CRANberries

Mon, 11 Dec 2023

New package EDCimport with initial version 0.4.0
Package: EDCimport
Version: 0.4.0
Title: Import Data from EDC Software
Description: A convenient toolbox to import data exported from Electronic Data Capture (EDC) software 'TrialMaster'.
License: GPL-3
URL: https://github.com/DanChaltiel/EDCimport, https://danchaltiel.github.io/EDCimport/
BugReports: https://github.com/DanChaltiel/EDCimport/issues
Depends: R (>= 3.1.0)
Imports: cli, dplyr, forcats, glue, ggplot2, haven, labelled, purrr, readr, rlang, stringr, tibble, tidyr, tidyselect, utils
Suggests: callr, gtools, janitor, knitr, plotly, testthat (>= 3.1.8), vdiffr, withr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-12-09 14:55:16 UTC; Dan
Author: Dan Chaltiel [aut, cre]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-11 09:00:06 UTC

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New package clinDataReview with initial version 1.5.0
Package: clinDataReview
Title: Clinical Data Review Tool
Version: 1.5.0
Date: 2023-12-08
Description: Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.
Imports: bookdown, clinUtils (>= 0.1.0), crosstalk, data.table, ggplot2, haven, htmltools, htmlwidgets, knitr, jsonlite, jsonvalidate, methods, plotly, plyr, rmarkdown, stats, stringr, utils, tools, yaml, xml2, xfun
Suggests: countrycode, inTextSummaryTable (>= 3.1.0), patientProfilesVis (>= 0.12.0), testthat, DT, scales
SystemRequirements: pandoc (to create a clinical data review report)
URL: https://github.com/openanalytics/clinDataReview
BugReports: https://github.com/openanalytics/clinDataReview/issues
License: MIT + file LICENSE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-08 22:09:54 UTC; root
Author: Laure Cougnaud [aut, cre], Michela Pasetto [aut], Lennart Tuijnder [aut], Adriaan Blommaert [aut], Arne De Roeck [ctb, rev] , Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Repository: CRAN
Date/Publication: 2023-12-11 08:30:02 UTC

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Sun, 10 Dec 2023

New package shinydbauth with initial version 1.0.0.1
Package: shinydbauth
Title: Simple Authentification for 'shiny' Applications
Version: 1.0.0.1
Description: Provides a simple authentification mechanism for single 'shiny' applications. Authentification and password change functionality are performed calling user provided functions that typically access some database backend. Source code of main applications is protected until authentication is successful.
License: GPL-3
URL: https://github.com/diegoefe/shinydbauth
Encoding: UTF-8
Imports: R6, shiny, htmltools, DT (>= 0.5), openssl, R.utils, billboarder, scrypt, yaml, glue
Suggests: keyring, testthat (>= 2.1.0), knitr, rmarkdown
NeedsCompilation: no
Packaged: 2023-12-08 14:40:08 UTC; diego
Author: Diego Florio [aut, cre]
Maintainer: Diego Florio <diegoefe@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-10 11:30:02 UTC

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New package pubmedtk with initial version 1.0.1
Package: pubmedtk
Title: 'Pubmed' Toolkit
Version: 1.0.1
Description: Provides various functions for retrieving and interpreting information from 'Pubmed' via the API, <https://www.ncbi.nlm.nih.gov/home/develop/api/>.
License: AGPL (>= 3)
URL: https://github.com/bgcarlisle/pubmedtk
BugReports: https://github.com/bgcarlisle/pubmedtk/issues
Imports: magrittr, dplyr, xml2, jsonlite, httr, assertthat, stringr, rlang, utils
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-12-08 12:34:49 UTC; researchfairy
Author: Benjamin Gregory Carlisle [aut, cre]
Maintainer: Benjamin Gregory Carlisle <murph@bgcarlisle.com>
Repository: CRAN
Date/Publication: 2023-12-10 11:20:02 UTC

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New package plot3logit with initial version 3.1.4
Package: plot3logit
Title: Ternary Plots for Trinomial Regression Models
Version: 3.1.4
Author: Flavio Santi [cre, aut] , Maria Michela Dickson [aut] , Giuseppe Espa [aut] , Diego Giuliani [aut]
Maintainer: Flavio Santi <flavio.santi@unitn.it>
URL: https://www.flaviosanti.it/software/plot3logit/
BugReports: https://github.com/f-santi/plot3logit/issues/
Description: An implementation of the ternary plot for interpreting regression coefficients of trinomial regression models, as proposed in Santi, Dickson and Espa (2019) <doi:10.1080/00031305.2018.1442368>. Ternary plots can be drawn using either 'ggtern' package (based on 'ggplot2') or 'Ternary' package (based on standard graphics). The package and its features are illustrated in Santi, Dickson, Espa and Giuliani (2022) <doi:10.18637/jss.v103.c01>.
Depends: R (>= 4.0), ggtern (>= 3.4.0), Ternary (>= 1.0.1)
Imports: dplyr, ellipse, forcats, generics, ggplot2 (>= 3.4.0), graphics, grDevices, lifecycle, magrittr (>= 1.5), purrr, Rdpack, stats, stringr, tibble, tidyr, tidyselect, utils
Suggests: knitr, MASS (>= 7.3-51), mlogit, nnet, ordinal, rmarkdown, VGAM, testthat
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Encoding: UTF-8
Repository: CRAN
VignetteBuilder: knitr
Packaged: 2023-12-08 13:14:01 UTC; flavio
Date/Publication: 2023-12-10 11:30:05 UTC

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New package parcats with initial version 0.0.5
Package: parcats
Title: Interactive Parallel Categories Diagrams for 'easyalluvial'
Version: 0.0.5
URL: https://erblast.github.io/parcats/
BugReports: https://github.com/erblast/parcats/issues/
Description: Complex graphical representations of data are best explored using interactive elements. 'parcats' adds interactive graphing capabilities to the 'easyalluvial' package. The 'plotly.js' parallel categories diagrams offer a good framework for creating interactive flow graphs that allow manual drag and drop sorting of dimensions and categories, highlighting single flows and displaying mouse over information. The 'plotly.js' dependency is quite heavy and therefore is outsourced into a separate package.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.0.0)
Suggests: testthat, covr, randomForest, knitr, rmarkdown, spelling, plotly, shiny
Imports: easyalluvial (>= 0.2.1.0), tidyr (>= 1.0.0), dplyr, purrr, forcats, magrittr, tibble, htmlwidgets, stringr
Language: en-US
NeedsCompilation: no
Packaged: 2023-12-08 15:42:50 UTC; koneswab
Author: Bjoern Koneswarakantha [aut, cre]
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-10 11:40:02 UTC

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New package florabr with initial version 1.0.1
Package: florabr
Title: Explore Brazilian Flora 2020 Database
Version: 1.0.1
Description: A collection of functions designed to retrieve, filter and spatialize data from the Brazilian Flora 2020 dataset. For more information about the dataset, please visit <https://floradobrasil.jbrj.gov.br/consulta/>.
Imports: XML (>= 3.99.0.14), data.table (>= 1.14.8), httr (>= 1.4.6), terra (>= 1.7.39), stats (>= 4.2.3), utils(>= 4.2.3)
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://wevertonbio.github.io/florabr/
BugReports: https://github.com/wevertonbio/florabr/issues
NeedsCompilation: no
Packaged: 2023-12-08 16:26:43 UTC; wever
Author: Weverton Trindade [aut, cre]
Maintainer: Weverton Trindade <wevertonf1993@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-10 11:40:05 UTC

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New package BTtest with initial version 0.10
Package: BTtest
Title: Estimate the Number of Factors in Large Nonstationary Datasets
Version: 0.10
Maintainer: Paul Haimerl <paul.haimerl@maastrichtuniversity.nl>
Description: Implementation of the Barigozzi and Trapani (2022) <doi:10.1080/07350015.2021.1901719> test for the number of common factors in large nonstationary panel data sets. The routine identifies the existence of (i) a factor subject to a linear trend, (ii) the number of zero-mean I(1) and (iii) zero-mean I(0) factors. Furthermore, the package includes the Integrated Panel Criteria by Bai (2004) <doi:10.1016/j.jeconom.2003.10.022> that provide a complementary measure for the number of factors in nonstationary panels.
License: MIT + file LICENSE
Encoding: UTF-8
BugReports: https://github.com/Paul-Haimerl/BTtest/issues
URL: https://github.com/Paul-Haimerl/BTtest
Imports: Rcpp
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2023-12-08 12:02:12 UTC; PaulAdmin
Author: Paul Haimerl [aut, cre]
Repository: CRAN
Date/Publication: 2023-12-10 11:20:05 UTC

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New package AccelStab with initial version 1.0.0
Package: AccelStab
Title: Accelerated Stability Kinetic Modelling
Version: 1.0.0
Description: Estimate the Šesták–Berggren kinetic model (degradation model) from experimental data. A closed-form (analytic) solution to the degradation model is implemented as a non-linear fit, allowing for the extrapolation of the degradation of a drug product - both in time and temperature (Campa C. et al, 2021 <doi:10.3390/vaccines9101114>). Parametric bootstrap, with kinetic parameters drawn from the multivariate t-distribution, and analytical formulae (the delta method) are available options to calculate the confidence and prediction intervals. The results (modelling, extrapolations and statistical intervals) can be visualised with multiple plots. The examples illustrate the accelerated stability modelling in drugs and vaccines development.
License: AGPL (>= 3)
Encoding: UTF-8
Imports: dplyr, ggplot2, minpack.lm, mvtnorm, stats
Suggests: testthat, knitr, rmarkdown, lifecycle
Depends: R (>= 4.1.0)
VignetteBuilder: knitr
LazyData: true
Language: en-GB
URL: https://github.com/AccelStab/AccelStab
BugReports: https://github.com/AccelStab/AccelStab/issues
NeedsCompilation: no
Packaged: 2023-12-08 12:42:15 UTC; alex_
Author: Bernard G Franq [aut, cph], Ben Wells [aut], Alex Ball [cre, ctb]
Maintainer: Alex Ball <alex_keith_ball@hotmail.com>
Repository: CRAN
Date/Publication: 2023-12-10 11:20:08 UTC

