Lang [aut], Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Repository: CRAN
Date/Publication: 2021-10-19 09:33:24 UTC

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New package visxhclust with initial version 1.0.0
Package: visxhclust
Title: A Shiny App for Visual Exploration of Hierarchical Clustering
Version: 1.0.0
Maintainer: Rafael Henkin <r.henkin@qmul.ac.uk>
Description: A Shiny application and functions for visual exploration of hierarchical clustering with numeric datasets. Allows users to iterative set hyperparameters, select features and evaluate results through various plots and computation of evaluation criteria.
License: GPL-3
URL: https://github.com/rhenkin/visxhclust
BugReports: https://github.com/rhenkin/visxhclust/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
biocViews:
Imports: shiny, shinyhelper, shinycssloaders, bsplus, DT, ggplot2, dplyr, readr, tidyr, cluster, fastcluster, clusterCrit, dunn.test, RColorBrewer, dendextend, ComplexHeatmap, circlize, patchwork, knitr, kableExtra
Suggests: testthat (>= 3.0.0), rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-18 14:50:38 UTC; rafaelhenkin
Author: Rafael Henkin [aut, cre]
Repository: CRAN
Date/Publication: 2021-10-19 07:20:02 UTC

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New package QBMS with initial version 0.6
Package: QBMS
Version: 0.6
Date: 2021-10-08
Title: Query the Breeding Management System 'BMS'
Author: Khaled Al-Shamaa [aut, cre], Mariano Omar Crimi [ctb], Zakaria Kehel [ctb], ICARDA [cph]
Maintainer: Khaled Al-Shamaa <k.el-shamaa@cgiar.org>
Depends: R (>= 3.1.0)
Description: Query the Breeding Management System 'BMS' database (using 'BrAPI' calls) to help breeders as targeted end-users retrieving data directly into their analyzing pipelines.
License: GPL (>= 3)
URL: https://github.com/icarda-git/QBMS
BugReports: https://github.com/icarda-git/QBMS/issues
LazyData: FALSE
Imports: utils, httr, tcltk, jsonlite
NeedsCompilation: no
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Packaged: 2021-10-18 11:10:57 UTC; Kel-shamaa
Repository: CRAN
Date/Publication: 2021-10-19 07:20:08 UTC

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New package npcs with initial version 0.1.0
Package: npcs
Title: Neyman-Pearson Classification via Cost-Sensitive Learning
Version: 0.1.0
Description: We connect the multi-class Neyman-Pearson classification (NP) problem to the cost-sensitive learning (CS) problem, and propose two algorithms (NPMC-CX and NPMC-ER) to solve the multi-class NP problem through cost-sensitive learning tools. Under certain conditions, the two algorithms are shown to satisfy multi-class NP properties. More details are available in the paper "Neyman-Pearson Multi-class Classification via Cost-sensitive Learning" (Ye Tian and Yang Feng, 2021), which will be posted on arXiv soon.
Imports: dfoptim, nnet, randomForest, e1071, magrittr, MASS, smotefamily, rpart, foreach, naivebayes, caret, formatR
License: GPL-2
Depends: R (>= 3.5.0)
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-18 14:16:01 UTC; yetian
Author: Ye Tian [aut, cre], Yang Feng [aut]
Maintainer: Ye Tian <ye.t@columbia.edu>
Repository: CRAN
Date/Publication: 2021-10-19 07:20:05 UTC

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New package Platypus with initial version 3.2.3
Package: Platypus
Title: Single-Cell Immune Repertoire and Gene Expression Analysis
Description: We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology (Yermanos A, et al (2021) <doi:10.1093/nargab/lqab023>).
Version: 3.2.3
Date: 2021-09-23
Maintainer: Alexander Yermanos <ayermanos@gmail.com>
Depends: R(>= 3.5.0)
Imports: BiocGenerics, Biostrings, dplyr, ggplot2, knitr, jsonlite, Matrix, plyr, reshape2, rmarkdown, seqinr, Seurat, SeuratObject, stringr, tibble, tidyr, utils, useful
Suggests: AnnotationDbi, ape, circlize, cowplot, data.table, doParallel, fda.usc, fgsea, ggrepel, ggridges, ggseqlogo, grid, gridExtra, harmony, igraph, IRanges, limma, keras, methods, msigdbr, org.Mm.eg.db, pheatmap, phytools, purrr, scales, SummarizedExperiment, stringdist, tensorflow, vegan, testthat (>= 3.0.0)
License: GPL-2
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-18 02:39:18 UTC; vickr
Author: Alexander Yermanos [aut, cre], Andreas Agrafiotis [ctb], Raphael Kuhn [ctb], Victor Kreiner [ctb], Damiano Robbiani [ctb], Josephine Yates [ctb], Jiami Han [ctb], Chrysa Papadopoulou [ctb], Cédric Weber [ctb], Danielle Shlesinger [ctb], Raphael Dizerens [ctb]
Repository: CRAN
Date/Publication: 2021-10-19 07:00:02 UTC

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Mon, 18 Oct 2021

New package rglobi with initial version 0.2.27
Encoding: UTF-8
Language: en-US
Package: rglobi
Title: R Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods provided by Global Biotic Interactions (GloBI) (<https://www.globalbioticinteractions.org/>). GloBI provides access to spatial-temporal species interaction records from sources all over the world. rglobi provides methods to search species interactions by location, interaction type, and taxonomic name. In addition, it supports Cypher, a graph query language, to allow for executing custom queries on the GloBI aggregate species interaction data set.
Version: 0.2.27
Date: 2021-10-14
URL: https://docs.ropensci.org/rglobi/, https://github.com/ropensci/rglobi
BugReports: https://github.com/ropensci/rglobi/issues
VignetteBuilder: knitr
Depends: R (>= 3.0.1)
License: MIT + file LICENSE
Imports: rjson (>= 0.2.13), readr (>= 1.3.1), RCurl (>= 0.3.4), curl (>= 0.3.3)
Suggests: testthat(>= 0.7), openssl, httr, markdown, knitr
NeedsCompilation: no
Packaged: 2021-10-18 21:30:06 UTC; jorrit
Author: Jorrit Poelen [aut, cre], Stephen Gosnell [aut], Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>
Repository: CRAN
Date/Publication: 2021-10-18 22:30:02 UTC

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New package abmR with initial version 1.0.4
Package: abmR
Title: Agent-Based Models in R
Version: 1.0.4
Maintainer: Benjamin Gochanour <ben.gochanour@gmail.com>
Description: Supplies tools for running agent-based models (ABM) in R, as discussed in Gochanour et al. (2021) <doi:10.1101/2021.09.15.460374> The package contains two movement functions, each of which is based on the Ornstein-Uhlenbeck (OU) model (Ornstein & Uhlenbeck, 1930) <doi:10.1103/PhysRev.36.823>. It also contains several visualization and data summarization functions to facilitate the presentation of simulation results.
License: GPL (>= 3)
Suggests: jpeg, knitr
Encoding: UTF-8
Depends: R (>= 3.5)
Imports: sp, rgdal, table1, googledrive, swfscMisc, geosphere, kableExtra, gtsummary, ggplot2, gstat, purrr, rnaturalearth, rnaturalearthdata, sf, tmap, raster, utils, stats, methods, rgeos
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-14 21:47:13 UTC; javifl
Author: Benjamin Gochanour [aut, cre], Javier Fernandez-Lopez [aut], Andrea Contina [aut]
Repository: CRAN
Date/Publication: 2021-10-18 18:10:08 UTC

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New package ctrialsgov with initial version 0.2.5
Package: ctrialsgov
Title: Query Data from U.S. National Library of Medicine's Clinical Trials Database
Version: 0.2.5
Maintainer: Taylor Arnold <tarnold2@richmond.edu>
Description: Tools to create and query database from the U.S. National Library of Medicine's Clinical Trials database <https://clinicaltrials.gov/>. Functions provide access a variety of techniques for searching the data using range queries, categorical filtering, and by searching for full-text keywords. Minimal graphical tools are also provided for interactively exploring the constructed data.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: dplyr, utils, ggplot2, lubridate, plotly, purrr, rlang, stringi, tibble, DBI, methods, Matrix, htmlwidgets
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0), usethis
VignetteBuilder: knitr
LazyData: true
LazyDataCompression: bzip2
NeedsCompilation: no
Packaged: 2021-10-18 02:25:35 UTC; admin
Author: Taylor Arnold [aut, cre] (<https://orcid.org/0000-0003-0576-0669>), Auston Wei [aut], Michael J. Kane [aut] (<https://orcid.org/0000-0003-1899-6662>)
Repository: CRAN
Date/Publication: 2021-10-18 16:00:02 UTC

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New package bayesPO with initial version 0.2.0
Package: bayesPO
Title: Bayesian Inference for Presence-Only Data
Version: 0.2.0
Date: 2021-10-13
Contact: Guido Alberti Moreira <guidoalber@gmail.com>
Maintainer: Guido Alberti Moreira <guidoalber@gmail.com>
Description: Presence-Only data is best modelled with a Point Process Model. The work of Moreira (2020) provides a way to use exact Bayesian inference to model this type of data, which is implemented in this package.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
LinkingTo: Rcpp, RcppEigen, RcppProgress
Imports: Rcpp, coda, parallel, methods, RcppProgress, graphics, stats, tools
Suggests: bayesplot, knitr, rmarkdown, webshot, ggplot2, MASS
URL: <http://www.pg.im.ufrj.br/teses/Estatistica/Doutorado/043.pdf>
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-10-16 10:51:06 UTC; anthorg
Author: Guido Alberti Moreira [cre, aut] (<https://orcid.org/0000-0001-7557-0874>)
Repository: CRAN
Date/Publication: 2021-10-18 15:20:02 UTC

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New package vntrs with initial version 0.1.0
Package: vntrs
Title: Variable Neighborhood Trust Region Search
Version: 0.1.0
Date: 2021-10-09
Description: An implementation of the variable neighborhood trust region algorithm Bierlaire et al. (2009) "A Heuristic for Nonlinear Global Optimization" <doi:10.1287/ijoc.1090.0343>.
Imports: trust
License: GPL-3
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-10-15 08:04:52 UTC; Lennart
Author: Lennart Oelschläger [aut, cre] (<https://orcid.org/0000-0001-5421-9313>)
Maintainer: Lennart Oelschläger <lennart.oelschlaeger@uni-bielefeld.de>
Repository: CRAN
Date/Publication: 2021-10-18 14:30:02 UTC

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New package TUFLOWR with initial version 0.1.0
Package: TUFLOWR
Title: Helper Functions for 'TUFLOW FV' Models
Version: 0.1.0
Author: Matt Gibbs [aut, cre]
Maintainer: Matt Gibbs <gibbs.ms@gmail.com>
URL: <https://github.com/matt-s-gibbs/TUFLOWR>
Description: Helper functions for 'TUFLOW FV' models. Current functionality includes reading in and plotting output POINTS files and generating initial conditions based on point observations.
License: GPL-3
Depends: R (>= 4.0.0)
Encoding: UTF-8
Imports: raster, readr, tibble, tidyr, stringr, rgdal, sp, dplyr, gstat, lubridate, ggplot2, rlang, magrittr
NeedsCompilation: no
Packaged: 2021-10-15 05:17:28 UTC; MGIBBS
Repository: CRAN
Date/Publication: 2021-10-18 14:30:05 UTC

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New package skilljaR with initial version 0.0.1
Package: skilljaR
Title: Connect to Your 'Skilljar' Data with R
Version: 0.0.1
Description: Functions that simplify calls to the 'Skilljar' API. See <https://api.skilljar.com/docs/> for documentation on the 'Skilljar' API. This package is not supported by 'Skilljar'.
Depends: R (>= 4.1.0)
License: CC0
Encoding: UTF-8
Imports: httr (>= 1.4.2), jsonlite (>= 1.7.2), purrr (>= 0.3.4), dplyr (>= 1.0.7), magrittr (>= 2.0.1)
NeedsCompilation: no
Packaged: 2021-10-15 20:12:28 UTC; c.umphlett
Author: Chris Umphlett [aut, cre]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-18 14:40:02 UTC

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New package ggokabeito with initial version 0.1.0
Package: ggokabeito
Title: 'Okabe-Ito' Scales for 'ggplot2' and 'ggraph'
Version: 0.1.0
Description: Discrete scales for the colorblind-friendly 'Okabe-Ito' palette, including 'color', 'fill', and 'edge_colour'. 'ggokabeito' provides 'ggplot2' and 'ggraph' scales to easily use the 'Okabe-Ito' palette in your data visualizations.
License: MIT + file LICENSE
URL: https://github.com/malcolmbarrett/ggokabeito, https://malcolmbarrett.github.io/ggokabeito/
BugReports: https://github.com/malcolmbarrett/ggokabeito/issues
Depends: R (>= 4.0.0)
Imports: ggplot2, grDevices
Suggests: covr, ggraph, igraph, spelling, testthat (>= 3.0.0), vdiffr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2021-10-15 19:30:07 UTC; malcolmbarrett
Author: Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-18 14:40:04 UTC

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New package klassR with initial version 0.1.7
Package: klassR
Title: Classifications and Codelists for Statistics Norway
Version: 0.1.7
Author: Susie Jentoft, Lisa Li, Diana-Cristina Iancu
Maintainer: Susie Jentoft <susie.jentoft@ssb.no>
Description: Functions to search, retrieve and apply classifications and codelists using Statistics Norway's API <https://www.ssb.no/klass> from the system 'KLASS'. Retrieves classifications by date with options to choose language, hierarchical level and formatting.
Imports: tm, httr, jsonlite
BugReports: https://github.com/statisticsnorway/klassR/issues
License: Apache License 2.0
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-10-17 09:14:33 UTC; coo
Repository: CRAN
Date/Publication: 2021-10-18 09:10:02 UTC

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Sun, 17 Oct 2021

New package RSC with initial version 2.0
Package: RSC
Title: Robust and Sparse Correlation Matrix
Description: Performs robust and sparse correlation matrix estimation. Robustness is achieved based on a simple robust pairwise correlation estimator, while sparsity is obtained based on thresholding. The optimal thresholding is tuned via cross-validation. See Serra, Coretto, Fratello and Tagliaferri (2018) <doi:10.1093/bioinformatics/btx642>.
Author: Luca Coraggio [cre, aut], Pietro Coretto [aut], Angela Serra [aut], Roberto Tagliaferri [ctb]
Maintainer: Luca Coraggio <luca.coraggio@unina.it>
NeedsCompilation: yes
Imports: stats, graphics, Matrix, methods, parallel, foreach, doParallel, utils
License: GPL (>= 2)
Version: 2.0
Date: 2021-10-14
Packaged: 2021-10-14 14:44:39 UTC; luco
Repository: CRAN
Date/Publication: 2021-10-17 20:00:08 UTC

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New package qra with initial version 0.2.6
Package: qra
Title: Quantal Response Analysis for Dose-Mortality Data
Date: 2021-10-10
Version: 0.2.6
Maintainer: John Maindonald <john@statsresearch.co.nz>
Description: Functions are provided that implement the use of the Fieller's formula methodology, for calculating a confidence interval for a ratio of (possibly, correlated) means. See Fieller (1954) <doi:10.1111/j.2517-6161.1954.tb00159.x>. Here, the application of primary interest is to studies of insect mortality response to increasing doses of a fumigant, or, e.g., to time in coolstorage. The formula is used to calculate a confidence interval for the dose or time required to achieve a specified mortality proportion, commonly 0.5 or 0.99. Vignettes demonstrate link functions that may be considered, checks on fitted models, and alternative choices of error family. Note in particular the betabinomial error family. See also Maindonald, Waddell, and Petry (2001) <doi:10.1016/S0925-5214(01)00082-5>.
Encoding: UTF-8
License: GPL-3
Depends: R (>= 4.1.0), lattice, latticeExtra, knitr, rmarkdown
Imports: lme4, splines, ggplot2
Suggests: robustlmm, MASS, fitODBOD, VGAM, glmmTMB (>= 1.1.2), gamlss, prettydoc, DHARMa, kableExtra (>= 1.2), plotrix, dfoptim, optimx, bookdown
VignetteBuilder: knitr, rmarkdown, bookdown, prettydoc
LazyData: TRUE
NeedsCompilation: no
Packaged: 2021-10-10 07:36:57 UTC; johnm1
Author: John Maindonald [aut, cre] (<https://orcid.org/0000-0002-0106-9224>)
Repository: CRAN
Date/Publication: 2021-10-17 20:00:02 UTC

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Sat, 16 Oct 2021

New package logib with initial version 0.1.1
Package: logib
Title: Salary Analysis by the Swiss Federal Office for Gender Equality
Version: 0.1.1
Description: Implementation of the Swiss Confederation's standard analysis model for salary analyses <https://www.ebg.admin.ch/dam/ebg/en/dokumente/lohngleichheit/infos-zu-analysen/standard-analysemodellzurueberpruefungderlohngleichheitzwischenf.pdf.download.pdf/methodological_approachformonitoringcompliancewithwageequalitybe.pdf> in R. The analysis is run at company-level and the model is intended for companies with 50 or more employees (apprentices, trainees/interns and expats are not included in the analysis). Employees with at least 100 employees are required by the Gender Equality Act to conduct an equal pay analysis. This package allows users to run the equal salary analysis in R, providing additional transparency with respect to the methodology and simple automation possibilities.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: lubridate (>= 1.7.9), readxl (>= 1.3.1)
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-10-16 15:04:15 UTC; 09607938
Author: Jonathan Chassot [aut, cre], Jeremy Kolly [ctb], Federal Office for Gender Equality of Switzerland [cph, fnd]
Maintainer: Jonathan Chassot <jonathanlaurentdominique.chassot@ebg.admin.ch>
Repository: CRAN
Date/Publication: 2021-10-16 23:30:13 UTC

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New package basket with initial version 0.10.11
Package: basket
Title: Basket Trial Analysis
Version: 0.10.11
Description: Implementation of multisource exchangeability models for Bayesian analyses of prespecified subgroups arising in the context of basket trial design and monitoring. The R 'basket' package facilitates implementation of the binary, symmetric multi-source exchangeability model (MEM) with posterior inference arising from both exact computation and Markov chain Monte Carlo sampling. Analysis output includes full posterior samples as well as posterior probabilities, highest posterior density (HPD) interval boundaries, effective sample sizes (ESS), mean and median estimations, posterior exchangeability probability matrices, and maximum a posteriori MEMs. In addition to providing "basketwise" analyses, the package includes similar calculations for "clusterwise" analyses for which subgroups are combined into meta-baskets, or clusters, using graphical clustering algorithms that treat the posterior exchangeability probabilities as edge weights. In addition plotting tools are provided to visualize basket and cluster densities as well as their exchangeability. References include Hyman, D.M., Puzanov, I., Subbiah, V., Faris, J.E., Chau, I., Blay, J.Y., Wolf, J., Raje, N.S., Diamond, E.L., Hollebecque, A. and Gervais, R (2015) <doi:10.1056/NEJMoa1502309>; Hobbs, B.P. and Landin, R. (2018) <doi:10.1002/sim.7893>; Hobbs, B.P., Kane, M.J., Hong, D.S. and Landin, R. (2018) <doi:10.1093/annonc/mdy457>; and Kaizer, A.M., Koopmeiners, J.S. and Hobbs, B.P. (2017) <doi:10.1093/biostatistics/kxx031>.
Depends: R (>= 3.5.0)
License: LGPL-2
Maintainer: Michael J. Kane <michael.kane@yale.edu>
Imports: GenSA, foreach, ggplot2, stats, tibble, tidyr, dplyr, igraph, gridExtra, itertools, crayon, cli, RColorBrewer, tidygraph, ggraph,
LazyData: true
Encoding: UTF-8
URL: https://github.com/kaneplusplus/basket
BugReports: https://github.com/kaneplusplus/basket/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), doParallel
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-14 19:42:41 UTC; mike
Author: Nan Chen [aut], Ryan Hafen [ctb], Brian Hobbs [aut], Alex Kaizer [aut], Michael J. Kane [aut, cre] (<https://orcid.org/0000-0003-1899-6662>)
Repository: CRAN
Date/Publication: 2021-10-16 23:30:22 UTC

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Fri, 15 Oct 2021

New package MALDIrppa with initial version 1.0.5-1
Package: MALDIrppa
Title: MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis
Version: 1.0.5-1
Date: 2021-10-09
Maintainer: Javier Palarea-Albaladejo <javier.palarea@udg.edu>
Depends: R (>= 3.2.5), MALDIquant, signal, robustbase, lattice
ByteCompile: yes
Description: Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data (Palarea-Albaladejo et al. (2018) <doi:10.1093/bioinformatics/btx628>).
License: GPL (>= 2)
Repository: CRAN
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-10-11 14:43:03 UTC; Japal
Author: Javier Palarea-Albaladejo [cre, aut] (<https://orcid.org/0000-0003-0162-669X>), Paolo Ribeca [ctb] (<https://orcid.org/0000-0001-5599-3933>), William Constantine [ctb] (Author of original C code used in archived wtmsa and ifultools R packages.), Keith L. Davidson [ctb] (Author of original C code used in archived wtmsa and ifultools R packages.), Insightful Corp. [cph] (Copyright holder named in some original C code used in archived wtmsa and ifultools R packages.)
Date/Publication: 2021-10-15 09:30:05 UTC

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New package L1mstate with initial version 1.0.1
Package: L1mstate
Title: L1-Regularized Multi-State Models
Version: 1.0.1
Date: 2021-10-7
Author: Xuan Dang
Maintainer: Xuan Dang <xuandang11289@gmail.com>
Description: Fitting the regularization path of the L1-regularized multi-state models since they can exploit sparsity structure of input. Different tuning regularization parameter methods are provided. The cumulative hazard rate estimation and the transition probability predictions can be made from the fitted models.
License: GPL (>= 2)
Encoding: UTF-8
Imports: Rcpp (>= 1.0.1)
LinkingTo: Rcpp, RcppEigen
Depends: Matrix (>= 1.2-10), MASS, mstate, colorspace
NeedsCompilation: yes
Packaged: 2021-10-11 13:43:10 UTC; xuand
Repository: CRAN
Date/Publication: 2021-10-15 09:10:12 UTC

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New package uniset with initial version 0.2.1
Package: uniset
Title: Dynamic Settings File
Version: 0.2.1
Maintainer: Bernhard Pollner <bernhard.pollner@mac.com>
Description: Any package (subsequently called 'target package') is enabled to provide its users an easily accessible, user-friendly and human readable text file where key=value pairs (used by functions defined in the target package) can be saved. This settings file lives in a location defined by the user of the target package, and its user-defined values remain unchanged even when the author of the target package is introducing or deleting keys, or when the target package is updated or re-installed.
URL: https://bpollner.github.io/uniset/
BugReports: https://github.com/bpollner/uniset/issues
Language: en-US
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.3.2)
Imports: easycsv
Suggests: covr, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-10-14 12:36:42 UTC; bernhard
Author: Bernhard Pollner [cre, aut], Zoltan Kovacs [aut]
Repository: CRAN
Date/Publication: 2021-10-15 07:50:01 UTC

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New package slasso with initial version 1.0.0
Package: slasso
Title: S-LASSO Estimator for the Function-on-Function Linear Regression
Version: 1.0.0
Description: Implements the smooth LASSO estimator for the function-on-function linear regression model described in Centofanti et al. (2020) <arXiv:2007.00529>.
License: GPL (>= 3)
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo
Depends: inline
Imports: Rcpp, RcppArmadillo, fda, fda.usc, matrixcalc, parallel, matrixStats, MASS, plot3D, methods, cxxfunplus
URL: https://github.com/unina-sfere/slasso
BugReports: https://github.com/unina-sfere/slasso
SystemRequirements: GNU make
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: yes
Packaged: 2021-10-14 12:23:55 UTC; fabio
Author: Fabio Centofanti [cre, aut], Antonio Lepore [aut], Simone Vantini [aut], Matteo Fontana [aut]
Maintainer: Fabio Centofanti <fabio.centofanti@unina.it>
Repository: CRAN
Date/Publication: 2021-10-15 07:40:02 UTC

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New package pharmr with initial version 0.33.1
Package: pharmr
Encoding: UTF-8
Version: 0.33.1
Date: 2021-10-13
Title: Interface to the 'Pharmpy' 'Pharmacometrics' Library
Maintainer: Rikard Nordgren <rikard.nordgren@farmaci.uu.se>
Depends: R (>= 3.3.0), altair (>= 4.0.0)
SystemRequirements: Python (>= 3.6.0)
Imports: reticulate (>= 1.19), utils
Suggests: testthat, magrittr, here
NeedsCompilation: no
Description: Interface to the 'Pharmpy' 'pharmacometrics' library. The 'Reticulate' package is used to interface Python from R.
Config/reticulate: list( packages = list( list(package = "altair"), list(package = "pharmpy-core") ) )
URL: https://github.com/pharmpy/pharmr
BugReports: https://github.com/pharmpy/pharmr/issues
License: BSD_2_clause + file LICENSE
Packaged: 2021-10-14 11:49:57 UTC; rikard
Author: Rikard Nordgren [aut, cre, cph], Stella Belin [aut, cph], Mats O. Karlsson [sad], Andrew C. Hooker [sad], Sebastian Ueckert [sad] (<https://orcid.org/0000-0002-3712-0255>), Simon Carter [rev], Simon Buatois [rev], João A. Abrantes [rev], F. Hoffmann-La Roche Ltd. [fnd]
Repository: CRAN
Date/Publication: 2021-10-15 07:30:02 UTC

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New package palmid with initial version 0.0.3
Package: palmid
Title: RdRP Analysis Suite
Description: R Analysis suite for viral RNA dependent RNA polymerase (RdRP). Statistical and meta-data analysis of 'palmscan' output and 'palmDB'/ 'DIAMOND' alignment files. Cross reference an input RNA virus against 145,000 RdRP identified in the Serratus project.
Version: 0.0.3
URL: https://serratus.io/palmid
BugReports: https://github.com/ababaian/palmid/issues
License: AGPL-3
Encoding: UTF-8
LazyData: true
Suggests: sf, rnaturalearth, rnaturalearthdata
Imports: dbplyr, downloadthis, DBI, DT, ggplotify, ggwordcloud, ggExtra, grDevices, gridExtra (>= 2.3), htmltools, htmlwidgets, leaflet, methods, plotly, rmarkdown, RPostgreSQL, scales, stats, utils, viridisLite
Depends: R (>= 3.5.0), dplyr, ggplot2 (>= 3.3.3)
NeedsCompilation: no
Packaged: 2021-10-14 13:45:13 UTC; ab
Author: Artem Babaian [aut, cre]
Maintainer: Artem Babaian <artem@rRNA.ca>
Repository: CRAN
Date/Publication: 2021-10-15 07:50:04 UTC

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New package paletteknife with initial version 0.4.1
Package: paletteknife
Title: Create Colour Scales and Legend from Continuous or Categorical Vectors
Version: 0.4.1
Description: Streamlines the steps for adding colour scales and associated legends when working with base R graphics, especially for interactive use. Popular palettes are included and pretty legends produced when mapping a large variety of vector classes to a colour scale. An additional helper for adding axes and grid lines complements the base::plot() work flow.
License: MIT + file LICENSE
URL: https://github.com/johnxhobbs/paletteknife
BugReports: https://github.com/johnxhobbs/paletteknife/issues
Encoding: UTF-8
Depends: graphics, grDevices
NeedsCompilation: no
Packaged: 2021-10-14 12:30:26 UTC; john
Author: John Hobbs [aut, cre]
Maintainer: John Hobbs <johnxhobbs@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-15 07:40:05 UTC

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New package owidR with initial version 1.0.0
Package: owidR
Title: A Package for Importing Data from Our World in Data
Version: 1.0.0
Author: Piers York
Maintainer: Piers York <piersyork@gmail.com>
Description: Scrapes data from the Our World in Data website to offer easy to use functions for searching for datasets and downloading them into R.
URL: <https://github.com/piersyork/owidR>, https://github.com/owid/covid-19-data/, <https://ourworldindata.org/>
Imports: dplyr, rvest, readr, leaflet, stringr, ggplot2, sf, magrittr, forcats, jsonlite, htmltools, purrr, xml2, curl, ggrepel, scales, rlang, grDevices
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-GB
Suggests: testthat (>= 3.0.0), utils, showtext, sysfonts
NeedsCompilation: no
Packaged: 2021-10-14 14:28:54 UTC; piers
Repository: CRAN
Date/Publication: 2021-10-15 07:50:07 UTC

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Thu, 14 Oct 2021

New package tidybins with initial version 0.1.0
Package: tidybins
Title: Make Tidy Bins
Version: 0.1.0
Maintainer: Harrison Tietze <Harrison4192@gmail.com>
Description: Multiple ways to bin numeric columns with a tidy output. Wraps a variety of existing binning methods into one function, and includes a new method for binning by equal value, which is useful for sales data. Provides a function to automatically summarize the properties of the binned columns.
Encoding: UTF-8
URL: https://github.com/Harrison4192/tidybins
BugReports: https://github.com/Harrison4192/tidybins/issues
Imports: magrittr, dplyr, stringr, tidyselect, purrr, janitor, tibble, rlang, lubridate, stats, scales, ggplot2, rlist, OneR, strex, ClusterR, framecleaner, xgboost, badger
Suggests: knitr, rmarkdown, arulesCBA, embed, woeBinning, recipes
VignetteBuilder: knitr
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2021-10-14 09:34:13 UTC; Harrison
Author: Harrison Tietze [aut, cre]
Repository: CRAN
Date/Publication: 2021-10-14 12:20:02 UTC

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New package transmdl with initial version 0.1.0
Package: transmdl
Title: Semiparametric Transformation Models
Version: 0.1.0
Maintainer: Fengyu Wen <Wenfy1207@qq.com>
Description: To make the semiparametric transformation models easier to apply in real studies, we introduce this R package, in which the MLE in transformation models via an EM algorithm proposed by Zeng D, Lin DY(2007) <doi:10.1111/j.1369-7412.2007.00606.x> and adaptive lasso method in transformation models proposed by Liu XX, Zeng D(2013) <doi:10.1093/biomet/ast029> are implemented. C++ functions are used to compute complex loops. The coefficient vector and cumulative baseline hazard function can be estimated, along with the corresponding standard errors and P values.
License: GPL (>= 2)
Encoding: UTF-8
Imports: graphics, Rcpp, statmod, stats, survival
LinkingTo: Rcpp, RcppEigen
Suggests: MASS
NeedsCompilation: yes
Packaged: 2021-10-13 13:30:03 UTC; wenfy
Author: Fengyu Wen [aut, cre], Baosheng Liang [aut]
Repository: CRAN
Date/Publication: 2021-10-14 11:50:02 UTC

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New package simFrame with initial version 0.5.4
Package: simFrame
Version: 0.5.4
Title: Simulation Framework
Date: 2021-10-11
Depends: R (>= 3.0.0), Rcpp (>= 0.8.6), lattice, parallel
Imports: methods, stats4
LinkingTo: Rcpp
Description: A general framework for statistical simulation, which allows researchers to make use of a wide range of simulation designs with minimal programming effort. The package provides functionality for drawing samples from a distribution or a finite population, for adding outliers and missing values, as well as for visualization of the simulation results. It follows a clear object-oriented design and supports parallel computing to increase computational performance.
License: GPL (>= 2)
LazyLoad: yes
Author: Andreas Alfons [aut, cre], Yves Tille [ctb] (original R code of certain sampling algorithms), Alina Matei [ctb] (original R code of certain sampling algorithms)
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2021-10-11 10:19:15 UTC; andreas
Repository: CRAN
Date/Publication: 2021-10-14 11:10:02 UTC

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New package landmap with initial version 0.0.13
Package: landmap
Title: Automated Spatial Prediction using Ensemble Machine Learning
Version: 0.0.13
Description: Functions and tools for spatial interpolation and/or prediction of environmental variables (points to grids) based on using Ensemble Machine Learning with geographical distances. Package also provides access to Global Environmental Layers (<https://www.OpenLandMap.org>) produced by the OpenGeoHub.org foundation and collaborators. Some functions have been migrated and adopted from the Global Soil Information Facilities package.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/envirometrix/landmap/
BugReports: https://github.com/envirometrix/landmap/issues/
Imports: methods, utils, parallel, matrixStats, mlr, parallelMap, sp, geoR, plyr, rgdal, gdalUtils, raster, ranger, rpart, forestError, nnet, xgboost, kernlab, glmnet, ParamHelpers, spdep, maptools
Suggests: boot, nabor, meteo, mda, psych, fossil, rjson, spatstat, spatstat.core, maxlike, RCurl, deepnet, RSAGA, plotKML
SystemRequirements: C++11, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0)
NeedsCompilation: no
Packaged: 2021-10-07 18:23:41 UTC; tomhe
Author: Tomislav Hengl [aut, cre]
Maintainer: Tomislav Hengl <tom.hengl@opengeohub.org>
Repository: CRAN
Date/Publication: 2021-10-14 12:00:02 UTC

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New package dissCqN with initial version 0.1.0
Package: dissCqN
Title: Multiple Assemblage Dissimilarity for Orders q = 0-N
Version: 0.1.0
Description: Calculate multiple or pairwise dissimilarity for orders q = 0-N (CqN; Chao et al. 2008 <doi:10/fcvn63>) for a set of species assemblages or interaction networks.
URL: https://murphymv.github.io/dissCqN/, https://github.com/murphymv/dissCqN
BugReports: https://github.com/murphymv/dissCqN/issues
Depends: R (>= 4.0.0)
Imports: parallel, stats
Suggests: knitr, markdown, rmarkdown, SpadeR, vegan
VignetteBuilder: knitr
License: GPL (>= 3)
Encoding: UTF-8
Language: en-GB
NeedsCompilation: no
Packaged: 2021-10-13 14:44:19 UTC; murph
Author: Mark Murphy [aut, cre]
Maintainer: Mark Murphy <murphymv@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-14 11:50:05 UTC

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New package BBcor with initial version 1.0.3
Package: BBcor
Title: Bayesian Bootstrapping Correlations
Version: 1.0.3
Description: Efficiently draw samples from the posterior distribution of various correlation coefficients with the Bayesian bootstrap described in Rubin (1981) <doi:10.1214/aos/1176345338>. There are six correlation coefficients, including Pearson, Kendall, Spearman, Gaussian Rank, Blomqvist, and polychoric.
Depends: R (>= 4.0.0)
License: GPL-2
Imports: parallel, pbapply (>= 1.4-2), psych (>= 1.9.12.31), wdm (>= 0.2.1), ggplot2 (>= 3.3.4), stats, utils, methods, bayeslincom (>= 1.2.0), Rdpack
Suggests: BGGM
RdMacros: Rdpack
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-13 00:46:59 UTC; josue
Author: Donald Williams [aut, cre], Josue Rodriguez [aut]
Maintainer: Donald Williams <drwwilliams@ucdavis.edu>
Repository: CRAN
Date/Publication: 2021-10-14 11:20:01 UTC

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New package rassta with initial version 1.0.1
Package: rassta
Title: Raster-Based Spatial Stratification Algorithms
Version: 1.0.1
Maintainer: Bryan A. Fuentes <bryandrep@gmail.com>
Description: Algorithms for the spatial stratification of landscapes, sampling and modeling of spatially-varying phenomena. These algorithms offer a simple framework for the stratification of geographic space based on raster layers representing landscape factors and/or factor scales. The stratification process follows a hierarchical approach, which is based on first level units (i.e., classification units) and second-level units (i.e., stratification units). Nonparametric techniques allow to measure the correspondence between the geographic space and the landscape configuration represented by the units. These correspondence metrics are useful to define sampling schemes and to model the spatial variability of environmental phenomena.
License: AGPL (>= 3)
Encoding: UTF-8
URL: https://github.com/bafuentes/rassta
BugReports: https://github.com/bafuentes/rassta/issues/
Imports: cluster (>= 2.1.2), data.table (>= 1.14.0), dplyr (>= 1.0.7), DT (>= 0.18), foreach (>= 1.5.1), GGally (>= 2.1.2), ggplot2 (>= 3.3.5), grDevices (>= 4.1.0), histogram (>= 0.0.25), KernSmooth (>= 2.23.18), kohonen (>= 3.0.10), plotly (>= 4.9.4.1), raster (>= 3.4.13), rlang (>= 0.4.11), scales (>= 1.1.1), shiny (>= 1.6.0), stats (>= 4.1.0), stringdist (>= 0.9.6.3), stringi (>= 1.7.2), terra (>= 1.3.4), utils (>= 4.1.0)
Suggests: testthat (>= 3.0.0), tinytest (>= 1.3.1), doParallel (>= 1.0.16)
NeedsCompilation: no
Packaged: 2021-10-13 21:00:06 UTC; bryan
Author: Bryan A. Fuentes [aut, cre] (<https://orcid.org/0000-0003-3506-7101>), Minerva J. Dorantes [aut] (<https://orcid.org/0000-0002-2877-832X>), John Tipton [aut] (<https://orcid.org/0000-0002-6135-8141>), Robert J. Hijmans [ctb] (<https://orcid.org/0000-0001-5872-2872>)
Repository: CRAN
Date/Publication: 2021-10-14 09:40:02 UTC

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Wed, 13 Oct 2021

New package vegtable with initial version 0.1.7
Package: vegtable
Version: 0.1.7
Encoding: UTF-8
Title: Handling Vegetation Data Sets
Depends: R (>= 3.5.0), taxlist
Imports: foreign, methods, knitr, qdapRegex, sp, stringi, vegdata
Suggests: rmarkdown, roxygen2, testthat, vegan
Description: Import and handling data from vegetation-plot databases, especially data stored in 'Turboveg 2' (<https://www.synbiosys.alterra.nl/turboveg/>). Also import/export routines for exchange of data with 'Juice' (<https://www.sci.muni.cz/botany/juice/>) are implemented.
LazyData: true
License: GPL (>= 2)
URL: https://github.com/kamapu/vegtable
BugReports: https://github.com/kamapu/vegtable/issues
NeedsCompilation: no
Packaged: 2021-10-13 15:23:38 UTC; miguel
Author: Miguel Alvarez [aut, cre] (<https://orcid.org/0000-0003-1500-1834>)
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-13 21:10:02 UTC

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New package effectFusion with initial version 1.1.3
Package: effectFusion
Version: 1.1.3
Date: 2021-10-13
Title: Bayesian Effect Fusion for Categorical Predictors
Depends: R (>= 3.3), mcclust
Imports: Matrix, MASS, bayesm, cluster, GreedyEPL, gridExtra, ggplot2, methods, utils, stats
Description: Variable selection and Bayesian effect fusion for categorical predictors in linear and logistic regression models. Effect fusion aims at the question which categories have a similar effect on the response and therefore can be fused to obtain a sparser representation of the model. Effect fusion and variable selection can be obtained either with a prior that has an interpretation as spike and slab prior on the level effect differences or with a sparse finite mixture prior on the level effects. The regression coefficients are estimated with a flat uninformative prior after model selection or by taking model averages. Posterior inference is accomplished by an MCMC sampling scheme which makes use of a data augmentation strategy (Polson, Scott & Windle (2013) <doi:10.1080/01621459.2013.829001>) based on latent Polya-Gamma random variables in the case of logistic regression. The code for data augmentation is taken from Polson et al. (2013) <doi:10.1080/01621459.2013.829001>, who own the copyright.
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Repository: CRAN
Packaged: 2021-10-13 19:20:51 UTC; User
Author: Daniela Pauger [aut], Magdalena Leitner [aut, cre], Helga Wagner [aut] (<https://orcid.org/0000-0002-7003-9512>), Gertraud Malsiner-Walli [aut] (<https://orcid.org/0000-0002-1213-4749>), Nicholas G. Polson [ctb], James G. Scott [ctb], Jesse Windle [ctb], Bettina Grün [ctb] (<https://orcid.org/0000-0001-7265-4773>)
Maintainer: Magdalena Leitner <effectfusion.jku@gmail.com>
Date/Publication: 2021-10-13 21:10:05 UTC

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New package previsionio with initial version 11.3.0
Package: previsionio
Title: 'Prevision.io' R SDK
Version: 11.3.0
Description: For working with the 'Prevision.io' AI model management platform's API <https://prevision.io/>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Imports: data.table, futile.logger, httr, jsonlite, Metrics, graphics, stats, utils, XML, magrittr, plotly
Suggests: testthat
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-10-13 08:37:12 UTC; Florian
Author: Florian Laroumagne [aut, cre], Prevision.io Inc [cph]
Maintainer: Florian Laroumagne <florian.laroumagne@prevision.io>
Repository: CRAN
Date/Publication: 2021-10-13 10:20:02 UTC

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New package lmForc with initial version 0.0.1
Package: lmForc
Title: Linear Model Forecasting
Version: 0.0.1
Description: Introduces in-sample, out-of-sample, pseudo out-of-sample, and benchmark linear model forecast tests and a new class for working with forecast data: Forecast.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.6.0)
Imports: methods
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-12 22:35:13 UTC; nelsonrayl
Author: Nelson Rayl [aut, cre]
Maintainer: Nelson Rayl <nelsonrayl14@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-13 10:10:02 UTC

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New package igcop with initial version 1.0.1
Package: igcop
Title: Computational Tools for the IG and IGL Copula Families
Version: 1.0.1
Description: Compute distributional quantities for an Integrated Gamma (IG) or Integrated Gamma Limit (IGL) copula, such as a cdf and density. Compute corresponding conditional quantities such as the cdf and quantiles. Generate data from an IG or IGL copula.
License: MIT + file LICENSE
Suggests: testthat, knitr, rmarkdown, tibble, covr, ggplot2
Encoding: UTF-8
VignetteBuilder: knitr
Imports: stats, vctrs, Rcpp, rlang
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2021-10-13 05:12:53 UTC; vincenzocoia
Author: Vincenzo Coia [aut, cre], Harry Joe [aut]
Maintainer: Vincenzo Coia <vincenzo.coia@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-13 10:20:06 UTC

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New package saotd with initial version 0.3.0
Package: saotd
Title: Sentiment Analysis of Twitter Data
Version: 0.3.0
Date: 2021-10-11
Maintainer: Evan Munson <evan.l.munson@gmail.com>
BugReports: https://github.com/evan-l-munson/saotd/issues
Description: This analytic is an in initial foray into sentiment analysis. This analytic will allow a user to access the Twitter API (once they create their own developer account), ingest tweets of their interest, clean / tidy data, perform topic modeling if interested, compute sentiment scores utilizing the Bing Lexicon, and output visualizations.
License: GPL (>= 2)
URL: https://github.com/evan-l-munson/saotd
Language: en-US
Imports: dplyr, widyr, stringr, tidytext, rtweet, tidyr, igraph, ggplot2, ggraph, scales, reshape2, lubridate, utils, stats, magrittr, ldatuning, topicmodels
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, httr, base64enc, tibble, covr
Depends: R (>= 3.5.0)
VignetteBuilder: knitr
SystemRequirements: GSL (>=2.4), MPFR (>= 4.0.0), udunits2 (>=2.2.26-3)
Encoding: UTF-8
LazyLoad: true
NeedsCompilation: no
Packaged: 2021-10-12 14:00:34 UTC; munson
Author: Evan Munson [aut, cre] (<https://orcid.org/0000-0002-9958-6800>), Christopher Smith [aut] (<https://orcid.org/0000-0002-8288-270X>), Bradley Boehmke [aut] (<https://orcid.org/0000-0002-3611-8516>), Jason Freels [aut] (<https://orcid.org/0000-0002-2415-0340>)
Repository: CRAN
Date/Publication: 2021-10-13 09:50:02 UTC