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Fri, 08 Dec 2023

New package rgeoboundaries with initial version 1.2.9
Package: rgeoboundaries
Title: A Client to 'geoBoundaries', a Political Administrative Boundaries Dataset
Version: 1.2.9
Description: Client the access data from the 'geoBoundaries' API <https://www.geoboundaries.org/api/current/> who provides country political administrative boundaries dataset.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/wmgeolab/rgeoboundaries
BugReports: https://github.com/wmgeolab/rgeoboundaries/issues
Depends: R (>= 4.1)
Imports: crul (>= 1.4.0), jsonlite, sf (>= 1.0.0), hoardr, glue, memoise, countrycode (>= 1.2.0), lifecycle
Suggests: roxygen2, knitr, rmarkdown, testthat, covr,
NeedsCompilation: no
Packaged: 2023-12-07 19:20:16 UTC; rohith
Author: Ahmadou Dicko [aut, cre], Andy South [ctb], Daniel Runfola [ctb], Rohith Reddy Mandala [ctb]
Maintainer: Ahmadou Dicko <team@geoboundaries.org>
Repository: CRAN
Date/Publication: 2023-12-08 11:20:03 UTC

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New package RcppCGAL with initial version 5.6.0
Package: RcppCGAL
Title: 'Rcpp' Integration for 'CGAL'
Version: 5.6.0
Date: 2023-11-13
Author: Eric Dunipace [aut, cre]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Description: Creates a header only package to link to the 'CGAL' (Computational Geometry Algorithms Library) header files in 'Rcpp'. There are a variety of potential uses for the software such as Hilbert sorting, K-D Tree nearest neighbors, and convex hull algorithms. For more information about how to use the header files, see the 'CGAL' documentation at <https://www.cgal.org>. Currently downloads the 'CGAL' version 5.6 stable release.
License: GPL-3
Imports: Rcpp
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
BugReports: https://github.com/ericdunipace/RcppCGAL/issues
NeedsCompilation: no
Encoding: UTF-8
VignetteBuilder: knitr
Biarch: TRUE
Language: en-US
URL: https://github.com/ericdunipace/RcppCGAL
Packaged: 2023-12-07 23:00:05 UTC; eifer
Repository: CRAN
Date/Publication: 2023-12-08 11:20:24 UTC

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New package PACVr with initial version 1.0.5
Package: PACVr
Version: 1.0.5
Date: 2023-12-07
Title: Plastome Assembly Coverage Visualization
Maintainer: Michael Gruenstaeudl <m_gruenstaeudl@fhsu.edu>
Depends: R (>= 3.3.0)
Imports: Biostrings (>= 2.48.0), dplyr, GenomicAlignments (>= 1.18.1), GenomicRanges, IRanges, logger, read.gb, RCircos (>= 1.2.0)
Description: Visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes. For more information, please see Gruenstaeudl and Jenke (2020) <doi:10.1186/s12859-020-3475-0>.
License: BSD 3-clause License + file LICENSE
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-12-08 01:15:50 UTC; mi
Author: Gregory Smith [ctb], Nils Jenke [ctb], Michael Gruenstaeudl [aut, cre]
Repository: CRAN
Date/Publication: 2023-12-08 11:20:28 UTC

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New package mergen with initial version 0.1.0
Package: mergen
Title: AI-Driven Code Generation, Explanation and Execution for Data Analysis
Version: 0.1.0
Description: Employing artificial intelligence to convert data analysis questions into executable code, explanations, and algorithms. The self-correction feature ensures the generated code is optimized for performance and accuracy. 'mergen' features a user-friendly chat interface, enabling users to interact with the AI agent and extract valuable insights from their data effortlessly.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5.0),
Imports: openai, rmarkdown, BiocManager, assertthat (>= 0.2.1), httr, jsonlite
Suggests: knitr, readxl, data.table (>= 1.9.6), testthat (>= 3.0.0), purrr (>= 0.3.4),
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-07 23:03:43 UTC; aakalin
Author: Altuna Akalin [aut, cre] , Jacqueline Anne Jansen [aut]
Maintainer: Altuna Akalin <aakalin@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-08 11:20:05 UTC

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New package MadanTextNetwork with initial version 0.1.0
Package: MadanTextNetwork
Title: Persian Text Mining Tool for Co-Occurrence Network
Version: 0.1.0
Description: Provides an extension to 'MadanText' for creating and analyzing co-occurrence networks in Persian text data. This package mainly makes use of the 'PersianStemmer' (Safshekan, R., et al. (2019). <https://CRAN.R-project.org/package=PersianStemmer>), 'udpipe' (Wijffels, J., et al. (2023). <https://CRAN.R-project.org/package=udpipe>), and 'shiny' (Chang, W., et al. (2023). <https://CRAN.R-project.org/package=shiny>) packages.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: xlsx, glue, lattice, stopwords,textmineR, tidytext, tidyr, udpipe, PersianStemmer, shiny (>= 1.8.0), shinythemes, tm, dplyr, hwordcloud, stringr, stringi, topicmodels, igraph, ngram, visNetwork
NeedsCompilation: no
Packaged: 2023-12-08 03:48:05 UTC; trial
Author: Kido Ishikawa [aut, cre], Hasan Khosravi [aut]
Maintainer: Kido Ishikawa <kido.ishikawa6@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-08 11:30:05 UTC

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New package fishRman with initial version 1.2.2
Package: fishRman
Title: The Fisheries Scientist's Toolbox
Version: 1.2.2
Description: A bundle of analytics tools for fisheries scientists. Data on fishing effort by 'Global Fishing Watch' can be retrieved via the package's API <https://fishrman.ddnsfree.com/gfw>, as well as data on Exclusive Economic Zones by 'Marine Regions'. A 'shiny' R App is included for a 'no-code' solution for retrieval, analysis, and visualization.
License: AGPL (>= 3)
Depends: R (>= 2.10)
Imports: config (>= 0.3.1), countrycode, dplyr, ggplot2, golem (>= 0.3.3), httr, jsonlite, maps, sf, shiny (>= 1.7.1), shinyBS, shinyjs, shinyWidgets, stats, utils, viridis
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
Date: 2023-12-07
URL: https://github.com/Shyentist/fish-r-man
BugReports: https://github.com/Shyentist/fish-r-man/issues
NeedsCompilation: no
Packaged: 2023-12-08 08:57:03 UTC; pico
Author: Pasquale Buonomo [cre, aut]
Maintainer: Pasquale Buonomo <pasqualebuonomo@hotmail.it>
Repository: CRAN
Date/Publication: 2023-12-08 11:30:02 UTC

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New package dsem with initial version 1.0.0
Package: dsem
Title: Fit Dynamic Structural Equation Models
Version: 1.0.0
Date: 2023-12-04
Imports: TMB (>= 1.9.7), Matrix (>= 1.6.3), sem, igraph, methods
Depends: R (>= 4.0.0),
Suggests: knitr, AER, phylopath, rmarkdown, reshape, gridExtra, dynlm, MARSS, ggplot2, ggpubr, ggraph, grid, vars, testthat
Enhances: rstan, tmbstan
LinkingTo: TMB, RcppEigen
Description: Applies dynamic structural equation models to time-series data with generic and simplified specification for simultaneous and lagged effects. Methods are described in Thorson et al. (In revision) "Dynamic structural equation models synthesize ecosystem dynamics constrained by ecological mechanisms."
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2023-12-08 01:09:20 UTC; James.Thorson
Author: James Thorson [aut, cre]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Repository: CRAN
Date/Publication: 2023-12-08 11:20:08 UTC

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New package blackmarbler with initial version 0.1.0
Package: blackmarbler
Title: Black Marble Data and Statistics
Version: 0.1.0
Description: Geographically referenced data and statistics of nighttime lights from NASA Black Marble <https://blackmarble.gsfc.nasa.gov/>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://worldbank.github.io/blackmarbler/
BugReports: https://github.com/worldbank/blackmarbler/issues
Imports: readr, hdf5r, dplyr, purrr, lubridate, raster, sf, exactextractr, stringr, httr
Suggests: geodata, ggplot2, tidyr, knitr
NeedsCompilation: no
Packaged: 2023-12-07 19:17:45 UTC; robmarty
Author: Robert Marty [aut, cre] , Gabriel Stefanini Vicente [aut]
Maintainer: Robert Marty <rmarty@worldbank.org>
Repository: CRAN
Date/Publication: 2023-12-08 11:20:21 UTC

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New package civ with initial version 0.1.0
Package: civ
Title: Categorical Instrumental Variables
Version: 0.1.0
Date: 2023-12-07
Description: Implementation of the categorical instrumental variable (CIV) estimator proposed by Wiemann (2023) <arXiv:2311.17021>. CIV allows for optimal instrumental variable estimation in settings with relatively few observations per category. To obtain valid inference in these challenging settings, CIV leverages a regularization assumption that implies existence of a latent categorical variable with fixed finite support achieving the same first stage fit as the observed instrument.
License: GPL (>= 3)
URL: https://github.com/thomaswiemann/civ
BugReports: https://github.com/thomaswiemann/civ/issues
Encoding: UTF-8
Depends: R (>= 3.6)
Imports: stats, AER, kcmeans
Suggests: testthat (>= 3.0.0), covr, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-07 22:09:29 UTC; thomas
Author: Thomas Wiemann [aut, cre]
Maintainer: Thomas Wiemann <wiemann@uchicago.edu>
Repository: CRAN
Date/Publication: 2023-12-08 11:00:06 UTC

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Thu, 07 Dec 2023

New package bdvis with initial version 0.2.37
Package: bdvis
Title: Biodiversity Data Visualizations
Version: 0.2.37
Date: 2023-12-07
Maintainer: Vijay Barve <vijay.barve@gmail.com>
Description: Provides a set of functions to create basic visualizations to quickly preview different aspects of biodiversity information such as inventory completeness, extent of coverage (taxonomic, temporal and geographic), gaps and biases. Barve & Otegui (2016) <DOI:10.1093/bioinformatics/btw333>.
License: GPL-3
Encoding: UTF-8
Imports: maps, plotrix, sqldf, plyr, taxize, treemap, ggplot2, lattice, chron, sf
Suggests: rinat
BugReports: https://github.com/vijaybarve/bdvis/issues
NeedsCompilation: no
Packaged: 2023-12-08 00:11:39 UTC; barve
Author: Vijay Barve [aut, cre] , Javier Otegui [aut]
Repository: CRAN
Date/Publication: 2023-12-08 00:50:02 UTC