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New package pvcurveanalysis with initial version 1.0.0
Package: pvcurveanalysis
Title: Analysis of Pressure Volume Curves
Version: 1.0.0
Depends: ggplot2, R (>= 3.5.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Description: Enables the manufacturing, analysis and display of pressure volume curves. From the progression of the curves, turgor loss point, osmotic potential and apoplastic fraction can be derived. Methods adapted from Bartlett, Scoffoni and Sack (2012) <doi:10.1111/j.1461-0248.2012.01751.x>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-12 16:17:09 UTC; anna.raesch
Author: Anna Raesch [aut, cre, cph]
Maintainer: Anna Raesch <annaraesch@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-13 10:00:02 UTC

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New package KingCountyHouses with initial version 0.1.0
Package: KingCountyHouses
Title: Data on House Sales in King County WA
Version: 0.1.0
Description: Data on houses in and around Seattle WA are included. Basic characteristics are given along with sale prices.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: spelling
Language: en-US
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-12 19:37:28 UTC; max
Author: Max Kuhn [aut, cre] (<https://orcid.org/0000-0003-2402-136X>)
Maintainer: Max Kuhn <max@rstudio.com>
Repository: CRAN
Date/Publication: 2021-10-13 10:00:08 UTC

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New package hydropeak with initial version 0.1.0
Package: hydropeak
Title: Detect and Characterize Sub-Daily Flow Fluctuations
Version: 0.1.0
Description: An important environmental impact on running water ecosystems is caused by hydropeaking - the discontinuous release of turbine water because of peaks of energy demand. An event-based algorithm is implemented to detect flow fluctuations referring to increase events (IC) and decrease events (DC). For each event, a set of parameters related to the fluctuation intensity is calculated: maximum flow fluctuation rate mafr(), mean flow fluctuation rate mefr(), amplitude amp(), flow ratio fr(), and duration dur(). The framework is introduced in Greimel et al. (2016) "A method to detect and characterize sub-daily flow fluctuations" <doi:10.1002/hyp.10773> and can be used to identify different fluctuation types according to the potential source: e.g., sub-daily flow fluctuations caused by hydropeaking, rainfall, or snow and glacier melt.
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), data.table
Imports: utils, parallel
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-12 14:05:58 UTC; gruen
Author: Bettina Grün [cre, ctb] (<https://orcid.org/0000-0001-7265-4773>), Julia Haider [aut], Franz Greimel [ctb] (<https://orcid.org/0000-0002-8000-1227>)
Maintainer: Bettina Grün <Bettina.Gruen@R-project.org>
Repository: CRAN
Date/Publication: 2021-10-13 10:00:05 UTC

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Tue, 12 Oct 2021

New package ttservice with initial version 0.1.2
Package: ttservice
Title: A Service for Tidy Transcriptomics Software Suite
Version: 0.1.2
Description: It provides generic methods that are used by more than one package, avoiding conflicts. This package will be imported by 'tidySingleCellExperiment' and 'tidyseurat'. The implemented method is join_features().
License: GPL-3
Depends: R (>= 4.0.0)
Imports: methods
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-10-12 07:00:31 UTC; mangiola.s
Author: Stefano Mangiola [aut, cre]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-12 12:30:02 UTC

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New package PKLMtest with initial version 1.0.0
Package: PKLMtest
Title: Classification Based MCAR Test
Version: 1.0.0
Author: Loris Michel, Meta-Lina Spohn, Jeffrey Naef
Maintainer: Meta-Lina Spohn <metalina.spohn@stat.math.ethz.ch>
Description: Implementation of a KL-based test for MCAR in the context of missing data as introduced in Michel et al. (2021) <arXiv:2109.10150>.
License: GPL-3
Encoding: UTF-8
Depends: parallel, stats, ranger
NeedsCompilation: no
Packaged: 2021-10-12 05:56:01 UTC; lorismichel
Repository: CRAN
Date/Publication: 2021-10-12 12:30:04 UTC

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New package text2sdg with initial version 0.1.0
Package: text2sdg
Version: 0.1.0
Date: 2021-10-08
Title: Detecting UN Sustainable Development Goals in Text
Description: The United Nations’ Sustainable Development Goals (SDGs) have become an important guideline for organisations to monitor and plan their contributions to social, economic, and environmental transformations. The 'text2sdg' package is an open-source analysis package that identifies SDGs in text using scientifically developed query systems, opening up the opportunity to monitor any type of text-based data, such as scientific output or corporate publications.
Maintainer: Dominik S. Meier <dominikmeier@outlook.com>
URL: https://github.com/dwulff/text2sdg
BugReports: https://github.com/dwulff/text2sdg/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: magrittr, dplyr, corpustools (>= 0.4.2), tidyr, tibble, stringr, ggplot2
Suggests: testthat, knitr, rmarkdown
LazyData: TRUE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-11 11:58:10 UTC; meidom02
Author: Dirk U. Wulff [aut] (<https://orcid.org/0000-0002-4008-8022>), Dominik S. Meier [aut, cre] (<https://orcid.org/0000-0002-3999-1388>), Rui Mata [ctb] (<https://orcid.org/0000-0002-1679-906X>)
Repository: CRAN
Date/Publication: 2021-10-12 08:20:02 UTC

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New package pylintR with initial version 0.1.0
Package: pylintR
Title: Lint 'Python' Files with a R Command or a 'RStudio' Addin
Version: 0.1.0
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Description: Allow to run 'pylint' on Python files with a R command or a 'RStudio' addin. The report appears in the RStudio viewer pane as a formatted HTML file.
License: GPL-3
Encoding: UTF-8
SystemRequirements: pylint
URL: https://github.com/stla/pylintR
BugReports: https://github.com/stla/pylintR/issues
Imports: fansi, utils, htmlwidgets, rstudioapi
NeedsCompilation: no
Packaged: 2021-10-11 19:14:26 UTC; SDL96354
Repository: CRAN
Date/Publication: 2021-10-12 09:00:01 UTC

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New package metaconfoundr with initial version 0.1.0
Package: metaconfoundr
Title: Visualize 'Confounder' Control in Meta-Analyses
Version: 0.1.0
Description: Visualize 'confounder' control in meta-analysis. 'metaconfoundr' is an approach to evaluating bias in studies used in meta-analyses based on the causal inference framework. Study groups create a causal diagram displaying their assumptions about the scientific question. From this, they develop a list of important 'confounders'. Then, they evaluate whether studies controlled for these variables well. 'metaconfoundr' is a toolkit to facilitate this process and visualize the results as heat maps, traffic light plots, and more.
License: MIT + file LICENSE
URL: https://github.com/malcolmbarrett/metaconfoundr
BugReports: https://github.com/malcolmbarrett/metaconfoundr/issues
Depends: R (>= 3.5.0)
Imports: dplyr (>= 1.0.0), ellipsis, forcats, ggplot2 (>= 3.3.1), glue, magrittr, purrr, rlang (>= 0.1.2), shiny, stringr, tibble, tidyr (>= 1.0.0), tidyselect
Suggests: covr, knitr, metafor, patchwork, readr, rio, rmarkdown, roxygen2, spelling, testthat (>= 3.0.0), vdiffr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-10 15:26:23 UTC; malcolmbarrett
Author: Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>), Julie M. Petersen [aut] (<https://orcid.org/0000-0001-7845-4545>), Ludovic Trinquart [aut] (<https://orcid.org/0000-0002-3028-4900>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-12 08:10:02 UTC

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New package GWPR.light with initial version 0.1.0
Package: GWPR.light
Title: Geographically Weighted Panel Regression
Version: 0.1.0
Author: Chao Li [aut, cre] (<https://orcid.org/0000-0002-6854-4456>), Shunsuke Managi [aut] (<https://orcid.org/0000-0001-7883-1427>)
Maintainer: Chao Li <chaoli0394@gmail.com>
Description: Geographically weighted panel regression is grounded in a branch of spatial statistics. Using geographically weights, the geographically weighted panel regression is try to solve the residuals from panel regression clustering spatially. To investigate whether the residuals cluster spatially, the Moran's I test is also improved. Furthermore, three local statistic tests are contained to help the users select model. The major references are Fotheringham et al. (2003, ISBN:978-0-470-85525-6) and Beenstock and Felsenstein (2019, ISBN:978-3-030-03614-0).
License: AGPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: data.table, doParallel, dplyr, foreach, GWmodel, iterators, lmtest, methods, parallel, plm, sp, stats
Depends: R (>= 2.10)
Suggests: rmarkdown, knitr, rgeos, tmap
VignetteBuilder: knitr
URL: https://github.com/MichaelChaoLi-cpu/GWPR.light
BugReports: https://github.com/MichaelChaoLi-cpu/GWPR.light/issues
NeedsCompilation: no
Packaged: 2021-10-11 06:57:09 UTC; li.chao.987@s.kyushu-u.ac.jp
Repository: CRAN
Date/Publication: 2021-10-12 08:20:05 UTC

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New package designsize with initial version 0.1.0
Title: Sample Size Calculation of Various Study Designs
Package: designsize
Version: 0.1.0
Date: 2021-10-03
Description: Different sample size calculations with different study designs. These techniques are explained by Chow (2007) <doi:10.1201/9781584889830>.
ByteCompile: Yes
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: stats
Maintainer: Atanu Bhattacharjee <atanustat@gmail.com>
NeedsCompilation: no
Packaged: 2021-10-11 19:22:55 UTC; atanu
Repository: CRAN
Date/Publication: 2021-10-12 09:00:04 UTC
Author: Atanu Bhattacharjee [aut, cre, ctb], Rajashree Dey [aut, ctb], Soutik Halder [aut, ctb], Akash Pawar [aut, ctb]

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Mon, 11 Oct 2021

New package processanimateR with initial version 1.0.4
Package: processanimateR
Title: Process Map Token Replay Animation
Version: 1.0.4
Description: Provides animated process maps based on the 'procesmapR' package. Cases stored in event logs created with with 'bupaR' S3 class eventlog() are rendered as tokens (SVG shapes) and animated according to their occurrence times on top of the process map. For rendering SVG animations ('SMIL') and the 'htmlwidget' package are used.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: bupaR, processmapR (>= 0.3.1), rlang, magrittr, dplyr, tidyr, htmlwidgets, DiagrammeR (>= 1.0.0), grDevices, stringr, htmltools
Suggests: eventdataR, edeaR, testthat, knitr, rmarkdown, shiny, RColorBrewer, lubridate
URL: https://github.com/bupaverse/processanimateR/
BugReports: https://github.com/bupaverse/processanimateR/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-11 15:35:50 UTC; fmannhar
Author: Felix Mannhardt [aut, cre], Gert Janssenswillen [ctb]
Maintainer: Felix Mannhardt <f.mannhardt@tue.nl>
Repository: CRAN
Date/Publication: 2021-10-11 18:50:02 UTC

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New package heuristicsmineR with initial version 0.2.5
Package: heuristicsmineR
Title: Discovery of Process Models with the Heuristics Miner
Version: 0.2.5
Description: Provides the heuristics miner algorithm for process discovery as proposed by Weijters et al. (2011) <doi:10.1109/CIDM.2011.5949453>. The algorithm builds a causal net from an event log created with the 'bupaR' package. Event logs are a set of ordered sequences of events for which 'bupaR' provides the S3 class eventlog(). The discovered causal nets can be visualised as 'htmlwidgets' and it is possible to annotate them with the occurrence frequency or processing and waiting time of process activities.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, BH
SystemRequirements: C++11
Depends: R (>= 2.10)
Imports: bupaR, processmapR (>= 0.3.1), rlang, magrittr, dplyr, tidyr, DiagrammeR (>= 1.0.0), petrinetR, purrr, scales, Rcpp, ggplot2, ggthemes, data.table, stringr
Suggests: eventdataR, svgPanZoom, DiagrammeRsvg
URL: https://github.com/bupaverse/heuristicsmineR
BugReports: https://github.com/bupaverse/heuristicsmineR/issues
NeedsCompilation: yes
Packaged: 2021-10-11 14:18:35 UTC; fmannhar
Author: Felix Mannhardt [aut, cre]
Maintainer: Felix Mannhardt <f.mannhardt@tue.nl>
Repository: CRAN
Date/Publication: 2021-10-11 18:50:05 UTC

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New package datapackage.r with initial version 1.3.4
Package: datapackage.r
Title: Data Package 'Frictionless Data'
Version: 1.3.4
Date: 2021-10-11
Maintainer: Kleanthis Koupidis <koupidis.okfgr@gmail.com>
Description: Work with 'Frictionless Data Packages' (<https://specs.frictionlessdata.io//data-package/>). Allows to load and validate any descriptor for a data package profile, create and modify descriptors and provides expose methods for reading and streaming data in the package. When a descriptor is a 'Tabular Data Package', it uses the 'Table Schema' package (<https://CRAN.R-project.org/package=tableschema.r>) and exposes its functionality, for each resource object in the resources field.
URL: https://github.com/frictionlessdata/datapackage-r
License: MIT + file LICENSE
BugReports: https://github.com/frictionlessdata/datapackage-r/issues
Encoding: UTF-8
Imports: config, future, httr, iterators, jsonlite, jsonvalidate, purrr, R6, R.utils, readr, rlist, stringr, tableschema.r, tools, urltools, utils, V8
Suggests: covr, curl, data.table, DBI, devtools, foreach, httptest, knitr, rmarkdown, RSQLite, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-11 15:19:18 UTC; akis_
Author: Kleanthis Koupidis [aut, cre], Lazaros Ioannidis [aut], Charalampos Bratsas [aut], Open Knowledge International [cph]
Repository: CRAN
Date/Publication: 2021-10-11 18:50:08 UTC

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New package stableGR with initial version 1.1
Package: stableGR
Title: A Stable Gelman-Rubin Diagnostic for Markov Chain Monte Carlo
Version: 1.1
Date: 2021-10-9
Maintainer: Christina Knudson <knud8583@stthomas.edu>
Description: Practitioners of Bayesian statistics often use Markov chain Monte Carlo (MCMC) samplers to sample from a posterior distribution. This package determines whether the MCMC sample is large enough to yield reliable estimates of the target distribution. In particular, this calculates a Gelman-Rubin convergence diagnostic using stable and consistent estimators of Monte Carlo variance. Additionally, this uses the connection between an MCMC sample's effective sample size and the Gelman-Rubin diagnostic to produce a threshold for terminating MCMC simulation. Finally, this informs the user whether enough samples have been collected and (if necessary) estimates the number of samples needed for a desired level of accuracy. The theory underlying these methods can be found in "Revisiting the Gelman-Rubin Diagnostic" by Vats and Knudson (2018) <arXiv:1812:09384>.
License: GPL-3
Depends: R (>= 3.5), mcmcse(>= 1.4-1)
Imports: mvtnorm
ByteCompile: TRUE
Repository: CRAN
NeedsCompilation: no
Packaged: 2021-10-10 00:22:29 UTC; admin
Author: Christina Knudson [aut, cre], Dootika Vats [aut]
Date/Publication: 2021-10-11 08:40:02 UTC

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New package fipio with initial version 1.0.0
Package: fipio
Title: Lightweight Federal Information Processing System (FIPS) Code Information Retrieval
Version: 1.0.0
Description: Provides a lightweight suite of functions for retrieving information about 5-digit or 2-digit US FIPS codes.
URL: https://fipio.justinsingh.me, https://github.com/program--/fipio
BugReports: https://github.com/program--/fipio/issues
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 2.10)
Suggests: testthat (>= 3.0.0), mockery (>= 0.4.2), sfheaders, covr
NeedsCompilation: no
Packaged: 2021-10-10 06:41:37 UTC; jsinghm
Author: Justin Singh-Mohudpur [aut, cre] (<https://orcid.org/0000-0002-5233-5799>)
Maintainer: Justin Singh-Mohudpur <justin@justinsingh.me>
Repository: CRAN
Date/Publication: 2021-10-11 08:40:05 UTC

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New package excessmort with initial version 0.6.1
Package: excessmort
Title: Excess Mortality
Version: 0.6.1
Depends: R (>= 3.5.0),
Imports: stats, datasets, dplyr, tidyr, rlang, lubridate, splines, ggplot2, scales
Suggests: tidycensus, knitr, rmarkdown
VignetteBuilder: knitr
Description: Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2021-10-08 20:22:32 UTC; rafa
Author: Rafael A. Irizarry [aut, cre], Rolando Acosta [aut]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Repository: CRAN
Date/Publication: 2021-10-11 08:10:12 UTC

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New package drpop with initial version 0.0.1
Package: drpop
Title: Efficient Doubly Robust Population Size Estimation
Version: 0.0.1
Description: Estimation of the total population size from capture-recapture data efficiently and with low bias implementing the methods from Das M, Kennedy EH, and Jewell NP (2021) <arXiv:2104.14091>. The estimator is doubly robust against errors in the estimation of the intermediate nuisance parameters. Users can choose from the flexible estimation models provided in the package, or use any other preferred model.
Depends: stats
Imports: gam, janitor, reshape2, stringr, tidyr, dplyr, SuperLearner, ggplot2, nnet, nnls, parallel, ranger
License: GPL-3
Encoding: UTF-8
Suggests: testthat (>= 2.0.0)
NeedsCompilation: no
Packaged: 2021-10-09 16:12:06 UTC; manja
Author: Manjari Das [aut, cre] (<https://orcid.org/0000-0002-6781-6368>), Edward H. Kennedy [aut] (<https://orcid.org/0000-0002-1510-8175>)
Maintainer: Manjari Das <manjari8d@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-11 08:20:02 UTC

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New package apache.sedona with initial version 1.1.0
Package: apache.sedona
Title: R Interface for Apache Sedona
Version: 1.1.0
Maintainer: Apache Sedona <private@sedona.apache.org>
Description: R interface for 'Apache Sedona' based on 'sparklyr' (<https://sedona.apache.org>).
License: Apache License 2.0
Depends: R (>= 3.2)
Imports: rlang, sparklyr (>= 1.3), DBI (>= 0.6-1), dplyr (>= 0.7.2), dbplyr (>= 1.1.0)
Suggests: knitr, rmarkdown
Encoding: UTF-8
SystemRequirements: 'Apache Spark' 2.4.x or 3.x
NeedsCompilation: no
Packaged: 2021-10-09 01:54:24 UTC; jiayu
Author: Apache Sedona [aut, cre], Jia Yu [ctb, cph], Yitao Li [aut, cph] (<https://orcid.org/0000-0002-1261-905X>), The Apache Software Foundation [cph], RStudio [cph]
Repository: CRAN
Date/Publication: 2021-10-11 08:10:15 UTC

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New package niaidMI with initial version 1.0.0
Package: niaidMI
Title: Markov Model Multiple Imputation for NIAID OS
Version: 1.0.0
Date: 2021-10-08
Description: The implementation of Markov Model Multiple Imputation with the application to COVID-19 scale, NIAID OS.
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Suggests: testthat
Imports: Rcpp (>= 1.0.3)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2021-10-08 14:59:35 UTC; c300194
Author: Nathan Morris [aut, cre], Chaoran Hu [aut], Eli Lilly and Company [cph]
Maintainer: Nathan Morris <morris_nathan@lilly.com>
Repository: CRAN
Date/Publication: 2021-10-11 07:50:10 UTC

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New package gapclosing with initial version 1.0.2
Package: gapclosing
Title: Estimate Gaps Under an Intervention
Version: 1.0.2
Description: Provides functions to estimate the disparities across categories (e.g. Black and white) that persists if a treatment variable (e.g. college) is equalized. Makes estimates by treatment modeling, outcome modeling, and doubly-robust augmented inverse probability weighting estimation, with standard errors calculated by a nonparametric bootstrap. Cross-fitting is supported. Survey weights are supported for point estimation but not for standard error estimation; those applying this package with complex survey samples should consult the data distributor to select an appropriate approach for standard error construction, which may involve calling the functions repeatedly for many sets of replicate weights provided by the data distributor. The methods in this package are described in Lundberg (2021) <doi:10.31235/osf.io/gx4y3>.
License: MIT + file LICENSE
URL: https://ilundberg.github.io/gapclosing/
BugReports: https://github.com/ilundberg/gapclosing/issues
Encoding: UTF-8
Imports: stats, mgcv, ranger, glmnet, magrittr, dplyr, forcats, ggplot2, tidyr, foreach, tidyselect, parallel, doParallel
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, spelling
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-30 01:53:22 UTC; ilundberg
Author: Ian Lundberg [aut, cre] (<https://orcid.org/0000-0002-1909-2270>)
Maintainer: Ian Lundberg <ianlundberg@ucla.edu>
Language: en-US
Repository: CRAN
Date/Publication: 2021-10-11 07:40:22 UTC

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New package factset.protobuf.stach.v2 with initial version 1.0.0
Package: factset.protobuf.stach.v2
Title: 'FactSet' 'STACH' Library
Version: 1.0.0
Author: analytics-reporting
Maintainer: Charlie Mathis<chmathis@factset.com>
Description: Generates 'RProtobuf' classes for 'FactSet' 'STACH' tabular format which represents complex multi-dimensional array of data. These classes help in the 'serialization' and 'deserialization' of 'STACH' formatted data. See 'GitHub' repository <https://github.com/factset/stachschema-sdks/tree/master/r/factset.protobuf.stach.v2> documentation for more information.
URL: https://github.com/factset/stachschema-sdks
BugReports: https://github.com/factset/stachschema-sdks/issues
License: Apache License 2.0
Encoding: UTF-8
Imports: R6
Depends: RProtoBuf
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-10-08 09:55:03 UTC; vaddala
Repository: CRAN
Date/Publication: 2021-10-11 08:00:05 UTC

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New package csodata with initial version 1.2.1
Package: csodata
Title: Download Data from the CSO 'PxStat' API
Version: 1.2.1
Date: 2021-10-07
Maintainer: Conor Crowley <conor.crowley@cso.ie>
Description: Imports 'PxStat' data in JSON-stat format and (optionally) reshapes it into wide format. The Central Statistics Office (CSO) is the national statistical institute of Ireland and 'PxStat' is the CSOs online database of Official Statistics. This database contains current and historical data series compiled from CSO statistical releases and is accessed at <http://data.cso.ie>. The CSO 'PxStat' Application Programming Interface (API), which is accessed in this package, provides access to 'PxStat' data in JSON-stat format at <http://data.cso.ie>. This dissemination tool allows developers machine to machine access to CSO 'PxStat' data.
Imports: dplyr, httr, jsonlite, reshape2, rjstat, R.cache, sf, lubridate
License: GPL-3
Encoding: UTF-8
Suggests: knitr, rmarkdown, tmap, viridisLite
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-07 12:59:27 UTC; crowleyco
Author: Eoin Horgan [aut] (<https://orcid.org/0000-0002-3446-6154>), Conor Crowley [aut, cre], Vytas Vaiciulis [aut], Mervyn O'Luing [aut]
Repository: CRAN
Date/Publication: 2021-10-11 07:40:32 UTC

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New package cartogramR with initial version 1.0-3
Package: cartogramR
Version: 1.0-3
Date: 2021-10-01
Title: Continuous Cartogram
Description: Procedures for making continuous cartogram. Procedures available are: flow based cartogram (Gastner & Newman (2004) <doi:10.1073/pnas.0400280101>), fast flow based cartogram (Gastner, Seguy & More (2018) <doi:10.1073/pnas.1712674115>), rubber band based cartogram (Dougenik et al. (1985) <doi:10.1111/j.0033-0124.1985.00075.x>).
Depends: R (>= 3.5.0)
Imports: sf, data.table
Suggests: lwgeom
SystemRequirements: FFTW (>=3.3.1); possible package: fftw-devel (rpm), fftw-dev (deb) or fftw (brew).
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2021-10-07 14:30:24 UTC; pac
Author: Pierre-Andre Cornillon [aut, cre], Florent Demoraes [aut], Flow-Based-Cartograms [cph] (Author of core C code for gsm and gn procedures)
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Repository: CRAN
Date/Publication: 2021-10-11 07:40:35 UTC

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Sat, 09 Oct 2021

New package PandemicLP with initial version 1.1.1
Package: PandemicLP
Title: Long Term Prediction for Epidemic and Pandemic Data
Version: 1.1.1
Date: 2021-10-08
Contact: CovidLP team <covidlp.team@gmail.com>
Maintainer: Guido Alberti Moreira <guidoalber@gmail.com>
Description: Implementation of the methodology described in <http://est.ufmg.br/covidlp/home/pt/> which can be also found in help(models). Implemented models are currently the Poisson distribution. The mean function can be the basic generalized logistic form, or the seasonal effect which has under- or over-reporting effects in up to three weekdays, or the two curves form. Bayesian inference is made available through the 'stan' software and its diagnostic functions pool can be used. Plot methods are implemented to mimic the graphics from the 'shiny' app in the URL using the 'plotly' library.
License: GPL-3
Encoding: UTF-8
LazyData: true
Biarch: true
Depends: R (>= 3.5.0), rstan (>= 2.18.1), rstantools (>= 2.1.1), stats
Imports: utils, methods, Rcpp (>= 0.12.0), plotly (>= 4.9.2.1), dplyr (>= 1.0.1), curl (>= 4.3), tidyr (>= 1.1.1), covid19br
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests: knitr, rmarkdown, webshot
URL: <http://est.ufmg.br/covidlp/home/pt/>
VignetteBuilder: knitr
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2021-10-08 14:27:52 UTC; anthorg
Author: Débora de Freitas Magalhães [aut], Marta Cristina Colozza Bianchi da Costa [aut], Guido Alberti Moreira [cre, aut] (<https://orcid.org/0000-0001-7557-0874>), Thais Pacheco Menezes [aut], Marcos Oliveira Prates [ctb] (<https://orcid.org/0000-0001-8077-4898>)
Repository: CRAN
Date/Publication: 2021-10-09 21:10:22 UTC

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New package PAMpal with initial version 0.14.4
Package: PAMpal
Title: Load and Process Passive Acoustic Data
Version: 0.14.4
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Description: Tools for loading and processing passive acoustic data. Read in data that has been processed in 'Pamguard' (<https://www.pamguard.org/>), apply a suite processing functions, and export data for reports or external modeling tools. Parameter calculations implement methods by Oswald et al (2007) <doi:10.1121/1.2743157>, Griffiths et al (2020) <doi:10.1121/10.0001229> and Baumann-Pickering et al (2010) <doi:10.1121/1.3479549>.
License: GNU General Public License
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), PamBinaries (>= 1.3.0), dplyr, tuneR
Imports: seewave, gam, data.table, PAMmisc, RSQLite, stringr, purrr, methods, magrittr, signal, readr, tidyr, ggplot2, manipulate, knitr, rstudioapi, xml2, rjson, rlang, reticulate, lubridate
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-10-08 23:42:58 UTC; tnsak
Author: Taiki Sakai [aut, cre], Jay Barlow [ctb], Emily Griffiths [ctb], Michael Oswald [ctb], Simone Baumann-Pickering [ctb], Julie Oswald [ctb]
Repository: CRAN
Date/Publication: 2021-10-09 21:10:26 UTC

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Fri, 08 Oct 2021

New package switchboard with initial version 0.1
Package: switchboard
Version: 0.1
Date: 2021-10-8
Title: An Agile Widget Engine for Real-Time, Dynamic Visualizations
Description: An unsorted collection of visualization widgets rendered in 'Tcl/Tk'<https://www.tcl.tk/> to generate agile dashboards for your iterative simulations. Widgets include progress bars, counters, eavesdroppers, injectors, switches, and sliders for dynamic manipulation and visualization of simulation parameters.
Depends: R (>= 3.3.2)
Imports: magrittr
SystemRequirements: Tcl/Tk toolkit (X11 Quarts for Mac)
VignetteBuilder: R.rsp
License: GPL (>= 2)
URL: http://lajeunesse.myweb.usf.edu/ https://github.com/mjlajeunesse/ https://www.youtube.com/c/LajeunesseLab/
Encoding: UTF-8
Suggests: R.rsp
NeedsCompilation: no
Packaged: 2021-10-08 12:35:49 UTC; lajeunesse
Author: Marc J. Lajeunesse [aut, cre] (<https://orcid.org/0000-0002-9678-2080>)
Maintainer: Marc J. Lajeunesse <lajeunesse@usf.edu>
Repository: CRAN
Date/Publication: 2021-10-08 18:00:02 UTC

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New package spm2 with initial version 1.1.0
Package: spm2
Title: Spatial Predictive Modeling
Version: 1.1.0
Date: 2021-10-01
Description: An updated and extended version of 'spm' package, by introducing some further novel functions for modern statistical methods (i.e., generalised linear models, glmnet, generalised least squares), support vector machine, kriging methods (i.e., simple kriging, universal kriging, block kriging, kriging with an external drift), and novel hybrid methods (228 hybrids plus numerous variants) of modern statistical methods or machine learning methods with mathematical and/or univariate geostatistical methods for spatial predictive modelling. For each method, two functions are provided, with one function for assessing the predictive errors and accuracy of the method based on cross-validation, and the other for generating spatial predictions. It also contains a couple of functions for data preparation and predictive accuracy assessment.
Depends: R (>= 2.10)
Imports: spm, gstat, sp, randomForest, psy, gbm, stats, ranger, MASS, nlme, glmnet, e1071
License: GPL (>= 2)
LazyData: true
Encoding: UTF-8
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2021-10-08 06:42:53 UTC; Jin
Author: Jin Li [aut, cre]
Maintainer: Jin Li <jinli68@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-08 17:40:02 UTC

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New package retriever with initial version 0.1.0
Package: retriever
Title: Generate Disease-Specific Response Signatures from the LINCS-L1000 Data
Version: 0.1.0
Description: Generates disease-specific drug-response profiles that are independent of time, concentration, and cell-line. Based on the cell lines used as surrogates, the returned profiles represent the unique transcriptional changes induced by a compound in a given disease.
Depends: R (>= 3.5.0)
Imports: ccdata, pbapply, preprocessCore
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-08 13:10:52 UTC; danie
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>), Marieke Kuijjer [aut] (<https://orcid.org/0000-0001-6280-3130>)
Maintainer: Daniel Osorio <daniecos@uio.no>
Repository: CRAN
Date/Publication: 2021-10-08 18:00:07 UTC

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New package LIC with initial version 0.0.1
Package: LIC
Title: The LIC Criterion for Optimal Subset Selection
Version: 0.0.1
Description: The LIC criterion is to determine the most informative subsets so that the subset can retain most of the information contained in the complete data. The philosophy of the package is described in Guo G. (2020) <doi: 10.1007/s00180-020-00974-4>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: stats
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-10-08 08:04:16 UTC; H
Author: Guangbao Guo [aut, cre], Yue Sun [aut], Guoqi Qian [aut], Qian Wang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2021-10-08 17:50:02 UTC

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New package expDB with initial version 0.1.0
Package: expDB
Title: Database for Experiment Dataset
Version: 0.1.0
Maintainer: Bangyou Zheng <bangyou.zheng@csiro.au>
Description: A SQLite database is designed to store all information of experiment-based data including metadata, experiment design, managements, phenotypic values and climate records. The dataset can be imported from an excel file.
License: MIT + file LICENSE
URL: https://expdb.bangyou.me/, https://github.com/byzheng/expdb
BugReports: https://github.com/byzheng/expdb/issues
Encoding: UTF-8
Imports: DBI, RSQLite, utils, readxl, png, grid, tibble, lubridate, dplyr, methods, weaana (>= 0.1.1), tidyr, tidyverse, magrittr, stats, reshape2, stringr, rlang
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-10-08 05:00:13 UTC; zhe00a
Author: Bangyou Zheng [aut, cre]
Repository: CRAN
Date/Publication: 2021-10-08 17:40:06 UTC

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New package discretefit with initial version 0.0.0
Package: discretefit
Title: Simulated Goodness-of-Fit Tests for Discrete Distributions
Version: 0.0.0
Description: Implements fast, Monte Carlo simulations for goodness-of-fit (GOF) tests for discrete distributions. This includes tests based on the root-mean-square statistic, the Chi-squared statistic, the log-likelihood-ratio statistic (G^2), and the Kolmogorov-Smirnov statistic.
License: MIT + file LICENSE
Encoding: UTF-8
LinkingTo: Rcpp
Imports: Rcpp
Suggests: knitr, dgof, RVAideMemoire, bench, testthat (>= 3.0.0), rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-10-08 06:19:35 UTC; Josh
Author: Josh McCormick [aut, cre]
Maintainer: Josh McCormick <josh.mccormick@aya.yale.edu>
Repository: CRAN
Date/Publication: 2021-10-08 17:40:09 UTC

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New package CoMiRe with initial version 0.7.1
Package: CoMiRe
Title: Convex Mixture Regression
Version: 0.7.1
Date: 2021-10-08
Author: Antonio Canale [aut, cre], Daniele Durante [ctb], Arianna Falcioni [aut], Luisa Galtarossa [aut], Tommaso Rigon [ctb]
Maintainer: Antonio Canale <canale@stat.unipd.it>
Description: Posterior inference under the convex mixture regression (CoMiRe) models introduced by Canale, Durante, and Dunson (2018) <doi:10.1111/biom.12917>.
License: GPL-2
NeedsCompilation: yes
Imports: Rcpp (>= 1.0.5), KernSmooth, NonpModelCheck, ggplot2, gtools, mvtnorm, splines2 (>= 0.3.1), truncnorm, rlang
Depends: R (>= 4.0)
LinkingTo: RcppArmadillo, Rcpp (>= 1.0.5)
Encoding: UTF-8
Packaged: 2021-10-08 10:06:03 UTC; tony
Repository: CRAN
Date/Publication: 2021-10-08 10:50:02 UTC

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New package digitalDLSorteR with initial version 0.1.0
Package: digitalDLSorteR
Title: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
Version: 0.1.0
Maintainer: Diego Mañanes <dmananesc@cnic.es>
Description: Deconvolution of bulk RNA-Seq data using context-specific deconvolution models based on Deep Neural Networks using scRNA-Seq data as input. These models are able to make accurate estimates of the cell composition of bulk RNA-Seq samples from the same context using the advances provided by Deep Learning and the meaningful information provided by scRNA-Seq data. See Torroja and Sanchez-Cabo (2017) <doi:10.3389/fgene.2019.00978> for more details.
License: GPL-3
URL: https://diegommcc.github.io/digitalDLSorteR/, https://github.com/diegommcc/digitalDLSorteR
BugReports: https://github.com/diegommcc/digitalDLSorteR/issues
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: rlang, Matrix, Matrix.utils, methods, tidyr, SingleCellExperiment, SummarizedExperiment, splatter, zinbwave, stats, pbapply, S4Vectors, dplyr, tools, reshape2, gtools, edgeR, reticulate, keras, tensorflow, ggplot2, ggpubr, RColorBrewer
Suggests: knitr, rmarkdown, BiocParallel, rhdf5, DelayedArray, DelayedMatrixStats, HDF5Array, testthat
SystemRequirements: Python (>= 2.7.0), TensorFlow (https://www.tensorflow.org/)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-08 07:35:44 UTC; diegommcc
Author: Diego Mañanes [aut, cre] (<https://orcid.org/0000-0001-7247-6794>), Carlos Torroja [aut] (<https://orcid.org/0000-0001-8914-3400>), Fatima Sanchez-Cabo [aut] (<https://orcid.org/0000-0003-1881-1664>)
Repository: CRAN
Date/Publication: 2021-10-08 09:50:05 UTC

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New package SC.MEB with initial version 1.1
Package: SC.MEB
Title: Spatial Clustering with Hidden Markov Random Field using Empirical Bayes
Version: 1.1
Date: 2021-09-30
Description: Spatial clustering with hidden markov random field fitted via EM algorithm, details of which can be found in Yi Yang (2021) <doi:10.1101/2021.06.05.447181>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
License: GPL-3
Depends: mclust,parallel,ggplot2, Matrix, R (>= 3.5)
Imports: Rcpp (>= 1.0.6), SingleCellExperiment, purrr,BiocSingular, SummarizedExperiment, scater, scran, S4Vectors
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2021-10-06 14:54:38 UTC; yygao
Author: Yi Yang [aut, cre], Xingjie Shi [aut], Jin Liu [aut]
Maintainer: Yi Yang <yygaosansiban@sina.com>
Repository: CRAN
Date/Publication: 2021-10-08 08:40:21 UTC

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New package kdtools with initial version 0.6.0
Package: kdtools
Title: Tools for Working with Multidimensional Data
Version: 0.6.0
Description: Provides various tools for working with multidimensional data in R and C++, including extremely fast nearest-neighbor- and range- queries without the overhead of linked tree nodes.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: Rcpp (>= 0.12.14)
LinkingTo: Rcpp
Suggests: testthat, knitr, markdown, rmarkdown, covr, ggplot2, tidytext, printr, scales, BH, sf
VignetteBuilder: knitr
SystemRequirements: A compiler that conforms to the C++17 standard
URL: https://github.com/thk686/kdtools
BugReports: https://github.com/thk686/kdtools/issues
Biarch: true
NeedsCompilation: yes
Packaged: 2021-10-07 05:04:19 UTC; tkeitt
Author: Timothy Keitt [aut, cre]
Maintainer: Timothy Keitt <tkeitt@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-08 08:30:02 UTC

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New package fwildclusterboot with initial version 0.4
Package: fwildclusterboot
Title: Fast Wild Cluster Bootstrap Inference for Linear Regression Models
Version: 0.4
Date: 2021-10-03
Description: Implementation of the fast algorithm for wild cluster bootstrap inference developed in Roodman et al (2019, STATA Journal) for linear regression models <https://journals.sagepub.com/doi/full/10.1177/1536867X19830877>, which makes it feasible to quickly calculate bootstrap test statistics based on a large number of bootstrap draws even for large samples - as long as the number of bootstrapping clusters is not too large. Multiway clustering, regression weights, bootstrap weights, fixed effects and subcluster bootstrapping are supported. Further, both restricted (WCR) and unrestricted (WCU) bootstrap are supported. Methods are provided for a variety of fitted models, including 'lm()', 'feols()' (from package 'fixest') and 'felm()' (from package 'lfe').
URL: https://s3alfisc.github.io/fwildclusterboot/
BugReports: https://github.com/s3alfisc/fwildclusterboot/issues/
License: GPL-3
Imports: collapse, Formula, Rcpp, dreamerr, Matrix, Matrix.utils, generics, gtools
Suggests: fixest, lfe, plm, clusterSEs, data.table, fabricatr, tinytest, covr, knitr, rmarkdown, spelling, broom, modelsummary, RStata
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppEigen
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: yes
Packaged: 2021-10-06 17:57:11 UTC; alexa
Author: Alexander Fischer [aut, cre], David Roodman [aut], Achim Zeileis [ctb] (Author of included sandwich fragments), Nathaniel Graham [ctb] (Contributor to included sandwich fragments), Susanne Koell [ctb] (Contributor to included sandwich fragments), Laurent Berge [ctb] (Author of included fixest fragments), Sebastian Krantz [ctb]
Maintainer: Alexander Fischer <alexander-fischer1801@t-online.de>
Repository: CRAN
Date/Publication: 2021-10-08 08:30:05 UTC

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New package covid19br with initial version 0.1.2
Package: covid19br
Title: Brazilian COVID-19 Pandemic Data
Version: 0.1.2
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at country, region, state, and city-levels. The package also downloads the world-level COVID-19 data from the John Hopkins University's repository.
URL: https://fndemarqui.github.io/covid19br/
BugReports: https://github.com/fndemarqui/covid19br/issues
Encoding: UTF-8
License: AGPL (>= 3)
Depends: R (>= 3.5.0)
Imports: data.table, dplyr, httr, rio, rlang, sf, tidyr
Suggests: ggrepel, kableExtra, knitr, leaflet, pracma, plotly, rmarkdown, testthat, tidyverse
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-07 22:45:23 UTC; fndemarqui
Author: Fabio Demarqui [aut, cre], Cristiano Santos [aut], Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Repository: CRAN
Date/Publication: 2021-10-08 08:40:12 UTC

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New package cotram with initial version 0.3-1
Package: cotram
Title: Count Transformation Models
Version: 0.3-1
Date: 2021-09-21
Description: Count transformation models featuring parameters interpretable as discrete hazard ratios, odds ratios, reverse-time discrete hazard ratios, or transformed expectations. An appropriate data transformation for a count outcome and regression coefficients are simultaneously estimated by maximising the exact discrete log-likelihood using the computational framework provided in package 'mlt', technical details are given in Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>. The package also contains an experimental implementation of multivariate count transformation models with an application to multi-species distribution models.
Depends: R (>= 3.5.0), tram (>= 0.2-6), mlt (>= 1.2-1)
Imports: variables (>= 1.0-2), basefun (>= 1.0-5), alabama, Matrix, methods
Suggests: TH.data, knitr, lattice, colorspace, multcomp, mvtnorm, numDeriv
VignetteBuilder: knitr
URL: http://ctm.R-forge.R-project.org
Encoding: UTF-8
License: GPL-2
NeedsCompilation: no
Packaged: 2021-09-24 07:38:30 UTC; hothorn
Author: Sandra Siegfried [aut] (<https://orcid.org/0000-0002-7312-1001>), Luisa Barbanti [aut] (<https://orcid.org/0000-0001-5352-5802>), Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Repository: CRAN
Date/Publication: 2021-10-08 08:20:02 UTC

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New package quincunx with initial version 0.1.1
Package: quincunx
Title: REST API Client for the 'PGS' Catalog
Version: 0.1.1
Description: Programmatic access to the 'PGS' Catalog. This package provides easy access to 'PGS' Catalog data by accessing the REST API <https://www.pgscatalog.org/rest/>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, knitr, rmarkdown, ggplot2
Imports: stringr, magrittr, vroom, purrr, glue, dplyr, tidyjson, tibble, lubridate, rlang, tidyr, httr, utils, rvest, progress, methods, writexl, concatenate, memoise
Depends: R (>= 2.10)
URL: https://github.com/maialab/quincunx
BugReports: https://github.com/maialab/quincunx/issues
NeedsCompilation: no
Packaged: 2021-10-07 20:55:30 UTC; rmagno
Author: Ramiro Magno [aut, cre] (<https://orcid.org/0000-0001-5226-3441>), Isabel Duarte [aut] (<https://orcid.org/0000-0003-0060-2936>), Ana-Teresa Maia [aut] (<https://orcid.org/0000-0002-0454-9207>), CINTESIS [cph, fnd]
Maintainer: Ramiro Magno <ramiro.magno@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-08 07:10:02 UTC