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New package wallace with initial version 2.1.1
Package: wallace
Version: 2.1.1
Date: 2023-12-05
Title: A Modular Platform for Reproducible Modeling of Species Niches and Distributions
Description: The 'shiny' application Wallace is a modular platform for reproducible modeling of species niches and distributions. Wallace guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface. An extensive vignette, which guides users through most package functionality can be found on the package's GitHub Pages website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
Depends: R (>= 3.5.0), shiny (>= 1.6.0), leaflet (>= 2.0.2)
Imports: dplyr (>= 1.0.2), DT (>= 0.5), ecospat (>= 4.0.0), ENMeval (>= 2.0.3), knitcitations, leafem, leaflet.extras (>= 1.0.0), magrittr, methods, RColorBrewer, rJava, rlang, rmarkdown, sf, shinyalert, shinyjs, shinyWidgets (>= 0.6.0), spocc (>= 1.2.0), spThin, zip
Suggests: ade4, BIEN, dismo, glue, jsonlite, knitr, mapview, maxnet, occCite, rangeModelMetadata, raster, rgbif (>= 3.3.0), sp, terra, testthat, tools
License: GPL-3
URL: http://wallaceecomod.github.io/wallace/,
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-12-07 16:06:02 UTC; dlopezlozano
Author: Jamie M. Kass [aut], Gonzalo E. Pinilla-Buitrago [aut], Andrea Paz [aut], Bethany A. Johnson [aut], Valentina Grisales-Betancur [aut], Dean Attali [aut], Matthew E. Aiello-Lammens [aut], Cory Merow [aut], Mary E. Blair [aut, cre], Robert P. Anderson [...truncated...]
Maintainer: Mary E. Blair <mblair1@amnh.org>
Repository: CRAN
Date/Publication: 2023-12-07 17:30:02 UTC

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New package xtsum with initial version 0.1.0
Package: xtsum
Title: Summary Statistics for Panel Data
Version: 0.1.0
Depends: R (>= 3.2.0), knitr, magrittr, rlang, plm
Imports: dplyr, kableExtra, sampleSelection
Author: Joao Claudio Macosso
Maintainer: Joao Claudio Macosso <joaoclaudiomacosso@gmail.com>
URL: https://github.com/Macosso/xtsum
BugReports: https://github.com/Macosso/xtsum/issues
VignetteBuilder: knitr
Description: Based on 'STATA' xtsum command, it is used to compute summary statistics for a panel data set. It generates overall, between-group, and within-group statistics for specified variables in a panel data set, as presented in S. Porter (2023) <https://stephenporter.org/files/xtsum_handout.pdf>, StataCorp (2023) <https://www.stata.com/manuals/xtxtsum.pdf>.
License: GPL-3
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-12-07 14:48:54 UTC; Joaoc
Repository: CRAN
Date/Publication: 2023-12-07 16:20:02 UTC

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New package readmission with initial version 0.1.0
Package: readmission
Title: Hospital Readmission Data for Patients with Diabetes
Version: 0.1.0
Description: Clinical care data from 130 U.S. hospitals in the years 1999-2008 adapted from the study Strack et al. (2014) <doi:10.1155/2014/781670>. Each row describes an "encounter" with a patient with diabetes, including variables on demographics, medications, patient history, diagnostics, payment, and readmission.
License: MIT + file LICENSE
Suggests: knitr
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2023-12-07 14:40:43 UTC; simoncouch
Author: Simon Couch [aut, cre]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-07 16:20:05 UTC

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New package GenTwoArmsTrialSize with initial version 0.0.4.3
Package: GenTwoArmsTrialSize
Title: Generalized Two Arms Clinical Trial Sample Size Calculation
Version: 0.0.4.3
Description: Two arms clinical trials required sample size is calculated in the comprehensive parametric context. The calculation is based on the type of endpoints(continuous/binary/time-to-event/ordinal), design (parallel/crossover), hypothesis tests (equality/noninferiority/superiority/equivalence), trial arms noncompliance rates and expected loss of follow-up. Methods are described in: Chow SC, Shao J, Wang H, Lokhnygina Y (2017) <doi:10.1201/9781315183084>, Wittes, J (2002) <doi:10.1093/epirev/24.1.39>, Sato, T (2000) <doi:10.1002/1097-0258(20001015)19:19<2689::aid-sim555>3.0.co;2-0>, Lachin J M, Foulkes, M A (1986) <doi:10.2307/2531201>, Whitehead J(1993) <doi:10.1002/sim.4780122404>, Julious SA (2023) <doi:10.1201/9780429503658>.
License: GPL-3
Encoding: UTF-8
Imports: TrialSize, dplyr, Hmisc
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-07 14:43:27 UTC; chelhee.lee
Author: Mohsen Soltanifar [aut] , Chel Hee Lee [cre, aut]
Maintainer: Chel Hee Lee <chelhee.lee@ucalgary.ca>
Repository: CRAN
Date/Publication: 2023-12-07 16:20:08 UTC

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New package CohortSurvival with initial version 0.2.5
Package: CohortSurvival
Title: Estimate Survival from Common Data Model Cohorts
Version: 0.2.5
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
License: Apache License (>= 2)
Encoding: UTF-8
Imports: CDMConnector, checkmate, cli, DBI, dplyr, dbplyr, magrittr, methods, lubridate, broom, PatientProfiles, rlang (>= 0.4.11), survival, scales, stringr, tibble, tidyr
Suggests: testthat (>= 3.0.0), CodelistGenerator, roxygen2, knitr, tictoc, rmarkdown, ggplot2, duckdb
VignetteBuilder: knitr
URL: https://darwin-eu-dev.github.io/CohortSurvival/
NeedsCompilation: no
Packaged: 2023-12-07 15:02:55 UTC; eburn
Author: Edward Burn [aut, cre] , Kim Lopez [ctb] , Marti Catala [ctb] , Xintong Li [ctb] , Danielle Newby [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Repository: CRAN
Date/Publication: 2023-12-07 16:30:05 UTC

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New package easyalluvial with initial version 0.3.2
Package: easyalluvial
Title: Generate Alluvial Plots with a Single Line of Code
Version: 0.3.2
URL: https://github.com/erblast/easyalluvial/
Description: Alluvial plots are similar to sankey diagrams and visualise categorical data over multiple dimensions as flows. (Rosvall M, Bergstrom CT (2010) Mapping Change in Large Networks. PLoS ONE 5(1): e8694. <doi:10.1371/journal.pone.0008694> Their graphical grammar however is a bit more complex then that of a regular x/y plots. The 'ggalluvial' package made a great job of translating that grammar into 'ggplot2' syntax and gives you many options to tweak the appearance of an alluvial plot, however there still remains a multi-layered complexity that makes it difficult to use 'ggalluvial' for explorative data analysis. 'easyalluvial' provides a simple interface to this package that allows you to produce a decent alluvial plot from any dataframe in either long or wide format from a single line of code while also handling continuous data. It is meant to allow a quick visualisation of entire dataframes with a focus on different colouring options that can make alluvial plots a great tool for d [...truncated...]
License: CC0
Encoding: UTF-8
LazyData: true
Depends: R(>= 3.5)
Suggests: testthat, covr, ISLR, nycflights13, vdiffr (>= 0.3.1), pkgdown, mlbench, earth, workflows, future, furrr, e1071, caret, parsnip, vip, rpart, glmnet, xgboost
Imports: purrr , tidyr (>= 1.0.0) , dplyr , forcats , ggalluvial (>= 0.9.1) , ggplot2 (>= 3.2.0) , ggridges , RColorBrewer , recipes (>= 0.1.5) , rlang , stringr , magrittr , tibble , gridExtra , randomForest , progressr , progress
Language: en-US
NeedsCompilation: no
Packaged: 2023-12-07 12:44:05 UTC; koneswab
Author: Bjoern Koneswarakantha [aut, cre]
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-07 13:40:06 UTC

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New package ggthemeUL with initial version 0.1.3
Package: ggthemeUL
Title: A 'ggplot' Theme for University of Ljubljana
Version: 0.1.3
Description: Designed to customize 'ggplot' graphics according to the institutional identity of the University of Ljubljana.
License: GPL
Encoding: UTF-8
Depends: ggplot2
Suggests: knitr, rmarkdown, scales
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-07 09:31:15 UTC; marss
Author: Marjan Cugmas [aut, cre]
Maintainer: Marjan Cugmas <marjan.cugmas@fdv.uni-lj.si>
Repository: CRAN
Date/Publication: 2023-12-07 11:50:02 UTC

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New package g.ridge with initial version 1.0
Package: g.ridge
Title: Generalized Ridge Regression for Linear Models
Version: 1.0
Description: Ridge regression due to Hoerl and Kennard (1970)<DOI:10.1080/00401706.1970.10488634> and generalized ridge regression due to Yang and Emura (2017)<DOI:10.1080/03610918.2016.1193195> with optimized tuning parameters. These ridge regression estimators (the HK estimator and the YE estimator) are computed by minimizing the cross-validated mean squared errors. Both the ridge and generalized ridge estimators are applicable for high-dimensional regressors (p>n), where p is the number of regressors, and n is the sample size.
License: GPL-2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-12-07 05:29:27 UTC; takes
Author: Takeshi Emura [aut, cre], Szu-Peng Yang [ctb]
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-07 11:50:05 UTC

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New package cryptotrackr with initial version 1.1.0
Package: cryptotrackr
Title: An Interface to Crypto Data Sources
Version: 1.1.0
Maintainer: Trevor French <FrenchTrevor@outlook.com>
Description: Allows you to connect to data sources across the crypto ecosystem. This data can enable a range of activity such as portfolio tracking, programmatic trading, or industry analysis.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: httr, jsonlite, stringi, openssl, utils, digest
NeedsCompilation: no
Packaged: 2023-12-06 19:09:08 UTC; Trevor French
Author: Trevor French [aut, cre]
Repository: CRAN
Date/Publication: 2023-12-07 11:10:02 UTC

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New package BTdecayLasso with initial version 0.1.1
Package: BTdecayLasso
Title: Bradley-Terry Model with Exponential Time Decayed Log-Likelihood and Adaptive Lasso
Version: 0.1.1
Description: We utilize the Bradley-Terry Model to estimate the abilities of teams using paired comparison data. For dynamic approximation of current rankings, we employ the Exponential Decayed Log-likelihood function, and we also apply the Lasso penalty for variance reduction and grouping. The main algorithm applies the Augmented Lagrangian Method described by Masarotto and Varin (2012) <doi:10.1214/12-AOAS581>.
Imports: optimx, ggplot2, stats
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Packaged: 2023-12-07 09:07:49 UTC; micha
Author: Yunpeng Zhou [aut, cre], Jinfeng Xu [aut]
Maintainer: Yunpeng Zhou <u3514104@connect.hku.hk>
Repository: CRAN
Date/Publication: 2023-12-07 11:40:02 UTC

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Wed, 06 Dec 2023

New package RNAmf with initial version 0.1.0
Package: RNAmf
Title: Recursive Non-Additive Emulator for Multi-Fidelity Data
Version: 0.1.0
Maintainer: Junoh Heo <heojunoh@msu.edu>
Description: Performs RNA emulation and active learning proposed by Heo and Sung (2023+) <arXiv:2309.11772> for multi-fidelity computer experiments. The RNA emulator is particularly useful when the simulations with different fidelity level are nonlinearly correlated. The hyperparameters in the model are estimated by maximum likelihood estimation.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: plgp, stats, lhs, doParallel, foreach
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2023-12-06 15:34:04 UTC; junoh
Author: Junoh Heo [aut, cre], Chih-Li Sung [aut]
Repository: CRAN
Date/Publication: 2023-12-06 19:20:06 UTC

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New package covadap with initial version 1.0.1
Package: covadap
Date: 2023-12-06
Title: Implement Covariate-Adaptive Randomization
Version: 1.0.1
Author: Rosamarie Frieri [aut, cre], Marco Novelli [aut]
Maintainer: Rosamarie Frieri <rosamarie.frieri2@unibo.it>
Imports: stats
Description: Implementing seven Covariate-Adaptive Randomization to assign patients to two treatments. Three of these procedures can also accommodate quantitative and mixed covariates. Given a set of covariates, the user can generate a single sequence of allocations or replicate the design multiple times by simulating the patients' covariate profiles. At the end, an extensive assessment of the performance of the randomization procedures is provided, calculating several imbalance measures. See Baldi Antognini A, Frieri R, Zagoraiou M and Novelli M (2022) <doi:10.1007/s00362-022-01381-1> for details.
License: GPL (>= 3)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-12-06 16:47:46 UTC; marco
Repository: CRAN
Date/Publication: 2023-12-06 19:20:02 UTC

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New package WRestimates with initial version 0.1.0
Package: WRestimates
Title: Sample Size, Power and CI for the Win Ratio
Version: 0.1.0
Description: Calculates non-parametric estimates of the sample size, power and confidence intervals for the win-ratio. For more detail on the theory behind the methodologies implemented see Yu, R. X. and Ganju, J. (2022) <doi:10.1002/sim.9297>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-06 11:08:53 UTC; r2301007
Author: Autumn O'Donnell [aut, cre, cph]
Maintainer: Autumn O'Donnell <autumn.research@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-06 16:10:02 UTC

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New package PHENTHAUproc with initial version 0.9.9
Package: PHENTHAUproc
Title: Modelling Phenology of Oak Processionary Moth
Version: 0.9.9
Description: Methods to calculate and present 'PHENTHAUproc', an early warning and decision support system for hazard assessment and control of oak processionary moth (Thaumetopoea processionea) using local and spatial temperature data. It was created by Halbig et al. 2023 (in submission) at the FVA (<https://www.fva-bw.de>) a forest research institute in Baden-Wuerttemberg, Germany.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5)
Imports: grDevices, lubridate (>= 1.9), methods, rlang, stats, terra (>= 1.7), utils
Suggests: dplyr, geomtextpath, ggplot2 (>= 3.4), knitr, rmarkdown, testthat (>= 3.0.0), tidyterra (>= 0.4.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-06 09:26:11 UTC; Lorenz.Bachfischer
Author: Lorenz Bachfischer [aut, cre], Abt. Waldschutz, FVA [fnd]
Maintainer: Lorenz Bachfischer <lorenz.bachfischer@posteo.de>
Repository: CRAN
Date/Publication: 2023-12-06 16:10:04 UTC

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New package SID with initial version 1.1
Package: SID
Title: Structural Intervention Distance
Version: 1.1
Date: 2023-12-03
Encoding: UTF-8
Imports: pcalg, igraph, RBGL, Matrix, methods
Description: The code computes the structural intervention distance (SID) between a true directed acyclic graph (DAG) and an estimated DAG. Definition and details about the implementation can be found in J. Peters and P. Bühlmann: "Structural intervention distance (SID) for evaluating causal graphs", Neural Computation 27, pages 771-799, 2015 <doi:10.1162/NECO_a_00708>.
URL: https://github.com/fkgruber/SID_cran
License: FreeBSD
Repository: CRAN
NeedsCompilation: no
Packaged: 2023-12-06 04:46:38 UTC; fred
Author: Fred Gruber [cre], Jonas Peters [aut]
Maintainer: Fred Gruber <fgruber@gmail.com>
Date/Publication: 2023-12-06 10:10:02 UTC

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New package pmartR with initial version 2.4.1
Package: pmartR
Title: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data
Version: 2.4.1
Date: 2023-11-07
Description: Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.
License: BSD_2_clause + file LICENSE
Depends: R (>= 3.5.0)
URL: https://github.com/pmartR/pmartR
BugReports: https://github.com/pmartR/pmartR/issues
LinkingTo: Rcpp, RcppArmadillo, BH
Imports: Rcpp (>= 0.12.8), data.table, doParallel, dplyr, ggplot2, e1071, foreach, methods, mvtnorm, pcaMethods, plotly, purrr, rrcov, stringr, tidyr, RColorBrewer, magrittr, parallelly, patchwork, glmpca,
Suggests: knitr, limma, rmarkdown, edgeR, DESeq2, scales, S4Vectors, survival, testthat, trelliscopejs, pmartRdata, vdiffr
Additional_repositories: https://pmartR.github.io/drat
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2023-12-04 17:45:08 UTC; clab683
Author: Lisa Bramer [aut, cre], Kelly Stratton [aut], Daniel Claborne [aut], Evan Glasscock [ctb], Rachel Richardson [ctb], David Degnan [ctb], Evan Martin [ctb]
Maintainer: Lisa Bramer <lisa.bramer@pnnl.gov>
Repository: CRAN
Date/Publication: 2023-12-06 10:30:05 UTC

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New package NRAHDLTP with initial version 0.1.2
Package: NRAHDLTP
Title: Location Tests for High-Dimensional Problems Including Normal-Reference Approach
Version: 0.1.2
Author: Pengfei Wang [aut, cre], Shuqi Luo [aut], Tianming Zhu [aut], Bu Zhou [aut]
Maintainer: Pengfei Wang <nie23.wp8738@e.ntu.edu.sg>
Description: We provide a collection of various classical tests and latest normal-reference approach tests for comparing high-dimensional mean vectors including two-sample and general linear hypothesis testing (GLHT) problem. The others’ tests for two-sample problem [see Bai, Zhidong, and Hewa Saranadasa.(1996) <https://www.jstor.org/stable/24306018>; Chen, Song Xi, and Ying-Li Qin.(2010) <doi:10.1214/09-aos716>; Srivastava, Muni S., and Meng Du.(2008) <doi:10.1016/j.jmva.2006.11.002>; Srivastava, Muni S., Shota Katayama, and Yutaka Kano.(2013)<doi:10.1016/j.jmva.2012.08.014>]. Normal-reference approach based tests for two-sample problem [see Zhang, Jin-Ting, Jia Guo, Bu Zhou, and Ming-Yen Cheng.(2020) <doi:10.1080/01621459.2019.1604366>; Zhang, Jin-Ting, Bu Zhou, Jia Guo, and Tianming Zhu.(2021) <doi:10.1016/j.jspi.2020.11.008>; Zhang, Liang, Tianming Zhu, and Jin-Ting Zhang.(2020) <doi:10.1016/j.ecosta.2019.12.002>; Zhang, Liang, Tianming Zhu, and Jin-Tin [...truncated...]
License: GPL (>= 3)
BugReports: https://github.com/nie23wp8738/NRAHDLTP/issues
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo
Imports: expm, Rcpp, Rdpack, readr, stats
Suggests: devtools, dplyr, knitr, rmarkdown, spelling, testthat (>= 3.0.0), tidyr
Depends: R (>= 2.10)
LazyData: true
Language: en-US
NeedsCompilation: yes
Packaged: 2023-12-06 04:28:13 UTC; yehe
Repository: CRAN
Date/Publication: 2023-12-06 10:10:05 UTC

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New package MadanText with initial version 0.1.0
Package: MadanText
Title: Persian Text Mining Tool for Frequency Analysis, Statistical Analysis, and Word Clouds
Version: 0.1.0
Description: This is an open-source software designed specifically for text mining in the Persian language. It allows users to examine word frequencies, download data for analysis, and generate word clouds. This tool is particularly useful for researchers and analysts working with Persian language data. This package mainly makes use of the 'PersianStemmer' (Safshekan, R., et al. (2019). <https://CRAN.R-project.org/package=PersianStemmer>), 'udpipe' (Wijffels, J., et al. (2023). <https://CRAN.R-project.org/package=udpipe>), and 'shiny' (Chang, W., et al. (2023). <https://CRAN.R-project.org/package=shiny>) packages.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: xlsx, lattice, stopwords,textmineR, tidytext, stringi, tidyr, udpipe, PersianStemmer, shiny (>= 1.8.0), shinythemes, tm, dplyr, hwordcloud, stringr, topicmodels
NeedsCompilation: no
Packaged: 2023-12-06 02:27:00 UTC; trial
Author: Kido Ishikawa [aut, cre], Hasan Khosravi [aut]
Maintainer: Kido Ishikawa <kido.ishikawa6@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-06 10:10:09 UTC

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New package GrabSVG with initial version 0.0.2
Package: GrabSVG
Title: Granularity-Based Spatially Variable Genes Identifications
Version: 0.0.2
Description: Identifying spatially variable genes is critical in linking molecular cell functions with tissue phenotypes. This package implemented a granularity-based dimension-agnostic tool for the identification of spatially variable genes. The detailed description of this method is available at Wang, J. and Li, J. et al. 2023 (Wang, J. and Li, J. (2023), <doi:10.1038/s41467-023-43256-5>).
License: GPL (>= 2)
Encoding: UTF-8
Imports: Matrix, sparseMatrixStats, fitdistrplus, RANN, spam
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2023-12-05 21:54:00 UTC; lijinp
Author: Jinpu Li [aut, cre]
Maintainer: Jinpu Li <castle.lee.f@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-06 10:00:14 UTC