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New package PAMmisc with initial version 1.7.0
Package: PAMmisc
Title: Miscellaneous Functions for Passive Acoustic Analysis
Version: 1.7.0
Description: A collection of miscellaneous functions for passive acoustics. Much of the content here is adapted to R from code written by other people. If you have any ideas of functions to add, please contact Taiki Sakai.
License: GNU General Public License
Encoding: UTF-8
LazyData: true
Imports: ggplot2, tuneR, seewave, dplyr, magrittr, RcppRoll, PamBinaries, RSQLite, lubridate, rerddap, ncdf4, httr, purrr, xml2, hoardr, methods, geosphere, tcltk, stringr, viridisLite, viridis
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-10-07 18:30:55 UTC; tnsak
Author: Taiki Sakai [aut, cre], Jay Barlow [ctb], Julie Oswald [ctb], Val Schmidt [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2021-10-08 07:10:06 UTC

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New package FADPclust with initial version 0.1.0
Package: FADPclust
Title: Functional Data Clustering Using Adaptive Density Peak Detection
Version: 0.1.0
Author: Rui Ren <xmurr@stu.xmu.edu.cn>
Maintainer: Rui Ren <xmurr@stu.xmu.edu.cn>
Description: An implementation of a clustering algorithm for functional data based on adaptive density peak detection technique, in which the density is estimated by functional k-nearest neighbor density estimation based on a proposed semi-metric between functions. The proposed functional data clustering algorithm is computationally fast since it does not need iterative process. (Alex Rodriguez and Alessandro Laio (2014) <doi:10.1126/science.1242072>; Xiao-Feng Wang and Yifan Xu (2016) <doi:10.1177/0962280215609948>).
License: GPL (>= 2)
Depends: R (>= 3.5.0)
Imports: MFPCA, cluster, fda, fda.usc, funData, stats, graphics
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-07 19:39:16 UTC; renrui
Repository: CRAN
Date/Publication: 2021-10-08 07:10:09 UTC

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New package presenter with initial version 0.1.0
Package: presenter
Title: Present Data with Style
Version: 0.1.0
Maintainer: Harrison Tietze <Harrison4192@gmail.com>
Description: Consists of custom wrapper functions using packages 'openxlsx', 'flextable', and 'officer' to create highly formatted MS office friendly output of your data frames. These viewer friendly outputs are intended to match expectations of professional looking presentations in business and consulting scenarios. The functions are opinionated in the sense that they expect the input data frame to have certain properties in order to take advantage of the automated formatting.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: flextable, magrittr, dplyr, rlang, stringr, purrr, officer, randomcoloR, tidyr, openxlsx, lubridate, janitor, tibble, stringi, berryFunctions, rvg, tidyselect, formattable, badger, framecleaner
Suggests: knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
URL: https://github.com/Harrison4192/presenter
BugReports: https://github.com/Harrison4192/presenter/issues
NeedsCompilation: no
Packaged: 2021-10-07 17:03:26 UTC; Harrison
Author: Harrison Tietze [aut, cre]
Repository: CRAN
Date/Publication: 2021-10-08 07:00:02 UTC

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Thu, 07 Oct 2021

New package StanMoMo with initial version 1.0.0
Package: StanMoMo
Title: Bayesian Mortality Modelling with 'Stan'
Version: 1.0.0
Description: Implementation of popular mortality models using the 'rstan' package, which provides the R interface to the 'Stan' C++ library for Bayesian estimation. The package supports well-known models proposed in the actuarial and demographic literature including the Lee-Carter (1992) <doi:10.1080/01621459.1992.10475265> and the Cairns-Blake-Dowd (2006) <doi:10.1111/j.1539-6975.2006.00195.x> models. By a simple call, the user inputs deaths and exposures and the package outputs the MCMC simulations for each parameter, the log likelihoods and predictions. Moreover, the package includes tools for model selection and Bayesian model averaging by leave future-out validation.
License: GPL-3
Encoding: UTF-8
LazyData: true
Biarch: true
Depends: R (>= 3.5.0)
Imports: loo, methods, RcppParallel, Rcpp (>= 0.12.0), rstan (>= 2.18.1), rstantools (>= 2.0.0), tidyverse, dplyr, tibble, httr, bridgesampling, stats, utils, tidyselect, latex2exp, tidyr, ggplot2, ggfan
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), rstan (>= 2.18.1), StanHeaders (>= 2.18.0), RcppParallel
SystemRequirements: GNU make
Suggests: knitr, rmarkdown, shinystan, Cairo
VignetteBuilder: knitr
URL: https://github.com/kabarigou/StanMoMo
BugReports: https://github.com/kabarigou/StanMoMo/issues
NeedsCompilation: yes
Packaged: 2021-10-07 10:24:27 UTC; Karim Barigou
Author: Karim Barigou [aut, cre] (<https://orcid.org/0000-0003-3389-9596>), Pierre-Olivier Goffard [aut] (<https://orcid.org/0000-0002-2667-6207>)
Maintainer: Karim Barigou <karim290492@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-07 16:20:05 UTC

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New package optimg with initial version 0.1.2
Package: optimg
Title: General-Purpose Gradient-Based Optimization
Version: 0.1.2
Date: 2021-10-07
Author: Vithor Rosa Franco <vithorfranco@gmail.com>
Maintainer: Vithor Rosa Franco <vithorfranco@gmail.com>
Description: Provides general purpose tools for helping users to implement steepest gradient descent methods for function optimization; for details see Ruder (2016) <arXiv:1609.04747v2>. Currently, the Steepest 2-Groups Gradient Descent and the Adaptive Moment Estimation (Adam) are the methods implemented. Other methods will be implemented in the future.
Imports: ucminf (>= 1.1-4)
License: GPL-3
Encoding: UTF-8
URL: https://github.com/vthorrf/optimg
NeedsCompilation: no
Packaged: 2021-10-07 12:11:12 UTC; Avell
Repository: CRAN
Date/Publication: 2021-10-07 16:30:05 UTC

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New package gslnls with initial version 1.0.0
Package: gslnls
Title: GSL Nonlinear Least-Squares Fitting
Version: 1.0.0
Date: 2021-10-07
Description: An R interface to nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquadt algorithm with and without geodesic acceleration, and several variants of Powell's dogleg algorithm. Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
BugReports: https://github.com/JorisChau/gslnls/issues
URL: https://github.com/JorisChau/gslnls
Depends: R (>= 3.5)
Encoding: UTF-8
Language: en-US
License: GPL-3
SystemRequirements: GSL (>= 2.2)
NeedsCompilation: yes
Packaged: 2021-10-07 08:01:59 UTC; jchau
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Repository: CRAN
Date/Publication: 2021-10-07 16:10:02 UTC

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New package SIMPLE.REGRESSION with initial version 0.1.2
Package: SIMPLE.REGRESSION
Title: Multiple Regression and Moderated Regression Made Simple
Version: 0.1.2
Date: 2021-10-06
Author: Brian P. O'Connor
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Description: Provides SPSS- and SAS-like output for least squares multiple regression and moderated regression, as well as interaction plots and Johnson-Neyman regions of significance for interactions. The output includes standardized coefficients, partial and semi-partial correlations, collinearity diagnostics, plots of residuals, and detailed information about simple slopes for interactions. There are numerous options for designing interaction plots, including plots of interactions for both lm and lme models.
Imports: graphics, stats, utils, nlme
LazyLoad: yes
LazyData: yes
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2021-10-06 10:28:10 UTC; brianoconnor
Repository: CRAN
Date/Publication: 2021-10-07 10:30:02 UTC

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New package pecora with initial version 0.1.0
Package: pecora
Title: Permutation Conditional Random Tests
Version: 0.1.0
Date: 2021-10-06
Description: It provides functions to perform permutation conditional random one-sample and two-samples t-tests in a multivariate framework.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.3), matrixStats, stats
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
Language: en-US
NeedsCompilation: yes
Packaged: 2021-10-06 16:20:14 UTC; Angela Andreella
Author: Angela Andreella [aut, cre] (Main author, <https://orcid.org/0000-0002-1141-3041>)
Maintainer: Angela Andreella <angela.andreella@unipd.it>
Repository: CRAN
Date/Publication: 2021-10-07 10:40:02 UTC

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New package BoneProfileR with initial version 2.0
Package: BoneProfileR
Title: Tools to Study Bone Compactness
Version: 2.0
Date: 2021-10-06
Author: Marc Girondot <marc.girondot@gmail.com>
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Depends: imager, HelpersMG (>= 4.7), knitr, rmarkdown, R (>= 4.1), shiny
Suggests: tiff, ijtiff, openxlsx, parallel
Description: Bone Profiler is a scientific method and a software used to model bone section for paleontological and ecological studies. See Girondot and Laurin 2003 <https://www.researchgate.net/publication/280021178_Bone_profiler_A_tool_to_quantify_model_and_statistically_compare_bone-section_compactness_profiles>.
License: GPL-2
LazyData: yes
LazyLoad: yes
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-10-06 17:16:22 UTC; marcgirondot
Repository: CRAN
Date/Publication: 2021-10-07 10:50:02 UTC

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New package SpatialBSS with initial version 0.12-0
Package: SpatialBSS
Title: Blind Source Separation for Multivariate Spatial Data
Version: 0.12-0
Date: 2021-10-05
Maintainer: Christoph Muehlmann <christoph.muehlmann@tuwien.ac.at>
Description: Blind source separation for multivariate spatial data based on simultaneous/joint diagonalization of local covariance matrices. This package is an implementation of the methods described in Bachoc, Genton, Nordhausen, Ruiz-Gazen and Virta (2020) <doi:10.1093/biomet/asz079>.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.2), JADE, sp, stats
Suggests: sf, RandomFields, knitr, rmarkdown, markdown
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2021-10-05 13:17:39 UTC; cmuehlmann
Author: Christoph Muehlmann [aut, cre] (<https://orcid.org/0000-0001-7330-8434>), Klaus Nordhausen [aut] (<https://orcid.org/0000-0002-3758-8501>), Joni Virta [aut] (<https://orcid.org/0000-0002-2150-2769>)
Repository: CRAN
Date/Publication: 2021-10-07 08:20:26 UTC

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Wed, 06 Oct 2021

New package RareComb with initial version 1.0
Package: RareComb
Title: Combinatorial and Statistical Analyses of Rare Events
Version: 1.0
Description: A custom implementation of the apriori algorithm and binomial tests to identify combinations of features (genes, variants etc) significantly enriched for simultaneous mutations/events from sparse Boolean input, see Vijay Kumar Pounraja, Santhosh Girirajan (2021). <doi:10.1101/2021.10.01.462832>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: magrittr, arules, dplyr, methods, pwr, stringr, tidyr, reshape2, sqldf
NeedsCompilation: no
Packaged: 2021-10-05 12:28:40 UTC; Vijay
Author: Vijay Kumar Pounraja [aut, cre] (<https://orcid.org/0000-0002-9710-189X>)
Maintainer: Vijay Kumar Pounraja <vijaykumar.mp@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-06 06:30:02 UTC

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New package ggalignment with initial version 1.0.0
Package: ggalignment
Title: Plots 'D&D'-Style Alignment Charts
Version: 1.0.0
Description: 'D&D' alignment charts show 9 boxes with values for good through evil and values for chaotic through lawful. This package easily creates these alignment charts from user-provided image paths and alignment values.
License: MIT + file LICENSE
Depends: R (>= 3.4)
Imports: dplyr (>= 1.0.0), ggimage (>= 0.2.0), ggplot2 (>= 3.3.0), magrittr (>= 1.0.0), rlang (>= 0.1.2)
Suggests: rmarkdown (>= 2.0.0), knitr (>= 1.0), testthat (>= 3.0.0), vdiffr (>= 1.0.0), roxygen2
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-06 04:44:37 UTC; aftoncoombs
Author: Afton Coombs [aut, cre, cph], Tan Ho [ctb] (<https://orcid.org/0000-0001-8388-5155>)
Maintainer: Afton Coombs <aftoncoombs@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-06 06:40:02 UTC

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Tue, 05 Oct 2021

New package stratEst with initial version 1.1.4
Package: stratEst
Title: Strategy Estimation
Version: 1.1.4
Author: Fabian Dvorak
Maintainer: Fabian Dvorak <fabian.dvorak@uni.kn>
Date: 2021-09-22
Description: Variants of strategy estimation (Dal Bo & Frechette, 2011, <doi:10.1257/aer.101.1.411>), including the model with parameters for the choice probabilities of the strategies (Breitmoser, 2015, <doi:10.1257/aer.20130675>), and the model with individual level covariates for the selection of strategies by individuals (Dvorak & Fehrler, 2018, <doi:10.2139/ssrn.2986445>).
Copyright: See the file COPYRIGHTS for copyright, authorship and license details
License: GPL-3
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo (>= 0.9.900.0.0)
Imports: Rcpp (>= 0.12.18), stats, graphics
Suggests: DiagrammeR (>= 1.0.6.1), DiagrammeRsvg (>= 0.1), spelling, testthat
Depends: R (>= 3.5)
URL: https://github.com/fdvorak/stratEst
BugReports: https://github.com/fdvorak/stratEst/issues
NeedsCompilation: yes
Language: en-US
Packaged: 2021-09-22 11:39:18 UTC; anon
Repository: CRAN
Date/Publication: 2021-10-05 23:20:02 UTC

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New package libproj with initial version 8.1.0-1
Package: libproj
Title: Generic Coordinate Transformation Library ('PROJ') C API
Version: 8.1.0-1
Description: Provides a 'PROJ' <https://proj.org> C API that can be used to write high-performance C and C++ coordinate transformation operations using R as an interface. This package contains an internal version of the 'PROJ' library to guarantee the best possible consistency on multiple platforms, and to provide a means by which 'PROJ' can be used on platforms where it may be impractical or impossible to install a binary version of the library.
License: MIT + file LICENSE
Encoding: UTF-8
SystemRequirements: C++11, libcurl, libtiff, zlib
Suggests: gh, testthat
URL: https://paleolimbot.github.io/libproj/, https://github.com/paleolimbot/libproj
BugReports: https://github.com/paleolimbot/libproj/issues
Imports: rappdirs
LinkingTo: cpp11
NeedsCompilation: yes
Packaged: 2021-09-26 12:59:37 UTC; deweydunnington
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>), PROJ authors [aut], Jeroen Ooms [cph] (configure script), Evan Roualt [cph], Thomas Knudsen [cph], SDFE [cph], Kristan Evers [cph], Frank Warmerdam [cph], Charles Karney [cph], Evan Roualt [cph]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Repository: CRAN
Date/Publication: 2021-10-05 23:10:02 UTC

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New package BayesSenMC with initial version 0.1.4
Package: BayesSenMC
Title: Different Models of Posterior Distributions of Adjusted Odds Ratio
Version: 0.1.4
Author: Jinhui Yang, Haitao Chu, and Lifeng Lin
Maintainer: Jinhui Yang <james.yangjinhui@gmail.com>
URL: https://github.com/formidify/BayesSenMC
BugReports: https://github.com/formidify/BayesSenMC/issues
Description: Generates different posterior distributions of adjusted odds ratio under different priors of sensitivity and specificity, and plots the models for comparison. It also provides estimations for the specifications of the models using diagnostics of exposure status with a non-linear mixed effects model. It implements the methods that are first proposed in <doi:10.1016/j.annepidem.2006.04.001> and <doi:10.1177/0272989X09353452>.
License: GPL-2
Encoding: UTF-8
LazyData: true
Biarch: true
Depends: R (>= 3.4.0)
Imports: methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.1.1), dplyr, ggplot2, lme4
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2021-09-28 14:35:06 UTC; james
Repository: CRAN
Date/Publication: 2021-10-05 23:10:12 UTC

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New package ttcg with initial version 1.0.1
Package: ttcg
Title: Three-Term Conjugate Gradient for Unconstrained Optimization
Version: 1.0.1
Date: 2021-10-04
Maintainer: Hao Chi Kiang <hello@hckiang.com>
Description: Some accelerated three-term conjugate gradient algorithms implemented purely in R with the same user interface as optim(). The search directions and acceleration scheme are described in Andrei, N. (2013) <doi:10.1016/j.amc.2012.11.097>, Andrei, N. (2013) <doi:10.1016/j.cam.2012.10.002>, and Andrei, N (2015) <doi:10.1007/s11075-014-9845-9>. Line search is done by a hybrid algorithm incorporating the ideas in Oliveia and Takahashi (2020) <doi:10.1145/3423597> and More and Thuente (1994) <doi:10.1145/192115.192132>.
License: GPL-3
Encoding: UTF-8
URL: https://git.sr.ht/~hckiang/ttcg
Depends: R (>= 3.3.0)
Imports: numDeriv
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-10-04 21:13:58 UTC; hckiang
Author: Hao Chi Kiang [cre, aut]
Repository: CRAN
Date/Publication: 2021-10-05 12:30:02 UTC

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New package multIntTestFunc with initial version 0.1.1
Package: multIntTestFunc
Title: Provides Test Functions for Multivariate Integration
Version: 0.1.1
Author: Klaus Herrmann [aut, cre]
Maintainer: Klaus Herrmann <klaus.herrmann@usherbrooke.ca>
Description: Provides implementations of functions that can be used to test multivariate integration routines. The package covers five different integration domains (unit hypercube, unit ball, unit sphere, standard simplex and R^n). For each domain several functions with different properties (smooth, non-differentiable, ...) are available. The functions are available in all dimensions n >= 1. For each function the exact value of the integral is known and implemented to allow testing the accuracy of multivariate integration routines. Details on the available test functions can be found at on the development website.
URL: https://github.com/KlausHerrmann/multIntTestFunc
Imports: gsl, pracma, methods
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-05 04:25:33 UTC; herk1401
Repository: CRAN
Date/Publication: 2021-10-05 12:30:05 UTC

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New package easylabel with initial version 0.1.0
Package: easylabel
Title: Interactive Scatter Plot and Volcano Plot Labels
Version: 0.1.0
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Description: Interactive labelling of scatter plots and volcano plots using a 'shiny' and 'plotly' interface. Users can hover over points to see where specific points are located and click points on/off to easily label them. Labels can be dragged around the plot to place them optimally. Plots can be exported directly to pdf for publication.
Language: en-gb
License: MIT + file LICENSE
Encoding: UTF-8
biocViews:
Suggests: AnnotationDbi, knitr, org.Hs.eg.db, qvalue, rmarkdown
Imports: plotly, shiny, RColorBrewer, DT
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-04 21:33:38 UTC; myles
Author: Myles Lewis [aut, cre] (<https://orcid.org/0000-0001-9365-5345>), Katriona Goldmann [aut] (<https://orcid.org/0000-0002-9073-6323>), Cankut Cubuk [ctb] (<https://orcid.org/0000-0003-4646-0849>)
Repository: CRAN
Date/Publication: 2021-10-05 12:30:12 UTC

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New package validata with initial version 0.1.0
Package: validata
Title: Validate Data Frames
Version: 0.1.0
Maintainer: Harrison Tietze <Harrison4192@gmail.com>
Description: Functions for validating the structure and properties of data frames. Answers essential questions about a data set after initial import or modification. What are the unique or missing values? What columns form a primary key? What are the properties of the numeric or categorical columns? What kind of overlap or mapping exists between 2 columns?
License: MIT + file LICENSE
URL: https://harrison4192.github.io/validata/, https://github.com/Harrison4192/validata
BugReports: https://github.com/Harrison4192/validata/issues
Encoding: UTF-8
LazyData: true
Imports: dplyr, stringr, janitor, rlang, tidyselect, purrr, magrittr, tidyr, tibble, gtools, listviewer, data.table, scales, utils, BBmisc, framecleaner, badger, rlist
Suggests: knitr, rmarkdown, testit, webshot
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-10-04 20:26:19 UTC; Harrison
Author: Harrison Tietze [aut, cre]
Repository: CRAN
Date/Publication: 2021-10-05 08:20:02 UTC

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New package tabularMLC with initial version 0.0.3
Package: tabularMLC
Title: Tabular Maximum Likelihood Classifier
Version: 0.0.3
Description: The maximum likelihood classifier (MLC) is one of the most common classifiers used for remote sensing imagery. This package uses 'RcppArmadillo' to provide a fast implementation of the MLC to train and predict over tabular data (data.frame). The algorithms were based on Mather (1985) <doi:10.1080/01431168508948456> method.
License: GPL-3
Depends: Rcpp, methods
Imports: stats
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
URL: https://github.com/caiohamamura/tabularMLC
BugReports: https://github.com/caiohamamura/tabularMLC/issues
Author: Caio Hamamura [aut, cre] (<https://orcid.org/0000-0001-6149-5885>)
Maintainer: Caio Hamamura <caiohamamura@gmail.com>
Repository: CRAN
Repository/R-Forge/Project: tabularmlc
Repository/R-Forge/Revision: 5
Repository/R-Forge/DateTimeStamp: 2021-10-04 20:39:29
Date/Publication: 2021-10-05 08:30:02 UTC
NeedsCompilation: yes
Packaged: 2021-10-04 20:48:40 UTC; rforge

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New package RCCPCA with initial version 0.1.0
Package: RCCPCA
Title: "Retained Component Criterion for Principal Component Analysis"
Version: 0.1.0
Date: 2021-10-01
Author: Fayed Alshammri
Maintainer: Dr. Fayed Alshammri <fayed333@hotmail.com>
Description: The RCC_PCA criterion is a tool to determine the optimal number of components to retain in PCA;See Alshammri (2021).
License: GPL-2
Depends: stats, graphics
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-10-04 16:00:01 UTC; User
Repository: CRAN
Date/Publication: 2021-10-05 08:10:10 UTC