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New package binpackr with initial version 0.1.1
Package: binpackr
Title: Fast 1d Bin Packing
Version: 0.1.1
Description: Implements the First Fit Decreasing algorithm to achieve one dimensional heuristic bin packing. Runtime is of order O(n log(n)) where n is the number of items to pack. See "The Art of Computer Programming Vol. 1" by Donald E. Knuth (1997, ISBN: 0201896834) for more details.
License: GPL (>= 3)
Encoding: UTF-8
LinkingTo: cpp11
Suggests: testthat (>= 3.0.0), hedgehog (>= 0.1)
URL: https://github.com/lschneiderbauer/binpackr
BugReports: https://github.com/lschneiderbauer/binpackr/issues
NeedsCompilation: yes
Packaged: 2023-12-05 21:55:53 UTC; lukas
Author: Lukas Schneiderbauer [aut, cre, cph]
Maintainer: Lukas Schneiderbauer <lukas.schneiderbauer@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-06 10:00:06 UTC

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Tue, 05 Dec 2023

New package mvst with initial version 1.1.1
Package: mvst
Title: Bayesian Inference for the Multivariate Skew-t Model
Version: 1.1.1
Date: 2023-12-05
Author: Antonio Parisi [aut, cre], Brunero Liseo [aut], Dirk Eddelbuettel [ctb], Romain Francois [ctb]
Maintainer: Antonio Parisi <antonio.parisi@uniroma2.it>
Description: Estimates the multivariate skew-t and nested models, as described in the articles Liseo, B., Parisi, A. (2013). Bayesian inference for the multivariate skew-normal model: a population Monte Carlo approach. Comput. Statist. Data Anal. <doi:10.1016/j.csda.2013.02.007> and in Parisi, A., Liseo, B. (2017). Objective Bayesian analysis for the multivariate skew-t model. Statistical Methods & Applications <doi: 10.1007/s10260-017-0404-0>.
SystemRequirements: GNU Scientific Library
License: GPL-3
Imports: MCMCpack, mvtnorm, mnormt
NeedsCompilation: yes
Packaged: 2023-12-05 13:29:21 UTC; user
Repository: CRAN
Date/Publication: 2023-12-05 23:10:02 UTC

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New package ZLAvian with initial version 0.1.0
Package: ZLAvian
Title: Zipf's Law of Abbreviation in Animal Vocalisations
Version: 0.1.0
Description: Assesses evidence for Zipf's Law of Abbreviation in animal vocalisation using IDs, note class and note duration. The package also provides a webplot function for visualisation. Davis, M. K., and Chen, G. (2007) <doi:10.2307/2346786>.
License: CC BY-SA 4.0
URL: https://github.com/CDr-er/ZLAvian
BugReports: https://github.com/CDr-er/ZLAvian/issues
Maintainer: CD Durrant <cbdurrantant@gmail.com>
Depends: R(>= 4.3.0)
Imports: lme4 (>= 1.1-34), performance (>= 0.10.4), doParallel (>= 1.0.17)
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
LazyData: true
NeedsCompilation: no
Packaged: 2023-12-04 10:01:57 UTC; dodge
Author: CD Durrant [com, cre, cph], Tucker Gilman [aut, cph]
Repository: CRAN
Date/Publication: 2023-12-05 17:30:02 UTC

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New package geostatsp with initial version 2.0.3
Package: geostatsp
Title: Geostatistical Modelling with Likelihood and Bayes
Version: 2.0.3
Date: 2023-11-24
Depends: Matrix, terra, R (>= 3.5.0)
Imports: abind, numDeriv, methods, stats
Suggests: RandomFields, parallel, mapmisc, ellipse, pracma, knitr
Enhances: INLA, diseasemapping, geoR, mvtnorm
LinkingTo: Matrix (>= 1.6-2)
Additional_repositories: https://inla.r-inla-download.org/R/testing
Description: Geostatistical modelling facilities using 'SpatRaster' and 'SpatVector' objects are provided. Non-Gaussian models are fit using 'INLA', and Gaussian geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>. The 'RandomFields' package is available at <https://www.wim.uni-mannheim.de/schlather/publications/software>.
License: GPL
NeedsCompilation: yes
VignetteBuilder: knitr
Packaged: 2023-12-04 23:12:43 UTC; patrick
Author: Patrick Brown [aut, cre, cph]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Repository: CRAN
Date/Publication: 2023-12-05 17:50:02 UTC

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New package genCountR with initial version 1.0.0
Package: genCountR
Title: Interacting with Roberts and Utych's (2019) Gendered Language Dictionary
Version: 1.0.0
Description: Allows users to generate a gendered language score according to the gendered language dictionary in Roberts and Utych (2019) <doi:10.1177/1065912919874883>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Suggests: devtools, knitr, rmarkdown, testthat
VignetteBuilder: knitr
URL: https://gencounter.app.damoncroberts.com, https://damoncharlesroberts.github.io/genCountR/
NeedsCompilation: no
Packaged: 2023-12-05 00:37:50 UTC; dcr
Author: Damon Roberts [aut, cre]
Maintainer: Damon Roberts <damon.charles.roberts@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-05 17:50:04 UTC

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New package fcp with initial version 0.1.0
Package: fcp
Title: Function Composition
Version: 0.1.0
Date: 2023-11-27
Description: A function composition operator to chain a series of calls into a single function, mimicking the math notion of (f o g o h)(x) = h(g(f(x))). Inspired by 'pipeOp' ('|>') since R4.1 and 'magrittr pipe' ('%>%'), the operator build a pipe without putting data through, which is best for anonymous function accepted by utilities such as apply() and lapply().
Depends: R (>= 3.5.0)
License: GPL (>= 2)
URL: https://github.com/xiaoran831213/R_fun_comp
Encoding: UTF-8
Author: Xiaoran Tong [aut, cre]
Maintainer: Xiaoran Tong <xiaoran.tong.cn@gmail.com>
NeedsCompilation: no
Packaged: 2023-12-04 02:03:17 UTC; xt
Repository: CRAN
Date/Publication: 2023-12-05 17:20:02 UTC

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New package CDSE with initial version 0.1.0
Package: CDSE
Title: 'Copernicus Data Space Ecosystem' API Wrapper
Version: 0.1.0
Description: Provides interface to the 'Copernicus Data Space Ecosystem' API <https://dataspace.copernicus.eu/analyse/apis>, mainly for searching the catalog of available data from Copernicus Sentinel missions and obtaining the images for just the area of interest based on selected spectral bands. The package uses the 'Sentinel Hub' REST API interface <https://dataspace.copernicus.eu/analyse/apis/sentinel-hub> that provides access to various satellite imagery archives. It allows you to access raw satellite data, rendered images, statistical analysis, and other features.
Depends: R (>= 3.6.0)
Imports: geojsonsf, httr2, jsonlite, lubridate, lutz, sf, stats, terra, utils
License: AGPL-3
Encoding: UTF-8
Suggests: maps, tibble
NeedsCompilation: no
Packaged: 2023-12-05 10:58:44 UTC; zivan
Author: Zivan Karaman [aut, cre, cph]
Maintainer: Zivan Karaman <zivan.karaman@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-05 18:00:02 UTC

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New package animbook with initial version 1.0.0
Package: animbook
Title: Visualizing Changes in Performance Measures and Demographic Affiliations using Animation
Version: 1.0.0
Description: Create an interactive visualization to be used for communication purposes. Providing the function for preparing, plotting, and animating the data.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/KrisanatA/animbook
BugReports: https://github.com/KrisanatA/animbook/issues
Depends: R (>= 2.10)
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: dplyr, gganimate, ggplot2, plotly, purrr, RColorBrewer, rlang, stats, tibble, tidyr, tidyselect
NeedsCompilation: no
Packaged: 2023-12-05 10:12:22 UTC; ottoi
Author: Krisanat Anukarnsakulchularp [aut, cre, cph] , Dianne Cook [aut]
Maintainer: Krisanat Anukarnsakulchularp <krisanat.anu@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-05 17:50:07 UTC

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New package misha with initial version 4.2.8
Package: misha
Title: Toolkit for Analysis of Genomic Data
Version: 4.2.8
Description: A toolkit for analysis of genomic data. The 'misha' package implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay (2011) <doi:10.1038/ng.947>.
License: MIT + file LICENSE
URL: https://tanaylab.github.io/misha/, https://github.com/tanaylab/misha
BugReports: https://github.com/tanaylab/misha/issues
Depends: R (>= 3.0.0)
Imports: magrittr, curl
Suggests: dplyr, glue, knitr, readr, rmarkdown, spelling, stats, testthat (>= 3.0.0), tibble, utils, withr
Encoding: UTF-8
Language: en-US
LazyLoad: yes
NeedsCompilation: yes
OS_type: unix
VignetteBuilder: knitr
Packaged: 2023-11-30 10:02:12 UTC; aviezerl
Author: Misha Hoichman [aut], Aviezer Lifshitz [aut, cre], Eitan Yaffe [aut], Amos Tanay [aut], Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Repository: CRAN
Date/Publication: 2023-12-05 15:20:02 UTC

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New package PracTools with initial version 1.4.2
Package: PracTools
Title: Designing and Weighting Survey Samples
Version: 1.4.2
Date: 2023-11-29
Author: Richard Valliant [aut, cre], Jill A. Dever [ctb], Frauke Kreuter [ctb], George Zipf [aut]
Maintainer: Richard Valliant <valliant@umich.edu>
Description: Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Suggests: doBy, foreign, lpSolve, markdown, plyr, pps, Rcpp, reshape, roxygen2, sampling, samplingbook, sp, survey, knitr, rmarkdown
Depends: R (>= 3.5.0)
Imports: dplyr, geosphere, ggplot2, graphics, usmap
License: GPL-3
LazyLoad: yes
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-29 20:27:21 UTC; rv
Repository: CRAN
Date/Publication: 2023-12-05 10:40:02 UTC