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New package predtools with initial version 0.0.2
Package: predtools
Title: Prediction Model Tools
Version: 0.0.2
Description: Provides additional functions for evaluating predictive models, including plotting calibration curves and model-based Receiver Operating Characteristic (mROC) based on Sadatsafavi et al (2021) <arXiv:2003.00316>.
License: GPL
Encoding: UTF-8
LazyData: true
URL: https://github.com/resplab/predtools
BugReports: https://github.com/resplab/predtools/issues
Depends: R (>= 3.6)
Imports: Rcpp, pROC, stats, graphics, RConics, ggplot2, dplyr, magrittr
LinkingTo: Rcpp
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-10-04 17:46:10 UTC; amin
Author: Mohsen Sadatsafavi [aut, cph] (<https://orcid.org/0000-0002-0419-7862>), Amin Adibi [cre] (<https://orcid.org/0000-0003-2748-4781>), Abdollah Safari [aut]
Maintainer: Amin Adibi <adibi@alumni.ubc.ca>
Repository: CRAN
Date/Publication: 2021-10-05 08:10:05 UTC

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New package OmicInt with initial version 1.1.5
Package: OmicInt
Title: Omics Network Exploration
Version: 1.1.5
Author: Auste Kanapeckaite
Maintainer: Auste Kanapeckaite <auste.kan@algorithm379.com>
Description: Omics integration and detailed gene network exploration to identify expression patterns, prepare for pathway building, and find disease candidate genes; the package compliments research "Insights into therapeutic targets and biomarkers using integrated multi-'omics' approaches for dilated and ischemic cardiomyopathies"; Auste Kanapeckaite and Neringa Burokiene; 2021, <doi:10.1093/intbio/zyab007>.
License: GPL (>= 3)
Encoding: UTF-8
VignetteBuilder: knitr
Suggests: viridis, utils, stats, graphics
Imports: cluster, stringr,RCurl, ggplot2, mclust,gtools,methods ,tidyr, dplyr, tidyselect,pheatmap,reshape2,plotly,knitr,rmarkdown,lattice, RColorBrewer, igraph, ggExtra, dendextend,STRINGdb
NeedsCompilation: no
Packaged: 2021-10-04 18:58:13 UTC; auste
Repository: CRAN
Date/Publication: 2021-10-05 08:20:06 UTC

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New package LMMstar with initial version 0.3.2
Package: LMMstar
Title: Repeated Measurement Models for Discrete Times
Version: 0.3.2
Date: 2021-10-04
Description: Companion R package for the course "Statistical analysis of correlated and repeated measurements for health science researchers" taught by the section of Biostatistics of the University of Copenhagen. It provides functions for computing summary statistics and obtaining graphical displays of longitudinal data, as well as for statistical modeling and statistical inference using linear mixed model.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/bozenne/LMMstar
BugReports: https://github.com/bozenne/LMMstar/issues
Depends: R (>= 3.5.0), ggplot2, nlme
Imports: emmeans, lava, Matrix, multcomp, numDeriv, reshape2, sandwich
Suggests: AICcmodavg, data.table, nlmeU, optimx, Publish, qqtest, R.rsp, testthat
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2021-10-04 21:05:26 UTC; bozenne
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>), Julie Forman [aut] (<https://orcid.org/0000-0001-7368-0869>)
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-05 08:30:12 UTC

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New package ECOTOXr with initial version 0.1.1
Package: ECOTOXr
Title: Download and Extract Data from US EPA's ECOTOX Database
Version: 0.1.1
Date: 2021-10-04
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Description: The US EPA ECOTOX database is a freely available database with a treasure of aquatic and terrestrial ecotoxicological data. As the online search interface doesn't come with an API, this package provides the means to easily access and search the database in R. To this end, all raw tables are downloaded from the EPA website and stored in a local SQLite database.
Depends: R (>= 3.5.0), RSQLite
Imports: crayon, dplyr, rappdirs, readr, rvest, stringr, utils
Suggests: testthat (>= 3.0.0), webchem
URL: <https://github.com/pepijn-devries/ECOTOXr>
BugReports: https://github.com/pepijn-devries/ECOTOXr/issues
License: GPL (>= 3)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-10-04 11:59:00 UTC; vries171
Repository: CRAN
Date/Publication: 2021-10-05 08:10:12 UTC

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New package rnpn with initial version 1.2.2
Package: rnpn
Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (<https://usanpn.org/>), which includes data on various life history events that occur at specific times.
Version: 1.2.2
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Imports: httr (>= 1.1.0), jsonlite (>= 0.9.19), data.table (>= 1.9.6), sp (>= 1.1-0), tibble, curl, raster, rgdal, plyr, XML, magrittr
Suggests: ggplot2, testthat, covr, knitr, markdown, rmarkdown, RColorBrewer, vcr
VignetteBuilder: knitr
URL: https://docs.ropensci.org/rnpn/ (website) https://github.com/ropensci/rnpn/ (devel)
NeedsCompilation: no
Packaged: 2021-10-04 20:47:14 UTC; usanpn
Author: Alyssa Rosemartin [aut, cre], Scott Chamberlain [aut], Lee Marsh [aut], Kevin Wong [aut]
Maintainer: Alyssa Rosemartin <alyssa@usanpn.org>
Repository: CRAN
Date/Publication: 2021-10-05 07:20:10 UTC

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New package rLiDAR with initial version 0.1.5
Package: rLiDAR
Title: LiDAR Data Processing and Visualization
Version: 0.1.5
Depends: R (>= 3.3.2)
Imports: bitops, deldir, geometry, methods, plyr, raster, rgeos, rgl, sp, spatstat.geom
Description: Set of tools for reading, processing and visualizing small set of LiDAR (Light Detection and Ranging) data for forest inventory applications. More details were published in Silva et al. (2016) <doi:10.1080/07038992.2016.1196582>.
License: GPL (>= 2)
Repository: CRAN
Repository/R-Forge/Project: rlidar
NeedsCompilation: no
Packaged: 2021-10-04 19:48:06 UTC; rforge
URL: https://github.com/carlos-alberto-silva/rLiDAR
Author: Carlos Alberto Silva [aut, cph, cre], Nicholas L. Crookston [aut, ctb], Andrew T. Hudak [aut, ctb], Lee A. Vierling [aut, ctb], Carine Klauberg [aut, ctb], Adrian Cardil [aut, ctb], Caio Hamamura [aut, ctb] (Maintenance and review)
Maintainer: Carlos Alberto Silva <carlos_engflorestal@outlook.com>
Repository/R-Forge/Revision: 129
Repository/R-Forge/DateTimeStamp: 2021-10-04 19:27:16
Date/Publication: 2021-10-05 07:30:02 UTC

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New package GNRS with initial version 0.3.2
Package: GNRS
Title: Access the 'Geographic Name Resolution Service'
Version: 0.3.2
Description: Provides tools for interacting with the 'geographic name resolution service' ('GNRS') API <https://github.com/ojalaquellueva/gnrs> and associated functionality. The 'GNRS' is a batch application for resolving & standardizing political division names against standard name in the geonames database <http://www.geonames.org/>. The 'GNRS' resolves political division names at three levels: country, state/province and county/parish. Resolution is performed in a series of steps, beginning with direct matching to standard names, followed by direct matching to alternate names in different languages, followed by direct matching to standard codes (such as ISO and FIPS codes). If direct matching fails, the 'GNRS' attempts to match to standard and then alternate names using fuzzy matching, but does not perform fuzzing matching of political division codes. The 'GNRS' works down the political division hierarchy, stopping at the current level if all matches fail. In other words, if a country cannot be matched, the 'GNRS' does not attempt to match state or county.
Depends: R (>= 3.4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: RCurl, jsonlite, httr
Suggests: knitr, rmarkdown, testthat, devtools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-04 20:17:26 UTC; Brian
Author: Brad Boyle [aut], Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-05 07:30:12 UTC

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New package fflr with initial version 1.9.2
Package: fflr
Title: Retrieve ESPN Fantasy Football Data
Version: 1.9.2
Description: Format the raw data from the ESPN fantasy football API <https://fantasy.espn.com/apis/v3/games/ffl/> as data frames. Retrieve data on public leagues, rosters, athletes, and matches.
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: httr (>= 1.4.2), jsonlite (>= 1.7.2), tibble (>= 3.1.3)
Suggests: knitr (>= 1.34), rmarkdown (>= 2.11), spelling (>= 2.2), testthat (>= 3.0.0), xml2 (>= 1.3.2)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-05 03:31:52 UTC; kiernan
Author: Kiernan Nicholls [aut, cre, cph]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Repository: CRAN
Date/Publication: 2021-10-05 07:30:05 UTC

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Mon, 04 Oct 2021

New package rbooster with initial version 1.0.2
Package: rbooster
Title: AdaBoost Framework for Any Classifier
Version: 1.0.2
Description: This is a simple package which provides a function that boosts pre-ready or custom-made classifiers. Package uses Discrete AdaBoost (<doi:10.1006/jcss.1997.1504>) for two class, SAMME (<doi:10.4310/SII.2009.v2.n3.a8>) for multiclass classification.
Depends: R (> 4.0.1)
Imports: stats, rpart, earth, Hmisc
Suggests: knitr, imbalance, nnet, rmarkdown
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-04 13:08:41 UTC; Fatih
Author: Fatih Saglam [aut, cre] (<https://orcid.org/0000-0002-2084-2008>), Hasan Bulut [ctb]
Maintainer: Fatih Saglam <fatih.saglam@omu.edu.tr>
Repository: CRAN
Date/Publication: 2021-10-04 20:20:02 UTC

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New package insiderTrades with initial version 0.0.1
Package: insiderTrades
Title: Tools to Download Insider Transactions and Holdings
Version: 0.0.1
Description: Download insider trading transactions and insider holdings from a public NoSQL SEC database (<https://www.sec.gov/Archives/edgar/full-index/>) using keyword criteria and generate a relational dataframe.
License: CC0
URL: https://github.com/US-Department-of-the-Treasury/insiderTrades
BugReports: https://github.com/US-Department-of-the-Treasury/insiderTrades/issues
Encoding: UTF-8
Imports: stringr (>= 1.4.0), magrittr (>= 2.0.1), RCurl (>= 1.98-1.3)
Suggests: knitr, rmarkdown, devtools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-04 15:27:11 UTC; HancuchJ
Author: Joseph Hancuch [aut, cre]
Maintainer: Joseph Hancuch <joseph.hancuch@treasury.gov>
Repository: CRAN
Date/Publication: 2021-10-04 20:20:05 UTC

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New package isokernel with initial version 0.1.0
Package: isokernel
Title: Isolation Kernel
Version: 0.1.0
Maintainer: Ye Zhu <ye.zhu@ieee.org>
Description: Implementation of Isolation kernel (Qin et al. (2019) <doi:10.1609/aaai.v33i01.33014755>).
License: GPL-3
URL: https://github.com/zhuye88/isokernel
BugReports: https://github.com/zhuye88/isokernel/issues
Depends: R (>= 3.5.0)
Imports: RANN (>= 2.6.1), Matrix (>= 1.3-4)
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2021-10-04 09:52:02 UTC; YE
Author: Ye Zhu [aut, cre, cph]
Repository: CRAN
Date/Publication: 2021-10-04 19:50:02 UTC

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New package deepregression with initial version 0.1
Package: deepregression
Title: Fitting Deep Distributional Regression
Version: 0.1
Description: Allows for the specification of semi-structured deep distributional regression models which are fitted in a neural network as proposed by Ruegamer et al. (2021) <arXiv:2104.02705>. Predictors can be modeled using structured (penalized) linear effects, structured non-linear effects or using an unstructured deep network model.
Config/reticulate: list( packages = list( list(package = "six", pip = TRUE), list(package = "tensorflow", version = "2.5.0rc0", pip = TRUE), list(package = "tensorflow_probability", version = "0.12", pip = TRUE), list(package = "keras", version = "2.5.0rc0", pip = TRUE)) )
Depends: R (>= 4.0.0)
Suggests: testthat, knitr
Imports: tensorflow (>= 2.2.0), tfprobability, keras, mgcv, dplyr, purrr, R6, reticulate (>= 1.14), Matrix, magrittr, Metrics, tfruns, methods, utils
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-10-04 08:59:25 UTC; david
Author: David Ruegamer [aut, cre], Florian Pfisterer [ctb], Philipp Baumann [ctb], Chris Kolb [ctb]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-04 19:50:04 UTC

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New package childesr with initial version 0.2.2
Package: childesr
Title: Accessing the 'CHILDES' Database
Description: Tools for connecting to 'CHILDES', an open repository for transcripts of parent-child interaction. For more information on the underlying data, see <https://childes-db.stanford.edu>.
Version: 0.2.2
Depends: R (>= 4.0)
License: GPL-3
URL: https://github.com/langcog/childesr
BugReports: https://github.com/langcog/childesr/issues
Encoding: UTF-8
Imports: DBI (>= 1.1), dbplyr (>= 2.1), dplyr (>= 1.0), jsonlite (>= 1.7), magrittr (>= 2.0), purrr (>= 0.3), RMySQL (>= 0.10.21)
Suggests: knitr, rmarkdown, curl
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-01 18:25:57 UTC; mikabr
Author: Mika Braginsky [aut, cre], Alessandro Sanchez [aut, ctb], Daniel Yurovsky [aut], Kyle MacDonald [ctb], Stephan Meylan [ctb], Jessica Mankewitz [ctb]
Maintainer: Mika Braginsky <mika.br@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-04 09:40:02 UTC

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New package wig with initial version 0.1.0
Package: wig
Title: Import WIG Data into R in Long Format
Version: 0.1.0
Description: Import WIG data into R in long format.
License: MIT + file LICENSE
URL: https://github.com/ramiromagno/wig
BugReports: https://github.com/ramiromagno/wig/issues
Encoding: UTF-8
Imports: dplyr, magrittr, stringr, tibble
Suggests: spelling
Language: en-US
NeedsCompilation: no
Packaged: 2021-10-02 10:57:25 UTC; rmagno
Author: Ramiro Magno [aut, cre] (<https://orcid.org/0000-0001-5226-3441>)
Maintainer: Ramiro Magno <ramiro.magno@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-04 08:20:02 UTC

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New package robustsur with initial version 0.0-7
Package: robustsur
Version: 0.0-7
Date: 2021-10-03
Title: Robust Estimation for Seemingly Unrelated Regression Models
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>
Description: Data sets are often corrupted by outliers. When data are multivariate outliers can be classified as case-wise or cell-wise. The latters are particularly challenge to handle. We implement a robust estimation procedure for Seemingly Unrelated Regression Models which is able to cope well with both type of outliers. Giovanni Saraceno, Fatemah Alqallaf, Claudio Agostinelli (2021) <arXiv:2107.00975>.
Depends: R (>= 3.0.0), robustbase, robreg3S
Imports: Matrix, GSE
Suggests: systemfit
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2021-10-03 14:59:00 UTC; claudio
Author: Claudio Agostinelli [aut, cre] (<https://orcid.org/0000-0001-6702-4312>), Giovanni Saraceno [aut] (<https://orcid.org/0000-0002-1753-2367>)
Repository: CRAN
Date/Publication: 2021-10-04 08:40:02 UTC

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New package iSFun with initial version 0.1.0
Package: iSFun
Title: Integrative Dimension Reduction Analysis for Multi-Source Data
Version: 0.1.0
Maintainer: Rui Ren <xmurr@stu.xmu.edu.cn>
Description: An implementation of integrative dimension reduction analysis procedures for multi-source data, which provides integrative sparse partial least squares, integrative sparse principal component analysis, integrative sparse canonical correlation analysis and corresponding meta-analysis versions, etc. The work is built and improved upon the references: (1) Fang, K., Fan, X., Zhang, Q., and Ma, S. (2018). "Integrative sparse principal component analysis." Journal of Multivariate Analysis, <doi:10.1016/j.jmva.2018.02.002>. (2) Liang, W., Ma, S., Zhang, Q., and Zhu, T. (2021). "Integrative sparse partial least squares." Statistics in Medicine, <doi:10.1002/sim.8900>.
License: GPL (>= 2)
Depends: R (>= 3.5.0)
Imports: caret, graphics, grDevices, irlba, stats
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-03 02:50:12 UTC; renrui
Author: Kuangnan Fang [aut], Rui Ren [aut, cre], Qingzhao Zhang [aut], Shuangge Ma [aut]
Repository: CRAN
Date/Publication: 2021-10-04 08:30:06 UTC

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New package gsbDesign with initial version 1.0-2
Package: gsbDesign
Version: 1.0-2
Date: 2021-10-02
Title: Group Sequential Bayes Design
Depends: gsDesign, lattice, grid,
Imports: stats, graphics, grDevices, utils
Description: Group Sequential Operating Characteristics for Clinical, Bayesian two-arm Trials with known Sigma and Normal Endpoints, as described in Gerber and Gsponer (2016) <doi: 10.18637/jss.v069.i11>.
License: GPL-3
LazyLoad: yes
NeedsCompilation: no
Packaged: 2021-10-02 12:17:47 UTC; bjoern
Repository: CRAN
Date/Publication: 2021-10-04 08:20:05 UTC
Author: Florian Gerber [aut], Thomas Gsponer [aut], Bjoern Bornkamp [cre] (maintainer)
Maintainer: Bjoern Bornkamp <bbnkmp@mail.de>

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New package ForestGapR with initial version 0.1.6
Package: ForestGapR
Title: Tropical Forest Canopy Gaps Analysis
Version: 0.1.6
Depends: R (>= 3.4.0)
Imports: raster, igraph, VGAM, sp, graphics, stats, viridis, rgeos, spatstat.core, spatstat.geom, poweRlaw
Description: Set of tools for detecting and analyzing Airborne Laser Scanning-derived Tropical Forest Canopy Gaps. Details were published in Silva et al. (2019) <doi:10.1111/2041-210X.13211>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Author: Carlos Alberto Silva [aut, cph, cre], Ekena Rangel Pinagé [aut] (Reviews the documentation), Midhun Mohan [aut] (Reviews the documentation), Danilo Roberti Alves de Almeida [aut] (Reviews the documentation), Eben North Broadbent [aut] (Reviews the documentation), Wan Shafrina Wan Mohd Jaafar [aut] (Reviews the documentation), Daniel de Almeida Papa [aut] (Reviews the documentation), Adrian Cardil [aut] (Reviews the documentation), Ruben Valbuena [cph, aut], Toby Jackson [aut], Caio Hamamura [aut] (Maintenance and review), Carine Klauberg [aut] (Reviews the documentation)
Maintainer: Carlos Alberto Silva <carlos_engflorestal@outlook.com>
Repository: CRAN
Repository/R-Forge/Project: forestgapr
Repository/R-Forge/Revision: 22
Repository/R-Forge/DateTimeStamp: 2021-10-02 18:18:11
Date/Publication: 2021-10-04 08:30:17 UTC
NeedsCompilation: no
Packaged: 2021-10-02 18:28:06 UTC; rforge

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New package rForest with initial version 0.1.4
Package: rForest
Title: Forest Inventory and Analysis
Version: 0.1.4
Depends: R (>= 3.1.2)
Imports: alphashape3d, geometry, rgl, sp
Description: Set of tools designed for forest inventory analysis.
License: GPL (>= 2)
URL: https://github.com/carlos-alberto-silva/rForest
Author: Carlos Alberto Silva [aut, cph, cre], Carine Klauberg [aut] (Reviews the documentation), Samuel P. C. Carvalho [aut], Manoela de O. Rosa [aut], Joao P. S. Madi [aut], Caio Hamamura [aut] (Maintenance and review)
Maintainer: Carlos Alberto Silva <carlos_engflorestal@outlook.com>
Repository: CRAN
Repository/R-Forge/Project: rforest
Repository/R-Forge/Revision: 15
Repository/R-Forge/DateTimeStamp: 2021-10-02 04:21:10
Date/Publication: 2021-10-04 08:00:02 UTC
NeedsCompilation: no
Packaged: 2021-10-02 04:28:54 UTC; rforge

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Sun, 03 Oct 2021

New package framecleaner with initial version 0.1.0
Package: framecleaner
Title: Clean Data Frames
Version: 0.1.0
Maintainer: Harrison Tietze <Harrison4192@gmail.com>
Description: Provides a friendly interface for modifying data frames with a sequence of piped commands built upon the 'tidyverse' Wickham et al., (2019) <doi:10.21105/joss.01686> . The majority of commands wrap 'dplyr' mutate statements in a convenient way to concisely solve common issues that arise when tidying small to medium data sets. Includes smart defaults and allows flexible selection of columns via 'tidyselect'.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, stringr, stringi, tidyselect, purrr, janitor, rlang, lubridate, magrittr, tibble, rstudioapi, tidyr, forcats, bit64, rio, readr, vroom, readxl, fs, rlist, printr
Suggests: knitr, rmarkdown, badger
VignetteBuilder: knitr
URL: https://github.com/Harrison4192/framecleaner, https://harrison4192.github.io/framecleaner/
BugReports: https://github.com/Harrison4192/framecleaner/issues
NeedsCompilation: no
Packaged: 2021-10-01 10:49:33 UTC; Harrison
Author: Harrison Tietze [aut, cre]
Repository: CRAN
Date/Publication: 2021-10-03 09:10:02 UTC

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New package ARTofR with initial version 0.2.2
Package: ARTofR
Title: Who Ever Care About the [Art of R] Scripts?
Version: 0.2.2
Description: Decorate your comments and keep them neat! Please check <https://github.com/Hzhang-ouce/ARTofR> for instructions.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: bannerCommenter, clipr, methods
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-01 12:59:24 UTC; Huanyuan
Author: Huanyuan Zhang [aut, cre] (<https://orcid.org/0000-0003-4801-8771>)
Maintainer: Huanyuan Zhang <hyzhang1996@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-03 09:10:05 UTC