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Mon, 04 Dec 2023

New package MarZIC with initial version 1.0.0
Package: MarZIC
Title: Marginal Mediation Effects with Zero-Inflated Compositional Mediator
Version: 1.0.0
Description: A way to estimate and test marginal mediation effects for zero-inflated compositional mediators. Estimates of Natural Indirect Effect (NIE), Natural Direct Effect (NDE) of each taxon, as well as their standard errors and confident intervals, were provided as outputs. Zeros will not be imputed during analysis. See Wu et al. (2022) <doi:10.3390/genes13061049>.
URL: https://www.mdpi.com/2073-4425/13/6/1049
License: GPL-2
Imports: Rcpp (>= 1.0.9), NlcOptim, betareg, doParallel, foreach, pracma, mathjaxr, dirmult, stats, parallel
Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2023-12-03 10:10:05 UTC; quranwu
Author: Quran Wu [aut], Zhigang Li [aut, cre]
Maintainer: Zhigang Li <lzg2151@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-04 20:00:02 UTC

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New package ebmstate with initial version 0.1.4
Package: ebmstate
Title: Empirical Bayes Multi-State Cox Model
Version: 0.1.4
Description: Implements an empirical Bayes, multi-state Cox model for survival analysis. Run "?'ebmstate-package'" for details. See also Schall (1991) <doi:10.1093/biomet/78.4.719>.
Depends: R (>= 3.6.0), survival (>= 2.44-1.1), mstate (>= 0.2.11)
Imports: Rcpp, HDInterval, stats, utils, methods
License: GPL (>= 3)
LinkingTo: Rcpp
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2023-12-02 16:42:33 UTC; RuiCosta
Author: Rui Costa [aut, cre], Moritz Gerstung [aut], Terry M Therneau [ctb] , Thomas Lumley [ctb] , Hein Putter [ctb] , Liesbeth de Wreede [ctb] , Marta Fiocco [ctb] , Ronald Geskus [ctb]
Maintainer: Rui Costa <ruibarrigana@hotmail.com>
Repository: CRAN
Date/Publication: 2023-12-04 17:10:02 UTC

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New package discFA with initial version 1.0.0
Package: discFA
Title: Discrete Factor Analysis
Version: 1.0.0
Description: Discrete factor analysis for dependent Poisson and negative binomial models with truncation, zero inflation, and zero inflated truncation.
License: GPL-3
Maintainer: Reza A. Belaghi <rezaarabi11@gmail.com>
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: VGAM, methods
NeedsCompilation: no
Packaged: 2023-12-02 13:18:40 UTC; yasinasar
Author: Yasin Asar [aut] , Reza A. Belaghi [aut, cre] , Rolf Larsson [aut]
Repository: CRAN
Date/Publication: 2023-12-04 17:10:06 UTC

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New package samplingin with initial version 1.0.1
Package: samplingin
Title: Dynamic Survey Sampling Solutions
Version: 1.0.1
Description: A robust solution employing both systematic and PPS (Probability Proportional to Size) sampling methods, ensuring a methodical and representative selection of data. Seamlessly allocate predetermined allocations to smaller levels. Kish, L. (1965) <https://books.google.co.id/books?id=xiZmAAAAIAAJ>.
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: data.table, dplyr, DT, magrittr, rio, rlang, stats, stringr, tidyr, utils
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-12-01 23:10:06 UTC; User
Author: Choerul Afifanto [aut, cre, cph]
Maintainer: Choerul Afifanto <choerulafifanto@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-04 16:40:02 UTC

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New package regmhmm with initial version 1.0.0
Package: regmhmm
Title: 'regmhmm' Fits Hidden Markov Models with Regularization
Version: 1.0.0
Date: 2023-11-29
Maintainer: Man Chong Leong <mc.leong26@gmail.com>
Description: Designed for longitudinal data analysis using Hidden Markov Models (HMMs). Tailored for applications in healthcare, social sciences, and economics, the main emphasis of this package is on regularization techniques for fitting HMMs. Additionally, it provides an implementation for fitting HMMs without regularization, referencing Zucchini et al. (2017, ISBN:9781315372488).
License: GPL (>= 3)
Encoding: UTF-8
Imports: glmnet, glmnetUtils, MASS, Rcpp, stats
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/HenryLeongStat/regmhmm
BugReports: https://github.com/HenryLeongStat/regmhmm/issues
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: yes
Packaged: 2023-12-01 18:08:55 UTC; mleong1
Author: Man Chong Leong [cre, aut]
Repository: CRAN
Date/Publication: 2023-12-04 16:40:05 UTC

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New package profrep with initial version 1.0.0
Package: profrep
Title: Profile Repeatability
Version: 1.0.0
Description: Calculates profile repeatability for replicate stress response curves, or similar time-series data. Profile repeatability is an individual repeatability metric that uses the variances at each timepoint, the maximum variance, the number of crossings (lines that cross over each other), and the number of replicates to compute the repeatability score. For more information see Reed et al. (2019) <doi:10.1016/j.ygcen.2018.09.015>.
Depends: R (>= 2.10)
License: MIT + file LICENSE
URL: https://ubeattie.github.io/profrep/
BugReports: https://github.com/ubeattie/profrep/issues
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Imports: stats
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-01 20:50:46 UTC; cleanaccount
Author: Ursula K. Beattie [cre, aut, cph] , David Harris [aut, cph], L. Michael Romero [aut, cph] , J. Michael Reed [aut, cph] , Zachary R. Weaver [aut, cph]
Maintainer: Ursula K. Beattie <ursula.beattie@tufts.edu>
Repository: CRAN
Date/Publication: 2023-12-04 16:40:08 UTC

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New package phdcocktail with initial version 0.1.0
Package: phdcocktail
Title: Enhance the Ease of R Experience as an Emerging Researcher
Version: 0.1.0
Description: A toolkit of functions to help: i) effortlessly transform collected data into a publication ready format, ii) generate insightful visualizations from clinical data, iii) report summary statistics in a publication-ready format, iv) efficiently export, save and reload R objects within the framework of R projects.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: ggplot2, here, RColorBrewer, rstudioapi, scales, stats
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
URL: https://dahhamalsoud.github.io/phdcocktail/, https://github.com/DahhamAlsoud/phdcocktail
BugReports: https://github.com/DahhamAlsoud/phdcocktail/issues
NeedsCompilation: no
Packaged: 2023-12-02 11:43:00 UTC; Dahham
Author: Dahham Alsoud [cre, aut, cph]
Maintainer: Dahham Alsoud <dahhamalsoud@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-04 17:00:03 UTC

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New package NAC with initial version 0.1.0
Package: NAC
Title: Network-Adjusted Covariates for Community Detection
Version: 0.1.0
Author: Yaofang Hu [aut, cre], Wanjie Wang [aut]
Maintainer: Yaofang Hu <yaofangh@smu.edu>
Description: Incorporating node-level covariates for community detection has gained increasing attention these years. This package provides the function for implementing the novel community detection algorithm known as Network-Adjusted Covariates for Community Detection (NAC), which is designed to detect latent community structure in graphs with node-level information, i.e., covariates. This algorithm can handle models such as the degree-corrected stochastic block model (DCSBM) with covariates. NAC specifically addresses the discrepancy between the community structure inferred from the adjacency information and the community structure inferred from the covariates information. For more detailed information, please refer to the reference paper: Yaofang Hu and Wanjie Wang (2023) <arXiv:2306.15616>. In addition to NAC, this package includes several other existing community detection algorithms that are compared to NAC in the reference paper. These algorithms are Spectral Clustering On Ratios-of E [...truncated...]
Imports: stats, pracma
License: GPL-2
Encoding: UTF-8
URL: https://arxiv.org/abs/2306.15616
Suggests: testthat, igraph
Depends: R (>= 4.2.2.0)
NeedsCompilation: no
Packaged: 2023-12-02 00:59:40 UTC; lu936
Repository: CRAN
Date/Publication: 2023-12-04 16:40:15 UTC

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New package ImVol with initial version 0.1.0
Package: ImVol
Title: Volume Prediction of Trees Using Linear and Nonlinear Allometric Equations
Version: 0.1.0
Author: M. Iqbal Jeelani [aut, cre], Fehim Jeelani [aut], Syed Naseem Geelani [aut], Md Yeasin [aut]
Maintainer: M. Iqbal Jeelani <jeelani.miqbal@gmail.com>
Description: Volume prediction is one of challenging task in forestry research. This package is a comprehensive toolset designed for the fitting and validation of various linear and nonlinear allometric equations (Linear, Log-Linear, Inverse, Quadratic, Cubic, Compound, Power and Exponential) used in the prediction of conifer tree volume. This package is particularly useful for forestry professionals, researchers, and resource managers engaged in assessing and estimating the volume of coniferous trees. This package has been developed using the algorithm of Sharma et al. (2017) <doi:10.13140/RG.2.2.33786.62407>.
License: GPL-3
Encoding: UTF-8
Imports: stats, tidyverse, nls2, caret, ggplot2, dplyr, tidyr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2023-12-02 07:26:08 UTC; YEASIN
Repository: CRAN
Date/Publication: 2023-12-04 16:50:05 UTC

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New package decompDL with initial version 0.1.0
Package: decompDL
Title: Decomposition Based Deep Learning Models for Time Series Forecasting
Version: 0.1.0
Maintainer: Kapil Choudhary <kapiliasri@gmail.com>
Description: Hybrid model is the most promising forecasting method by combining decomposition and deep learning techniques to improve the accuracy of time series forecasting. Each decomposition technique decomposes a time series into a set of intrinsic mode functions (IMFs), and the obtained IMFs are modelled and forecasted separately using the deep learning models. Finally, the forecasts of all IMFs are combined to provide an ensemble output for the time series. The prediction ability of the developed models are calculated using international monthly price series of maize in terms of evaluation criteria like root mean squared error, mean absolute percentage error and, mean absolute error. For method details see Choudhary, K. et al. (2023). <https://ssca.org.in/media/14_SA44052022_R3_SA_21032023_Girish_Jha_FINAL_Finally.pdf>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: keras, tensorflow, reticulate, tsutils, stats, BiocGenerics, utils, graphics, magrittr,Rlibeemd, TSdeeplearning, VMDecomp
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2023-12-02 01:12:13 UTC; kapil
Author: Kapil Choudhary [aut, cre], Girish Kumar Jha [aut, ths, ctb], Ronit Jaiswal [ctb], Rajeev Ranjan Kumar [ctb]
Repository: CRAN
Date/Publication: 2023-12-04 16:50:02 UTC

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New package IOHanalyzer with initial version 0.1.8.6
Package: IOHanalyzer
Title: Data Analysis Part of 'IOHprofiler'
Version: 0.1.8.6
Maintainer: Diederick Vermetten <d.l.vermetten@liacs.leidenuniv.nl>
Description: The data analysis module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides statistical analysis methods for the benchmark data generated by optimization heuristics, which can be visualized through a web-based interface. The benchmark data is usually generated by the experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://iohanalyzer.liacs.nl, https://github.com/IOHprofiler/IOHAnalyzer
BugReports: https://github.com/IOHprofiler/IOHAnalyzer/issues
Imports: magrittr, dplyr, data.table, ggplot2, plotly, colorspace, colorRamps, RColorBrewer, shiny, reshape2, stringi, httr, knitr, methods, rjson, eaf, viridis
LinkingTo: Rcpp
SystemRequirements: C++
Suggests: Rcpp, testthat, withr, ComplexHeatmap, grid, keyring, PlayerRatings, xtable, shinyjs, colourpicker, bsplus, DT, kableExtra, markdown, igraph, shinydashboard, RVCompare, reticulate
Depends: R (>= 2.10)
NeedsCompilation: yes
Packaged: 2023-12-04 10:18:31 UTC; diedi
Author: Hao Wang [aut] , Diederick Vermetten [cre, aut] , Carola Doerr [aut] , Thomas Baeck [aut]
Repository: CRAN
Date/Publication: 2023-12-04 14:30:07 UTC

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New package diseasemapping with initial version 2.0.5
Package: diseasemapping
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Version: 2.0.5
Date: 2023-12-01
Depends: R (>= 3.5.0)
Imports: stats, utils, terra, methods
Suggests: mgcv, mapmisc (>= 1.9.0), knitr
Enhances: INLA, XML
Additional_repositories: https://inla.r-inla-download.org/R/testing
Description: Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using 'INLA'. For details see Brown (2015) <doi:10.18637/jss.v063.i12>.
License: GPL
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-01 20:35:37 UTC; patrick
Author: Patrick Brown [aut, cre, cph], Lutong Zhou [aut]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Repository: CRAN
Date/Publication: 2023-12-04 14:30:04 UTC

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Sun, 03 Dec 2023

New package SSNbayes with initial version 0.0.3
Package: SSNbayes
Title: Bayesian Spatio-Temporal Analysis in Stream Networks
Version: 0.0.3
Depends: R (>= 4.0.0)
Imports: plyr, dplyr, rstan, sf, methods, SSN2
Description: Fits Bayesian spatio-temporal models and makes predictions on stream networks using the approach by Santos-Fernandez, Edgar, et al. (2022)."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, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/EdgarSantos-Fernandez/SSNbayes
BugReports: https://github.com/EdgarSantos-Fernandez/SSNbayes/issues
NeedsCompilation: no
Packaged: 2023-12-03 03:43:26 UTC; santosfe
Author: Edgar Santos-Fernandez [aut, cre, cph]
Maintainer: Edgar Santos-Fernandez <santosfe@qut.edu.au>
Repository: CRAN
Date/Publication: 2023-12-03 17:20:02 UTC

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Sat, 02 Dec 2023

New package FjordLight with initial version 0.7.0
Package: FjordLight
Version: 0.7.0
Date: 2023-11-30
Title: Available Light Within the Water Column and Seafloor of Arctic Fjords
Description: Satellite data collected between 2003 and 2022, in conjunction with gridded bathymetric data (50-150 m resolution), are used to estimate the irradiance reaching the bottom of a series of representative EU Arctic fjords. An Earth System Science Data (ESSD) manuscript, Schlegel et al. (2023, in review), that provides a detailed explanation of the methodology is currently in review.
Maintainer: Robert W. Schlegel <robert.schlegel@imev-mer.fr>
Depends: R (>= 3.3.0)
Imports: ncdf4, raster, curl
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/FACE-IT-project/FjordLight, http://obs-vlfr.fr/Pfunction/, www.obs-vlfr.fr, https://doi.pangaea.de/10.1594/PANGAEA.910898
NeedsCompilation: no
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Packaged: 2023-11-30 18:08:24 UTC; rws
Author: Bernard Gentili [aut], Jean-Pierre Gattuso [aut] , Robert W. Schlegel [aut, cre]
Repository: CRAN
Date/Publication: 2023-12-02 17:30:08 UTC

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Fri, 01 Dec 2023

New package survobj with initial version 1.0
Package: survobj
Title: Objects to Simulate Survival Times
Version: 1.0
Description: Generate objects that simulate survival times. Random values for the distributions are generated using the method described by Bender (2003) <https://epub.ub.uni-muenchen.de/id/eprint/1716>.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
Language: en-US
Imports: dplyr, tidyr, ggplot2, survival
VignetteBuilder: knitr
URL: https://johnaponte.github.io/survobj/, https://github.com/johnaponte/survobj
BugReports: https://github.com/johnaponte/survobj/issues
NeedsCompilation: no
Packaged: 2023-12-01 16:56:51 UTC; master
Author: Aponte John [aut, cre, cph]
Maintainer: Aponte John <john.j.aponte@gmail.com>
Repository: CRAN
Date/Publication: 2023-12-01 18:50:02 UTC

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New package rmerec with initial version 0.1.0
Package: rmerec
Title: MEREC - Method Based on the Removal Effects of Criteria
Version: 0.1.0
Maintainer: Lucas Sebastiao de Paula <lucas@ime.eb.br>
Description: Implementation of the MEthod based on the Removal Effects of Criteria - MEREC- a new objective weighting method for determining criteria weights for Multiple Criteria Decision Making problems, created by Mehdi Keshavarz-Ghorabaee (2021) <doi:10.3390/sym13040525>. Given a decision matrix, the function return the Merec´s weight vector and all intermediate matrix/vectors used to calculate it.
License: GPL (>= 3)
URL: https://github.com/lucassp/rmerec
Imports: utils
Language: en-US
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-12-01 17:24:34 UTC; lucas
Author: Lucas Sebastiao de Paula [aut, cre] , Bernardo Silva [ctb] , Marcos Santos [ctb]
Repository: CRAN
Date/Publication: 2023-12-01 19:00:02 UTC

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New package MCTrend with initial version 1.0.1
Package: MCTrend
Title: Monte Carlo Trend Analysis
Version: 1.0.1
Date: 2023-11-28
Description: Application of a test to rule out that trends detected in hydrological time series are explained exclusively by the randomness of the climate. Based on: Ricchetti, (2018) <https://repositorio.uchile.cl/handle/2250/168487>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: trend, reshape2, ggplot2, magrittr, lmomco, dplyr
Suggests: rmarkdown, knitr,
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2023-11-30 23:01:27 UTC; CLAA300697
Author: Alonso Arriagada [aut, cre]
Maintainer: Alonso Arriagada <alonso.arriagada@usach.cl>
Repository: CRAN
Date/Publication: 2023-12-01 14:40:03 UTC

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New package enmpa with initial version 0.1.5
Package: enmpa
Title: Ecological Niche Modeling using Presence-Absence Data
Version: 0.1.5
Maintainer: Luis F. Arias-Giraldo <lfarias.giraldo@gmail.com>
Date: 2023-11-30
Description: A set of tools to perform Ecological Niche Modeling with presence-absence data. It includes algorithms for data partitioning, model fitting, calibration, evaluation, selection, and prediction. Other functions help to explore signals of ecological niche using univariate and multivariate analyses, and model features such as variable response curves and variable importance. Unique characteristics of this package are the ability to exclude models with concave quadratic responses, and the option to clamp model predictions to specific variables. These tools are implemented following principles proposed in Cobos et al., (2022) <doi:10.17161/bi.v17i.15985>, Cobos et al., (2019) <doi:10.7717/peerj.6281>, and Peterson et al., (2008) <doi:10.1016/j.ecolmodel.2007.11.008>.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/Luisagi/enmpa
BugReports: https://github.com/Luisagi/enmpa/issues
Imports: doSNOW, ellipse, foreach, graphics, methods, mgcv, parallel, Rcpp, snow, stats, terra, utils, vegan
LazyData: true
Depends: R (>= 3.5.0)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2023-12-01 08:27:52 UTC; luisagi
Author: Luis F. Arias-Giraldo [aut, cre] , Marlon E. Cobos [aut] , A. Townsend Peterson [aut]
Repository: CRAN
Date/Publication: 2023-12-01 15:00:02 UTC

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New package acro with initial version 0.1.1
Package: acro
Title: A Tool for Automating the Statistical Disclosure Control of Research Outputs
Version: 0.1.1
Maintainer: Jim Smith <James.Smith@uwe.ac.uk>
Description: Assists researchers and output checkers by distinguishing between research output that is safe to publish, output that requires further analysis, and output that cannot be published because of substantial disclosure risk. A paper about the tool was presented at The United Nations Economic Commission for Europe Expert Meeting on Statistical Data Confidentiality <https://unece.org/statistics/events/SDC2023><https://uwe-repository.worktribe.com/output/11060964>.
License: MIT + file LICENSE
Encoding: UTF-8
SystemRequirements: Python (>= 3.8)
Imports: reticulate, admiraldev, png
Depends: R (>= 2.10)
LazyData: true
Suggests: spelling, testthat (>= 3.0.0)
Language: en-US
NeedsCompilation: no
Packaged: 2023-11-30 15:55:05 UTC; m-albashir
Author: Jim Smith [cre, ctb] , Maha Albashir [aut, ctb], Richard John Preen [ctb]
Repository: CRAN
Date/Publication: 2023-12-01 15:00:06 UTC