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New package hierbase with initial version 0.0.4
Package: hierbase
Title: Enabling Hierarchical Multiple Testing
Version: 0.0.4
Description: Implementation of hierarchical inference based on Renaux and Bühlmann (2021) 'Efficient Multiple Testing Adjustment for Hierarchical Inference' <arXiv:2104.15028>. The R-package hierbase offers tools to perform hierarchical inference for one or multiple data sets based on ready-to-use (group) test functions or alternatively a user specified (group) test function. The procedure is based on an efficient hierarchical multiple testing correction and controls the family-wise error rate (FWER). The functions can easily be run in parallel. Hierarchical inference can be applied to (low- or) high-dimensional data sets to find significant groups or single variables (depending on the signal strength and correlation structure) in a data-driven and automated procedure. Possible applications can for example be found in statistical genetics and statistical genomics.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: glmnet, hdi, methods, parallel, stats, SIHR
Suggests: knitr, MASS, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-30 20:54:49 UTC; renauxc
Author: Claude Renaux [aut, cre], Peter Bühlmann [ths]
Maintainer: Claude Renaux <renaux@stat.math.ethz.ch>
Repository: CRAN
Date/Publication: 2021-10-03 08:30:02 UTC

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New package EventWinRatios with initial version 0.1.0
Package: EventWinRatios
Title: Event-Specific Win Ratios for Terminal and Non-Terminal Events
Version: 0.1.0
Maintainer: Daewoo Pak <dpak@yonsei.ac.kr>
Description: Provides several confidence interval and testing procedures using event-specific win ratios for semi-competing risks data with non-terminal and terminal events, as developed in Yang et al. (2021, preprint). Compared with conventional methods for survival data, these procedures are designed to utilize more data for improved inference procedures with semi-competing risks data. The event-specific win ratios were introduced in Yang and Troendle (2021<doi:10.1177/1740774520972408>). In this package, the event-specific win ratios and confidence intervals are obtained for each event type, and several testing procedures are developed for the global null of no treatment effect on either terminal or non-terminal events. Furthermore, a test of proportional hazard assumptions, under which the event-specific win ratios converge to the hazard ratios, and a test of equal hazard ratios are provided. For summarizing the treatment effect on all events, confidence intervals for linear combinations of the event-specific win ratios are available using pre-determined or data-driven weights. Asymptotic properties of these inference procedures are discussed in Yang et al (2021, preprint). Also, transformations are used to yield better control of the type one error rates for moderately sized data sets.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-10-01 08:43:02 UTC; heavy
Author: Daewoo Pak [aut, cre], Song Yang [aut]
Repository: CRAN
Date/Publication: 2021-10-03 08:50:05 UTC

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New package edcpR with initial version 1.0.1
Package: edcpR
Title: Ecological Data Collection and Processing Package
Version: 1.0.1
Description: This is the course package for the exercise portion of the "Ecological Data Collection and Processing" course.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-10-01 08:19:16 UTC; u0134601
Author: Ward Fonteyn [aut, cre]
Maintainer: Ward Fonteyn <ward.fonteyn@kuleuven.be>
Repository: CRAN
Date/Publication: 2021-10-03 08:50:02 UTC

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Fri, 01 Oct 2021

New package ToxCrit with initial version 1.0
Package: ToxCrit
Title: Calculates Safety Stopping Boundaries for a Single-Arm Trial using Bayes
Version: 1.0
Author: NCT Trial Center, Heidelberg [aut], Lisa-Marie Lanz [cre]
Maintainer: Lisa-Marie Lanz <studienzentrale@nct-heidelberg.de>
Description: Computation of stopping boundaries for a single-arm trial using a Bayesian criterion; i.e., for each m<=n (n= total patient number of the trial) the smallest number of observed toxicities is calculated leading to the termination of the trial/accrual according to the specified criteria. The probabilities of stopping the trial/accrual at and up until (resp.) the m-th patient (m<=n) is also calculated. This design is more conservative than the frequentist approach (using Clopper Pearson CIs) which might be preferred as it concerns safety.See also Aamot et.al.(2010) "Continuous monitoring of toxicity in clinical trials - simulating the risk of stopping prematurely" <doi:10.5414/cpp48476>.
Language: en-US
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-09-30 13:22:12 UTC; Lisa
Repository: CRAN
Date/Publication: 2021-10-01 08:20:08 UTC

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New package ringostat with initial version 0.1.3
Package: ringostat
Title: Load Data from 'Ringostat API'
Version: 0.1.3
Description: Loading calls data from 'Ringostat API'. See <https://help.ringostat.com/knowledge-base/article/integration-with-ringostat-via-api>.
License: MIT + file LICENSE
Imports: httr2, stringr, cli, readr, lifecycle
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-09-30 19:06:28 UTC; SAMSUNG
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>), Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-01 08:30:02 UTC

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New package modnets with initial version 0.9.0
Package: modnets
Title: Modeling Moderated Networks
Version: 0.9.0
Maintainer: Trevor Swanson <trevorswanson222@gmail.com>
Description: Methods for modeling moderator variables in cross-sectional, temporal, and multi-level networks. Includes model selection techniques and a variety of plotting functions. Implements the methods described by Swanson (2020) <https://www.proquest.com/openview/d151ab6b93ad47e3f0d5e59d7b6fd3d3>.
License: GPL (>= 3)
URL: https://github.com/tswanson222/modnets
BugReports: https://github.com/tswanson222/modnets/issues
Imports: abind, corpcor, ggplot2, glinternet, glmnet, gridExtra, gtools, igraph, interactionTest, leaps, lme4, lmerTest, Matrix, methods, mvtnorm, parallel, pbapply, plyr, psych, qgraph, reshape2, systemfit
Suggests: sn, arm, hierNet, psychTools
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-09-30 16:28:09 UTC; t092s958@home.ku.edu
Author: Trevor Swanson [aut, cre]
Repository: CRAN
Date/Publication: 2021-10-01 08:20:02 UTC

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New package plotDK with initial version 0.1.0
Package: plotDK
Title: Plot Summary Statistics as Choropleth Maps of Danish Administrative Areas
Description: Provides a ggplot2 front end to plot summary statistics on danish provinces, regions, municipalities, and zipcodes. The needed geoms of each of the four levels are inherent in the package, thus making these types of plots easy for the user. This is essentially an updated port of the previously available 'mapDK' package by Sebastian Barfort.
Version: 0.1.0
Depends: R (>= 4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, ggplot2 (>= 3.1.0), mapproj, plotly, purrr, rlang
Suggests: testthat
NeedsCompilation: no
Packaged: 2021-09-30 12:43:23 UTC; W20201
Author: Kristian Stendorff Nielsen [aut, cre]
Maintainer: Kristian Stendorff Nielsen <krisdorff@hotmail.com>
Repository: CRAN
Date/Publication: 2021-10-01 08:00:02 UTC

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Thu, 30 Sep 2021

New package tremendousr with initial version 1.0.0
Package: tremendousr
Title: Easily Send Rewards and Incentives with 'Tremendous' from R
Version: 1.0.0
Description: A slightly-opinionated R interface for the 'Tremendous' API (<https://www.tremendous.com/>). In addition to supporting GET and POST requests, 'tremendousr' has, dare I say, tremendously intuitive functions for sending digital rewards and incentives directly from R.
License: MIT + file LICENSE
Encoding: UTF-8
Language: es
Imports: cli, crayon, crul, jsonlite
Suggests: testthat (>= 3.0.0), clipr, vcr (>= 0.6.0), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-30 09:45:18 UTC; jt
Author: Jonathan Trattner [aut, cre] (<https://orcid.org/0000-0002-1097-7603>), Scott Chamberlain [ctb] (Utility functions `err_catcher()` and `trem_ua()` from chimpr package.), R Computing Lab at Wake Forest University [fnd]
Maintainer: Jonathan Trattner <jdt@jdtrat.com>
Repository: CRAN
Date/Publication: 2021-09-30 12:20:02 UTC

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New package robis with initial version 2.8.1
Package: robis
Title: Ocean Biodiversity Information System (OBIS) Client
Description: Client for the Ocean Biodiversity Information System (<https://obis.org>).
Version: 2.8.1
Date: 2021-09-29
URL: https://github.com/iobis/robis
BugReports: https://github.com/iobis/robis/issues
Depends: R (>= 3.1.3)
Imports: httr, dplyr, jsonlite, leaflet, ggplot2, tidyr, httpcache, tibble, mapedit, sf, rlang, purrr, stringr, curl, data.table, tidyselect, xml2
License: MIT + file LICENSE
Suggests: testthat, knitr, rmarkdown, spelling
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2021-09-29 13:24:26 UTC; pieter
Author: Pieter Provoost [cre, aut], Samuel Bosch [aut], Ward Appeltans [ctb], OBIS [cph]
Maintainer: Pieter Provoost <pieterprovoost@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-30 12:10:10 UTC

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New package ractivecampaign with initial version 0.1.1
Package: ractivecampaign
Title: Loading Data from 'ActiveCampaign API v3'
Version: 0.1.1
Description: Interface for loading data from 'ActiveCampaign API v3' <https://developers.activecampaign.com/reference>. Provide functions for getting data by deals, contacts, accounts, campaigns and messages.
Imports: dplyr, httr, pbapply, stringr, tidyr, cli
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-09-30 09:53:49 UTC; Alsey
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>), Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-30 12:20:05 UTC

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New package perryExamples with initial version 0.1.0
Package: perryExamples
Title: Examples for Integrating Prediction Error Estimation into Regression Models
Version: 0.1.0
Date: 2021-09-30
Depends: R (>= 2.14.1), perry (>= 0.3.0), robustbase
Imports: stats, quantreg, lars
Description: Examples for integrating package 'perry' for prediction error estimation into regression models.
License: GPL (>= 2)
LazyLoad: yes
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-09-30 09:49:59 UTC; andreas
Repository: CRAN
Date/Publication: 2021-09-30 12:20:08 UTC

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New package LDLcalc with initial version 1.0
Package: LDLcalc
Title: Calculate and Predict the Low Density Lipoprotein Values
Version: 1.0
Author: Petros Paplomatas [aut, cre], Kostas Anagnostopoulos [aut, ctb]
Description: A wide variety of ways to calculate (through equations) or predict (using 9 Machine Learning methods as well as a stack algorithm combination of them all) the Low Density Lipoprotein values of patients based on the values of three other metrics as Total Cholesterol , Triglyceride and High Density Lipoprotein.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: data.table, caret, caretEnsemble, lares, corrplot, RColorBrewer, lattice, resample, glmnet, earth, kernlab, gbm, Cubist, randomForest
Depends: R (>= 3.5.0)
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-09-29 19:20:52 UTC; ppapl
Maintainer: Petros Paplomatas <P.paplomatas@hotmail.com>
Repository: CRAN
Date/Publication: 2021-09-30 11:20:02 UTC

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New package hwig with initial version 0.0.2
Package: hwig
Title: Half-Weight Index Gregariousness
Version: 0.0.2
Description: The half-weight index gregariousness (HWIG) is an association index used in social network analyses. It extends the half-weight association index (HWI), correcting for level of gregariousness in individuals. It is calculated using group by individual data according to methods described in Godde et al. (2013) <doi:10.1016/j.anbehav.2012.12.010>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: asnipe, spatsoc, data.table
Suggests: testthat
BugReports: https://github.com/robitalec/hwig/issues
URL: https://gitlab.com/robit.a/hwig, https://github.com/robitalec/hwig
NeedsCompilation: no
Packaged: 2021-09-30 06:22:36 UTC; alecr
Author: Alec L. Robitaille [aut, cre] (<https://orcid.org/0000-0002-4706-1762>)
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-30 11:50:09 UTC

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New package CatPredi with initial version 1.2
Package: CatPredi
Title: Optimal Categorisation of Continuous Variables in Prediction Models
Version: 1.2
Date: 2021-09-27
Imports: survival, rms, CPE, rgenoud, mgcv, stats, graphics
Description: Allows the user to categorise a continuous predictor variable in a logistic or a Cox proportional hazards regression setting, by maximising the discriminative ability of the model. I Barrio, I Arostegui, MX Rodriguez-Alvarez, JM Quintana (2015) <doi:10.1177/0962280215601873>. I Barrio, MX Rodriguez-Alvarez, L Meira-Machado, C Esteban, I Arostegui (2017) <https://www.idescat.cat/sort/sort411/41.1.3.barrio-etal.pdf>.
License: GPL
NeedsCompilation: no
Packaged: 2021-09-30 10:29:05 UTC; sarai
Author: Irantzu Barrio [aut, cre], Maria Xose Rodriguez-Alvarez [aut], Inmaculada Arostegui [ctb]
Maintainer: Irantzu Barrio <irantzu.barrio@ehu.eus>
Repository: CRAN
Date/Publication: 2021-09-30 12:00:07 UTC

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New package AntibodyTiters with initial version 0.1.4
Package: AntibodyTiters
Version: 0.1.4
Date: 2021-09-30
Title: Antibody Titer Analysis of Vaccinated Patients
Maintainer: Hiroaki Kato <hkato@med.shimane-u.ac.jp>
Depends: openxlsx (>= 4.2.4), R (>= 3.3.0)
Description: Visualization of antibody titer scores is valuable for examination of vaccination effects and usefulness of the antibody used for titer scoring. 'AntibodyTiters' visualizes antibody titers of all or selected patients. This package also produces empty excel files in a specified format, in which users can fill in experimental data for visualization. Excel files with toy data can also be produced, so that users can see how it is visualized before obtaining real data. The data should contain titer scores at pre-vaccination, after- 1st shot, after-2nd shot, and at least one additional sampling point. Patients with missing values can be included. The first three sampling points will be plotted discretely, whereas those following the after-2nd shot will be plotted on a continuous time scale starting from the day of second shot.
License: GPL-3
NeedsCompilation: no
Packaged: 2021-09-30 01:55:50 UTC; hrk_kato
Author: Yuuki Mizumoto [aut], Hiroaki Kato [aut, cre] (<https://orcid.org/0000-0001-9591-1875>), Takeshi Urano [ctb]
Repository: CRAN
Date/Publication: 2021-09-30 11:50:12 UTC

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New package CoNI with initial version 0.1.0
Package: CoNI
Title: Correlation Guided Network Integration (CoNI)
Version: 0.1.0
Date: 2021-09-28
Description: Integrates two numerical omics data sets from the same samples using partial correlations. The output can be represented as a network, bipartite graph or a hypergraph structure. The method used in the package refers to Klaus et al (2021) <doi:10.1016/j.molmet.2021.101295>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0)
Imports: igraph (>= 1.2.6), doParallel (>= 1.0.16), cocor (>= 1.1.3), ggplot2 (>= 3.3.3), forcats (>= 0.5.1), dplyr (>= 1.0.5), data.table (>= 1.13.7), tibble (>= 3.1.0), foreach (>= 1.5.1), genefilter (>= 1.72.1), ggrepel (>= 0.9.1), gplots (>= 3.1.1), gridExtra (>= 2.3), plyr (>= 1.8.6), ppcor (>= 1.1), tidyr (>= 1.1.3), Hmisc (>= 4.4.2), methods (>= 4.0.3), rlang (>= 0.4.10), tidyselect (>= 1.1.0)
Suggests: kableExtra (>= 1.3.2), knitr (>= 1.31), rmarkdown (>= 2.6)
VignetteBuilder: knitr
SystemRequirements: python3
NeedsCompilation: no
Packaged: 2021-09-29 16:18:07 UTC; manuel.kuhn
Author: José Manuel Monroy Kuhn [aut, cre], Dominik Lutter [ths], Valentina Klaus [ctb]
Maintainer: José Manuel Monroy Kuhn <nolozz@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-30 09:10:02 UTC

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New package BrainCon with initial version 0.1.0
Package: BrainCon
Title: Inference the Partial Correlations Based on Time Series Data
Version: 0.1.0
Author: Yunhaonan Yang [aut, cre], Peng Wu [aut], Xin Gai [aut], Yumou Qiu [aut], Xiaohua Zhou [aut]
Maintainer: Yunhaonan Yang <haonan_yy@pku.edu.cn>
Description: A statistical tool to inference the multi-level partial correlations based on multi-subject time series data. It combines both individual and population level inference by using the methods of Qiu and Zhou. (2021)<DOI: 10.1080/01621459.2021.1917417> and Genovese and Wasserman. (2006)<DOI: 10.1198/016214506000000339>. It can be used to identify nonzero individual- or population-level partial correlations, and find out unequal partial correlation coefficients between two populations.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: glmnet, MASS
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-09-29 16:26:01 UTC; Dinic
Repository: CRAN
Date/Publication: 2021-09-30 09:10:05 UTC

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New package SCEnt with initial version 0.0.1
Package: SCEnt
Title: Single Cell Entropy Analysis of Gene Heterogeneity in Cell Populations
Version: 0.0.1
Description: Analyse single cell RNA sequencing data using entropy to calculate heterogeneity and homogeneity of genes amongst the cell population. From the work of Michael J. Casey, Ruben J. Sanchez-Garcia and Ben D. MacArthur.
License: GPL (>= 3)
Encoding: UTF-8
Imports: entropy, tibble
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-29 12:47:02 UTC; hwarden
Author: Hugh Warden [aut, cre] (<https://orcid.org/0000-0002-4308-7316>)
Maintainer: Hugh Warden <hugh.warden@outlook.com>
Repository: CRAN
Date/Publication: 2021-09-30 08:30:04 UTC

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New package preregr with initial version 0.1.3
Package: preregr
Title: Specify (Pre)Registrations and Export Them Human- And Machine-Readably
Version: 0.1.3
Description: Preregistrations, or more generally, registrations, enable explicit timestamped and (often but not necessarily publicly) frozen documentation of plans and expectations as well as decisions and justifications. In research, preregistrations are commonly used to clearly document plans and facilitate justifications of deviations from those plans, as well as decreasing the effects of publication bias by enabling identification of research that was conducted but not published. Like reporting guidelines, (pre)registration forms often have specific structures that facilitate systematic reporting of important items. The 'preregr' package facilitates specifying (pre)registrations in R and exporting them to a human-readable format (using R Markdown partials or exporting to an 'HTML' file) as well as human-readable embedded data (using 'JSON'), as well as importing such exported (pre)registration specifications from such embedded 'JSON'.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: cli (>= 3.0), jsonlite (>= 1.7), rmdpartials (>= 0.5.8), yaml (>= 2.2)
Suggests: googlesheets4 (>= 1.0), haven (>= 2.4.3), justifier (>= 0.2.1), knitr (>= 1.34), markdown (>= 1.1), openxlsx (>= 4.2), readxl (>= 1.3), rvest (>= 1.0), testthat (>= 3.0), writexl (>= 1.4), XLConnect (>= 1.0), rmarkdown
Depends: R (>= 2.10)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-29 11:12:00 UTC; gjalt
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>)
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@behaviorchange.eu>
Repository: CRAN
Date/Publication: 2021-09-30 08:20:02 UTC

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New package powerly with initial version 1.5.2
Package: powerly
Title: Sample Size Analysis for Psychological Networks and More
Version: 1.5.2
Description: An implementation of the sample size computation method for network models proposed by Constantin et al. (2021) <doi:10.31234/osf.io/j5v7u> The implementation takes the form of a three-step recursive algorithm designed to find an optimal sample size given a model specification and a performance measure of interest. It starts with a Monte Carlo simulation step for computing the performance measure and a statistic at various sample sizes selected from an initial sample size range. It continues with a monotone curve-fitting step for interpolating the statistic across the entire sample size range. The final step employs stratified bootstrapping to quantify the uncertainty around the fitted curve.
License: MIT + file LICENSE
URL: https://github.com/mihaiconstantin/powerly
BugReports: https://github.com/mihaiconstantin/powerly/issues
Imports: R6, progress, parallel, splines2, quadprog, osqp, bootnet, qgraph, ggplot2, patchwork
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-09-29 14:12:04 UTC; mihai
Author: Mihai Constantin [aut, cre] (<https://orcid.org/0000-0002-6460-0107>)
Maintainer: Mihai Constantin <mihai@mihaiconstantin.com>
Repository: CRAN
Date/Publication: 2021-09-30 09:00:02 UTC

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New package nodeSub with initial version 1.2
Package: nodeSub
Title: Simulate DNA Alignments Using Node Substitutions
Version: 1.2
Author: Thijs Janzen
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Description: Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. The nodeSub package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1101/2020.08.19.256891>.
URL: https://github.com/thijsjanzen/nodeSub
BugReports: https://github.com/thijsjanzen/nodeSub
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
LinkingTo: Rcpp
Depends: Rcpp
Imports: nLTT, RPANDA, apTreeshape, phangorn, tibble, DDD, Rmpfr, assertthat, pbapply, phylobase, rappdirs, stringr, geiger, ape, testit, babette, beautier, beastier, mauricer, tracerer
Suggests: phytools, testthat, TreeSim, dplyr, knitr, rmarkdown, ggplot2, magrittr, tidyr
NeedsCompilation: yes
Packaged: 2021-09-29 11:16:02 UTC; janzen
Repository: CRAN
Date/Publication: 2021-09-30 08:30:02 UTC

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New package metaCluster with initial version 0.1.0
Package: metaCluster
Title: Metagenomic Clustering
Version: 0.1.0
Maintainer: Dipro Sinha <diprosinha@gmail.com>
Description: Clustering in metagenomics is the process of grouping of microbial contigs in species specific bins. This package contains functions that extract genomic features from metagenome data, find the number of clusters for that given data and find the best clustering algorithm for binning.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: factoextra, cluster, dbscan, dplyr, seqinr, Biostrings
Depends: R (>= 3.6)
NeedsCompilation: no
Packaged: 2021-09-29 10:06:44 UTC; SAYANTI
Author: Dipro Sinha [aut, cre], Sayanti Guha Majumdar [aut], Anu Sharma [aut], Dwijesh Chandra Mishra [aut]
Repository: CRAN
Date/Publication: 2021-09-30 08:10:02 UTC

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New package gJLS2 with initial version 0.2.0
Package: gJLS2
Title: A Generalized Joint Location and Scale Framework for Association Testing
Version: 0.2.0
Description: An update to the Joint Location-Scale (JLS) testing framework that identifies associated SNPs, gene-sets and pathways with main and/or interaction effects on quantitative traits (Soave et al., 2015; <doi:10.1016/j.ajhg.2015.05.015>). The JLS method simultaneously tests the null hypothesis of equal mean and equal variance across genotypes, by aggregating association evidence from the individual location/mean-only and scale/variance-only tests using Fisher's method. The generalized joint location-scale (gJLS) framework has been developed to deal specifically with sample correlation and group uncertainty (Soave and Sun, 2017; <doi:10.1111/biom.12651>). The current release: gJLS2, include additional functionalities that enable analyses of X-chromosome genotype data through novel methods for location (Chen et al., 2021; <doi:10.1002/gepi.22422>) and scale (Deng et al., 2019; <doi:10.1002/gepi.22247>).
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: knitr, markdown
VignetteBuilder: knitr
Imports: methods, nlme, quantreg, MCMCpack, MASS, plyr, ggplot2, moments
Depends: R (>= 3.6.0)
NeedsCompilation: no
Packaged: 2021-09-29 16:03:28 UTC; weideng
Author: Wei Deng [aut, cre], Lei Sun [aut]
Maintainer: Wei Deng <deng@utstat.toronto.edu>
Repository: CRAN
Date/Publication: 2021-09-30 09:00:05 UTC

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Wed, 29 Sep 2021

New package Guerry with initial version 1.7.4
Package: Guerry
Title: Maps, Data and Methods Related to Guerry (1833) "Moral Statistics of France"
Version: 1.7.4
Date: 2021-09-27
Author: Michael Friendly [aut, cre], Stephane Dray [aut], Roger Bivand [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Encoding: latin1
Language: en-US
Depends: R (>= 2.10)
Suggests: knitr, spdep, ade4, adegraphics, adespatial, maptools, RColorBrewer, corrgram, car, rmarkdown, ggplot2, ggrepel, heplots, patchwork, candisc, colorspace
Imports: sp
Description: Maps of France in 1830, multivariate datasets from A.-M. Guerry and others, and statistical and graphic methods related to Guerry's "Moral Statistics of France". The goal is to facilitate the exploration and development of statistical and graphic methods for multivariate data in a geospatial context of historical interest.
License: GPL
URL: https://github.com/friendly/Guerry
BugReports: https://github.com/friendly/Guerry/issues
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-28 13:52:26 UTC; friendly
Repository: CRAN
Date/Publication: 2021-09-29 13:40:05 UTC

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New package sdamr with initial version 0.1.0
Package: sdamr
Title: Statistics: Data Analysis and Modelling
Version: 0.1.0
Description: Data sets and functions to support the books "Statistics: Data analysis and modelling" by Speekenbrink, M. (2021) <https://mspeekenbrink.github.io/sdam-book/> and "An R companion to Statistics: data analysis and modelling" by Speekenbrink, M. (2021) <https://mspeekenbrink.github.io/sdam-r-companion/>. All datasets analysed in these books are provided in this package. In addition, the package provides functions to compute sample statistics (variance, standard deviation, mode), create raincloud and enhanced Q-Q plots, and expand Anova results into omnibus tests and tests of individual contrasts.
License: GPL-3
Encoding: UTF-8
Language: en-GB
LazyData: true
URL: https://mspeekenbrink.github.io/sdam-r/
Depends: R (>= 3.5.0)
Imports: methods, stats, dplyr, ggplot2, grid, car
NeedsCompilation: no
Packaged: 2021-09-28 13:20:11 UTC; maarten
Author: Maarten Speekenbrink [aut, cre] (<https://orcid.org/0000-0003-3221-1091>)
Maintainer: Maarten Speekenbrink <m.speekenbrink@ucl.ac.uk>
Repository: CRAN
Date/Publication: 2021-09-29 08:20:02 UTC

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New package ReDirection with initial version 1.0.0
Package: ReDirection
Title: Predict Dominant Direction of Reactions of a Biochemical Network
Version: 1.0.0
Author: Siddhartha Kundu <2021: Manuscript Under Preparation>
Maintainer: Siddhartha Kundu <siddhartha_kundu@aiims.edu>
Description: Biologically relevant, yet mathematically sound constraints are used to compute the propensity and thence infer the dominant direction of reactions of a generic biochemical network. The reactions must be unique and their number must exceed that of the reactants,i.e., reactions >= reactants + 2. 'ReDirection', computes the null space of a user-defined stoichiometry matrix. The spanning non-zero and unique reaction vectors (RVs) are combinatorially summed to generate one or more subspaces recursively. Every reaction is represented as a sequence of identical components across all RVs of a particular subspace. The terms are evaluated with (biologically relevant bounds, linear maps, tests of convergence, descriptive statistics, vector norms) and the terms are classified into forward-, reverse- and equivalent-subsets. Since, these are mutually exclusive the probability of occurrence is binary (all, 1; none, 0). The combined propensity of a reaction is the p1-norm of the sub-propensities, i.e., sum of the products of the probability and maximum numeric value of a subset (least upper bound, greatest lower bound). This, if strictly positive is the probable rate constant, is used to infer dominant direction and annotate a reaction as "Forward (f)", "Reverse (b)" or "Equivalent (e)". The inherent computational complexity (NP-hard) per iteration suggests that a suitable value for the number of reactions is around 20. Three functions comprise ReDirection. These are check_matrix() and reaction_vector() which are internal, and calculate_reaction_vector() which is external.
License: GPL-3
Encoding: UTF-8
Imports: gtools
Depends: stats, MASS, pracma
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-09-28 20:26:13 UTC; Siddhartha
Repository: CRAN
Date/Publication: 2021-09-29 08:20:14 UTC

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New package netie with initial version 1.0
Package: netie
Title: Antigen T Cell Interaction Estimation
Version: 1.0
Date: 2021-9-28
Author: Tianshi Lu
Maintainer: Tianshi Lu <tianshi.lu@utsouthwestern.edu>
Description: The Bayesian hierarchical model named antigen-T cell interaction estimation is to estimate the history of the immune pressure on the evolution of the tumor clones.The model is based on the estimation result from Andrew Roth (2014) <doi:10.1038/nmeth.2883>.
Depends: R (>= 3.6.0)
License: Apache License
NeedsCompilation: no
Packaged: 2021-09-28 14:47:19 UTC; s171162
Repository: CRAN
Date/Publication: 2021-09-29 08:20:05 UTC

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New package melt with initial version 1.0.0
Package: melt
Title: Multiple Empirical Likelihood Tests
Version: 1.0.0
Description: Multiple hypothesis testing via empirical likelihood in general block designs. It provides asymptotic generalized family-wise error rate control.
License: GPL (>= 2)
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 1.0.6), stats
LinkingTo: Rcpp, RcppEigen, RcppProgress
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2021-09-29 07:04:15 UTC; markean
Author: Eunseop Kim [aut, cre]
Maintainer: Eunseop Kim <kim.7302@osu.edu>
Repository: CRAN
Date/Publication: 2021-09-29 08:20:08 UTC

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New package mclustAddons with initial version 0.5
Package: mclustAddons
Version: 0.5
Date: 2021-09-28
Title: Addons for the 'mclust' Package
Description: Extend the functionality of the 'mclust' package for Gaussian finite mixture modelling by including: density estimation for data with bounded support (Scrucca, 2019 <doi:10.1002/bimj.201800174>); modal clustering using MEM algorithm for Gaussian mixtures (Scrucca, 2021 <doi:10.1002/sam.11527>).
Depends: R (>= 4.0), mclust (>= 5.4)
Imports: stats, graphics, grDevices, methods, foreach, iterators, utils, Rcpp (>= 0.12)
LinkingTo: Rcpp, RcppArmadillo
Suggests: parallel, doParallel, doRNG (>= 1.6), cli, crayon, knitr (>= 1.12), rmarkdown (>= 0.9)
License: GPL (>= 2)
URL: https://mclust-org.github.io/mclustAddons/
VignetteBuilder: knitr
Repository: CRAN
ByteCompile: true
NeedsCompilation: yes
LazyData: yes
Encoding: UTF-8
Packaged: 2021-09-28 17:26:39 UTC; luca
Author: Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Date/Publication: 2021-09-29 08:10:02 UTC

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New package marginaleffects with initial version 0.1.0
Package: marginaleffects
Title: Marginal Effects, Marginal Means, Predictions, and Contrasts
Version: 0.1.0
Description: Compute, summarize, and plot marginal effects, adjusted predictions, contrasts, and marginal means for a wide variety of models.
License: GPL (>= 3)
Copyright: inst/COPYRIGHTS
LazyData: true
Encoding: UTF-8
URL: https://vincentarelbundock.github.io/marginaleffects/ https://github.com/vincentarelbundock/marginaleffects
BugReports: https://github.com/vincentarelbundock/marginaleffects/issues
VignetteBuilder: knitr
Config/testthat/parallel: true
Depends: R (>= 3.5.0)
Imports: checkmate, generics, insight, methods, numDeriv
Suggests: bench, broom, dplyr, emmeans, ggplot2, ggbeeswarm, haven, kableExtra, knitr, margins, modelsummary, patchwork, rlang, rmarkdown, testthat (>= 3.0.0), tidyverse, vdiffr, AER, betareg, bife, brglm2, crch, estimatr, fixest, gam, geepack, glmx, ivreg, lme4, MASS, nlme, nnet, ordinal, plm, pscl, quantreg, rms, robustbase, sandwich, speedglm, survey, survival, truncreg, covr
NeedsCompilation: no
Packaged: 2021-09-28 13:36:05 UTC; vincent
Author: Vincent Arel-Bundock [aut, cre] (<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Repository: CRAN
Date/Publication: 2021-09-29 08:10:05 UTC

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New package GoogleImage2Array with initial version 0.99.2
Package: GoogleImage2Array
Title: Create Array Data from 2D Image Thumbnails via Google Image Search
Version: 0.99.2
Date: 2021-09-28
Depends: R (>= 4.1.0)
Imports: xml2, rvest, EBImage, magrittr
Suggests: testthat
Description: Images are provided as an array dataset of 2D image thumbnails from Google Image Search <https://www.google.com/search>. This array data may be suitable for a training data of machine learning or deep learning as a first trial.
License: Artistic-2.0
URL: https://github.com/kumeS/GoogleImage2Array
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-09-28 15:27:14 UTC; skume
Author: Satoshi Kume [aut, cre]
Maintainer: Satoshi Kume <satoshi.kume.1984@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-29 08:20:16 UTC

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New package DiNAMIC.Duo with initial version 1.0.0
Package: DiNAMIC.Duo
Title: Finding Recurrent DNA Copy Number Alterations and Differences
Version: 1.0.0
Description: In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. Here we use cyclic shift permutations to identify recurrent copy number alterations in a single cohort or recurrent copy number differences in two cohorts based on a common set of genomic markers. Additional functionality is provided to perform downstream analyses, including the creation of summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al. (2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al. (2015) <doi:10.1093/biomet/asv046>. A manuscript based on DiNAMIC.Duo is currently under development.
Config/reticulate: list( packages = list( list(package = "numpy") ) )
Depends: R (>= 3.5.0)
VignetteBuilder: R.rsp
Suggests: R.rsp
biocViews: biomaRt
Imports: biomaRt, dinamic, plyr, reticulate
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-09-28 19:46:12 UTC; vwalter1
Author: Vonn Walter [aut, cre] (<https://orcid.org/0000-0001-6114-6714>), Hyo Young Choi [aut] (<https://orcid.org/0000-0002-7627-8493>), Xiaobei Zhao [aut] (<https://orcid.org/0000-0002-5277-0846>), Yan Gao [aut] (<https://orcid.org/0000-0002-6852-2038>), David Neil Hayes [aut] (<https://orcid.org/0000-0001-6203-7771>)
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>
Repository: CRAN
Date/Publication: 2021-09-29 08:20:19 UTC

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New package chantrics with initial version 1.0.0
Package: chantrics
Title: Loglikelihood Adjustments for Econometric Models
Version: 1.0.0
Date: 2021-09-28
Description: Adjusts the loglikelihood of common econometric models for clustered data based on the estimation process suggested in Chandler and Bate (2007) <doi:10.1093/biomet/asm015>, using the 'chandwich' package <https://cran.r-project.org/package=chandwich>, and provides convenience functions for inference on the adjusted models.
Imports: AER, chandwich, graphics, sandwich, stats, utils, methods, lmtest, rlang, progress, purrr
Depends: R (>= 4.0.0)
URL: https://chantrics.theobruckbauer.eu, https://github.com/tbruckbauer/chantrics
BugReports: https://github.com/tbruckbauer/chantrics/issues
License: EUPL (>= 1.2)
Encoding: UTF-8
Language: en-GB
Suggests: knitr, rmarkdown, testthat, lax, covr, MASS, pscl
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-28 14:04:03 UTC; theobruckbauer
Author: Theo Bruckbauer [aut, cre] (<https://orcid.org/0000-0002-4764-9953>)
Maintainer: Theo Bruckbauer <chantrics@theobruckbauer.eu>
Repository: CRAN
Date/Publication: 2021-09-29 08:20:11 UTC

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New package isaeditor with initial version 0.1.1
Package: isaeditor
Title: Tools to Manipulate ISA-Tab Files
Version: 0.1.1
Description: ISA-Tab (Investigation/Study/Assay (ISA) tab-delimited (TAB) format) is a general purpose framework for storing complex metadata in omics applications. It is notoriously hard to manipulate due to the fact that it is a graph rather than a tab-delimited data frame. The 'isaeditor' package is meant to facilitate reading, writing, displaying, manipulating, modifying and populating ISA-Tab files in R.
License: GPL (>= 3)
URL: https://github.com/bihealth/isaeditor/
Encoding: UTF-8
Imports: colorDF, crayon, tibble, dplyr, glue, tidyr, readr, magrittr, methods, rlang
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-09-28 16:32:28 UTC; january
Author: January Weiner [aut, cre] (<https://orcid.org/0000-0003-1438-7819>)
Maintainer: January Weiner <january.weiner@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-29 08:00:02 UTC

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New package GenderInfer with initial version 0.1.0
Package: GenderInfer
Title: This is a Collection of Functions to Analyse Gender Differences
Version: 0.1.0
Maintainer: Rita Giordano <giordanor@rsc.org>
Description: Implementation of functions, which combines binomial calculation and data visualisation, to analyse the differences in publishing authorship by gender described in Day et al. (2020) <doi:10.1039/C9SC04090K>. It should only be used when self-reported gender is unavailable.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, binom
Depends: R (>= 2.10)
Suggests: dplyr, knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-28 08:03:26 UTC; giordanor
Author: Rita Giordano [aut, cre], Aileen Day [aut], John Boyle [aut], Colin Batchelor [ctb], Royal Society of Chemistry [cph]
Repository: CRAN
Date/Publication: 2021-09-29 08:00:05 UTC

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Tue, 28 Sep 2021

New package qmd with initial version 1.0.0
Package: qmd
Title: Quantification of Multivariate Dependence
Version: 1.0.0
Description: A multivariate copula-based dependence measure. For more information, see Griessenberger, Junker, Trutschnig (2021), On a multivariate copula-based dependence measure and its estimation, <arXiv:2109.12883>.
License: GPL (>= 2)
Imports: qad
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-09-28 05:42:02 UTC; Florian
Author: Florian Griessenberger [aut, cre], Robert R. Junker [aut], Wolfgang Trutschnig [aut]
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>
Repository: CRAN
Date/Publication: 2021-09-28 12:50:02 UTC

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New package flintyR with initial version 0.0.2
Package: flintyR
Title: Flexible and Interpretable Non-Parametric Tests of Exchangeability
Version: 0.0.2
Date: 2021-09-27
Description: Given a multivariate dataset and some knowledge about the dependencies between its features, it is important to ensure the observations or individuals are exchangeable before fitting a model to the data in order to make inferences from it, or assigning randomized treatments in order to estimate treatment effects. This package provides a flexible non-parametric test of exchangeability, allowing the user to specify the feature dependencies by hand. It can be used directly to evaluate whether a sample is exchangeable, and can also be piped into larger procedures that require exchangeable samples as outputs (e.g., clustering or community detection). See Aw, Spence and Song (2021+) for the accompanying paper.
License: GPL (>= 3)
Imports: Rcpp (>= 1.0.6), doParallel, foreach, assertthat, testthat, stats
Suggests: rmarkdown, knitr, devtools, tidyverse
LinkingTo: Rcpp, RcppArmadillo
URL: https://alanaw1.github.io/flintyR/
BugReports: https://github.com/alanaw1/flintyR/issues
NeedsCompilation: yes
Packaged: 2021-09-27 22:44:09 UTC; alanaw
Author: Alan Aw [cre, aut] (<https://orcid.org/0000-0001-9455-7878>), Jeffrey Spence [ctb]
Maintainer: Alan Aw <alanaw1@berkeley.edu>
Repository: CRAN
Date/Publication: 2021-09-28 12:40:07 UTC

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New package ccmEstimator with initial version 1.0.0
Package: ccmEstimator
Title: Comparative Causal Mediation Estimation
Version: 1.0.0
Maintainer: Xiaohan Wu <xiw021@ucsd.edu>
Description: Functions to perform comparative causal mediation analysis to compare the mediation effects of different treatments via a common mediator. Results contain the estimates and confidence intervals for the two comparative causal mediation analysis estimands, as well as the ATE and ACME for each treatment. Functions provided in the package will automatically assess the comparative causal mediation analysis scope conditions (i.e. for each comparative causal mediation estimand, a numerator and denominator that are both estimated with the desired statistical significance and of the same sign). Results will be returned for each comparative causal mediation estimand only if scope conditions are met for it. See details in Bansak(2020)<doi:10.1017/pan.2019.31>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, covr, testthat
VignetteBuilder: knitr
URL: https://github.com/xiw021/ccmEstimator
BugReports: https://github.com/xiw021/ccmEstimator/issues
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-09-14 16:45:31 UTC; wuxiaohan
Author: Kirk Bansak [aut], Xiaohan Wu [aut, cre]
Repository: CRAN
Date/Publication: 2021-09-28 12:20:02 UTC

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New package wordpiece.data with initial version 1.0.1
Package: wordpiece.data
Title: Data for Wordpiece-Style Tokenization
Version: 1.0.1
Description: Provides data to be used by the wordpiece algorithm in order to tokenize text into somewhat meaningful chunks. Included vocabularies were retrieved from <https://huggingface.co/bert-base-cased/resolve/main/vocab.txt> and <https://huggingface.co/bert-base-uncased/resolve/main/vocab.txt> and parsed into an R-friendly format.
License: Apache License (>= 2)
Encoding: UTF-8
URL: https://github.com/macmillancontentscience/wordpiece.data
BugReports: https://github.com/macmillancontentscience/wordpiece.data/issues
Depends: R (>= 3.5.0)
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-09-27 16:50:57 UTC; jonth
Author: Jonathan Bratt [aut] (<https://orcid.org/0000-0003-2859-0076>), Jon Harmon [aut, cre] (<https://orcid.org/0000-0003-4781-4346>), Bedford Freeman & Worth Pub Grp LLC DBA Macmillan Learning [cph], Google, Inc [cph] (original BERT base uncased vocabulary)
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-28 11:20:02 UTC

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New package ZIPBayes with initial version 1.0.1
Package: ZIPBayes
Title: Bayesian Methods in the Analysis of Zero-Inflated Poisson Model
Version: 1.0.1
Date: 2021-09-27
Description: Implementation of zero-inflated Poisson models under Bayesian framework using data augmentation as discussed in Chapter 5 of Zhang (2020) <https://hdl.handle.net/10012/16378>. This package is constructed in accommodating four different scenarios: the general scenario, the scenario with measurement error in responses, the external validation scenario, and the internal validation scenario.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.11), MASS
Depends: R (>= 3.5.0)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2021-09-27 16:05:38 UTC; qihua
Author: Qihuang Zhang [aut, cre, cph], Grace Y. Yi [aut, ths]
Maintainer: Qihuang Zhang <qihuang.zhang@uwaterloo.ca>
Repository: CRAN
Date/Publication: 2021-09-28 10:30:06 UTC

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New package statsearchanalyticsr with initial version 0.1.4
Package: statsearchanalyticsr
Title: An Interface for the 'STAT Search Analytics' 'API'
Version: 0.1.4
Description: Pull data from the 'STAT Search Analytics' API <https://help.getstat.com/knowledgebase/api-services/>. It was developed by the Search Discovery team to help analyze keyword ranking data.
License: MIT + file LICENSE
URL: https://searchdiscovery.github.io/statsearchanalyticsr/
BugReports: https://github.com/searchdiscovery/statsearchanalyticsr/issues
Encoding: UTF-8
Imports: glue, httr, jsonlite, purrr, tidyr, tibble, stringr, lubridate
Suggests: spelling
Language: en-US
NeedsCompilation: no
Packaged: 2021-09-27 13:05:42 UTC; ben.woodard
Author: Ben Woodard [aut, cre], Chima Umeakunne [ctb], Search Discovery, LLC [own] (Visit SearchDiscovery.com for more information)
Maintainer: Ben Woodard <ben.woodard@searchdiscovery.com>
Repository: CRAN
Date/Publication: 2021-09-28 10:20:02 UTC

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