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Thu, 30 Nov 2023

New package TaylorRussell with initial version 1.2
Package: TaylorRussell
Version: 1.2
Date: 2023-11-30
Title: A Taylor-Russell Function for Multiple Predictors
Maintainer: Niels Waller <nwaller@umn.edu>
Depends: R (>= 3.5)
Imports: mvtnorm, shiny, shinyWidgets,
Description: The Taylor Russell model is a widely used method for assessing test validity in personnel selections tasks. The three functions in this package extend this model in a number of notable ways. TR() estimates test validity for a single selection test via the original Taylor Russell model. It extends this model by allowing users greater flexibility in argument choice. For example, users can specify any three of the four parameters (base rate, selection ratio, criterion validity, and positive predictive value) of the Taylor Russell model and estimate the remaining parameter (see the help file for examples). The TaylorRussell() function generalizes the original Taylor Russell model to allow for multiple selection tests (predictors). To our knowledge, this is the first generalization of the Taylor Russell model to allow for three or more selection tests (it is also the first to correctly handle models with two selection tests). TRDemo() is a 'shiny' program for illustrating the underlying l [...truncated...]
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Suggests: rmarkdown, knitr
Packaged: 2023-11-30 19:41:18 UTC; nielswaller
Author: Niels Waller [aut, cre], Ziyu Ren [ctb]
Repository: CRAN
Date/Publication: 2023-11-30 20:40:02 UTC

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New package calibmsm with initial version 1.0.0
Package: calibmsm
Title: Calibration Plots for the Transition Probabilities from Multistate Models
Version: 1.0.0
Description: Assess the calibration of an existing (i.e. previously developed) multistate model through calibration plots. Calibration is assessed using one of three methods. 1) Calibration methods for binary logistic regression models applied at a fixed time point in conjunction with inverse probability of censoring weights. 2) Calibration methods for multinomial logistic regression models applied at a fixed time point in conjunction with inverse probability of censoring weights. 3) Pseudo-values estimated using the Aalen-Johansen estimator of observed risk. All methods are applied in conjunction with landmarking when required. These calibration plots evaluate the calibration (in a validation cohort of interest) of the transition probabilities estimated from an existing multistate model. While package development has focused on multistate models, calibration plots can be produced for any model which utilises information post baseline to update predictions (e.g. dynamic models); competing risks mod [...truncated...]
License: MIT + file LICENSE
Encoding: UTF-8
Imports: boot, dplyr, ggplot2, ggpubr, Hmisc, magrittr, mstate, rms, stats, survival, tidyr, VGAM
Depends: R (>= 2.10)
LazyData: true
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://alexpate30.github.io/calibmsm/
NeedsCompilation: no
Packaged: 2023-11-30 11:37:05 UTC; mbrxsap3
Author: Alexander Pate [aut, cre, cph] , Glen P Martin [fnd, rev]
Maintainer: Alexander Pate <alexander.pate@manchester.ac.uk>
Repository: CRAN
Date/Publication: 2023-11-30 19:50:02 UTC

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New package ADTSA with initial version 1.0
Package: ADTSA
Title: Time Series Analysis
Version: 1.0
Date: 2023-11-16
Description: Analyzes autocorrelation and partial autocorrelation using surrogate methods and bootstrapping, and computes the acceleration constants for the vectorized moving block bootstrap provided by this package. It generates percentile, bias-corrected, and accelerated intervals and estimates partial autocorrelations using Durbin-Levinson. This package calculates the autocorrelation power spectrum, computes cross-correlations between two time series, computes bandwidth for any time series, and performs autocorrelation frequency analysis.
License: GPL-3
Author: Hossein Hassani [aut], Masoud Yarmohammadi [aut], Mohammad Reza Yeganegi [aut], Leila Marvian Mashhad [aut, cre]
Maintainer: Leila Marvian Mashhad <Leila.marveian@gmail.com>
NeedsCompilation: no
Packaged: 2023-11-30 12:31:35 UTC; ne_da
Repository: CRAN
Date/Publication: 2023-11-30 17:20:02 UTC

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New package mgwrsar with initial version 1.0.5
Package: mgwrsar
Title: GWR and MGWR with Spatial Autocorrelation
Version: 1.0.5
Date: 2023-11-28
Author: Ghislain Geniaux and Davide Martinetti
Maintainer: Ghislain Geniaux <ghislain.geniaux@inrae.fr>
Description: Functions for computing (Mixed) Geographically Weighted Regression with spatial autocorrelation, Geniaux and Martinetti (2017) <doi:10.1016/j.regsciurbeco.2017.04.001>.
License: GPL (>= 2)
Depends: R (>= 3.5.0), Rcpp, sp, leaflet, Matrix
Imports: ggplot2, sf, knitr, spgwr, methods, doParallel, foreach, htmltools, nabor, mapview, microbenchmark, rlang, dplyr, gridExtra, grid, mboost, mgcv, caret
VignetteBuilder: knitr
LinkingTo: RcppEigen, Rcpp
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2023-11-30 13:14:49 UTC; geniaux
Repository: CRAN
Date/Publication: 2023-11-30 15:00:02 UTC

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New package scGOclust with initial version 0.2.0
Package: scGOclust
Title: Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq
Version: 0.2.0
Description: Traditional methods for analyzing single cell RNA-seq datasets focus solely on gene expression, but this package introduces a novel approach that goes beyond this limitation. Using Gene Ontology terms as features, the package allows for the functional profile of cell populations, and comparison within and between datasets from the same or different species. Our approach enables the discovery of previously unrecognized functional similarities and differences between cell types and has demonstrated success in identifying cell types' functional correspondence even between evolutionarily distant species.
URL: https://github.com/Papatheodorou-Group/scGOclust
BugReports: https://github.com/Papatheodorou-Group/scGOclust/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
LazyDataCompression: bzip2
Imports: limma, Seurat(>= 5.0.0), biomaRt, dplyr, magrittr, stats, tibble, tidyr, Matrix, utils, networkD3, slanter
Suggests: knitr, devtools, pheatmap, rmarkdown, httr
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2023-11-27 09:37:33 UTC; ysong
Author: Yuyao Song [aut, cre, ctb], Irene Papatheodorou [aut, ths]
Maintainer: Yuyao Song <ysong@ebi.ac.uk>
Repository: CRAN
Date/Publication: 2023-11-30 10:30:02 UTC

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New package kcmeans with initial version 0.1.0
Package: kcmeans
Title: Conditional Expectation Function Estimation with K-Conditional-Means
Version: 0.1.0
Date: 2023-11-28
Description: Implementation of the KCMeans regression estimator studied by Wiemann (2023) <arXiv:2311.17021> for expectation function estimation conditional on categorical variables. Computation leverages the unconditional KMeans implementation in one dimension using dynamic programming algorithm of Wang and Song (2011) <doi:10.32614/RJ-2011-015>, allowing for global solutions in time polynomial in the number of observed categories.
License: GPL (>= 3)
URL: https://github.com/thomaswiemann/kcmeans
BugReports: https://github.com/thomaswiemann/kcmeans/issues
Encoding: UTF-8
Depends: R (>= 3.6)
Imports: stats, Ckmeans.1d.dp, MASS, Matrix
Suggests: testthat (>= 3.0.0), covr, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-30 08:37:07 UTC; thomas
Author: Thomas Wiemann [aut, cre]
Maintainer: Thomas Wiemann <wiemann@uchicago.edu>
Repository: CRAN
Date/Publication: 2023-11-30 10:50:02 UTC

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New package iperform with initial version 0.0.1
Package: iperform
Title: Time Series Performance
Version: 0.0.1
Description: A tool to calculate the performance of a time series in a specific date or period. It is more intended for data analysis in the fields of finance, banking, telecommunications or operational marketing.
License: GPL-3
Encoding: UTF-8
Suggests: ggplot2, knitr, rmarkdown, testthat (>= 3.0.0)
Imports: lubridate, matrixStats
Language: en, fr
VignetteBuilder: knitr
LazyData: true
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2023-11-29 19:31:41 UTC; patrickilunga
Author: Patrick Ilunga [aut, cre], Ilunga Buabua Patrick [cph]
Maintainer: Patrick Ilunga <patrick.ilunga@unikin.ac.cd>
Repository: CRAN
Date/Publication: 2023-11-30 10:20:02 UTC

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New package flevr with initial version 0.0.4
Package: flevr
Title: Flexible, Ensemble-Based Variable Selection with Potentially Missing Data
Version: 0.0.4
Description: Perform variable selection in settings with possibly missing data based on extrinsic (algorithm-specific) and intrinsic (population-level) variable importance. Uses a Super Learner ensemble to estimate the underlying prediction functions that give rise to estimates of variable importance. For more information about the methods, please see Williamson and Huang (2023+) <arXiv:2202.12989>.
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1.0)
Imports: SuperLearner, dplyr, magrittr, tibble, caret, mvtnorm, kernlab, rlang, ranger
Suggests: vimp, stabs, testthat, knitr, rmarkdown, mice, xgboost, glmnet, polspline
URL: https://github.com/bdwilliamson/flevr
BugReports: https://github.com/bdwilliamson/flevr/issues
VignetteBuilder: knitr
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2023-11-29 19:23:19 UTC; L107067
Author: Brian D. Williamson [aut, cre]
Maintainer: Brian D. Williamson <brian.d.williamson@kp.org>
Repository: CRAN
Date/Publication: 2023-11-30 10:20:05 UTC

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New package gatoRs with initial version 1.0.1
Package: gatoRs
Title: Geographic and Taxonomic Occurrence R-Based Scrubbing
Version: 1.0.1
Date: 2023-11-29
Imports: ridigbio, dplyr (>= 1.1.0), rgbif, magrittr, CoordinateCleaner (>= 3.0.1), terra, spThin, stringr, leaflet, parsedate, spatstat.geom
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
Suggests: knitr, rmarkdown, testthat
License: GPL-3
Description: Streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).
Maintainer: Natalie N. Patten <natalienpatten@gmail.com>
URL: https://nataliepatten.github.io/gatoRs/, https://github.com/nataliepatten/gatoRs
BugReports: https://github.com/nataliepatten/gatoRs/issues
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2023-11-29 20:07:42 UTC; Natalie Patten
Author: Natalie N. Patten [aut, cre] , Michelle L. Gaynor [aut] , Douglas E. Soltis [ctb] , Pamela S. Soltis [ctb]
Repository: CRAN
Date/Publication: 2023-11-30 10:00:02 UTC

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New package historicalborrowlong with initial version 0.0.8
Package: historicalborrowlong
Title: Longitudinal Bayesian Historical Borrowing Models
Description: Historical borrowing in clinical trials can improve precision and operating characteristics. This package supports a longitudinal hierarchical model to borrow historical control data from other studies to better characterize the control response of the current study. It also quantifies the amount of borrowing through longitudinal benchmark models (independent and pooled). The hierarchical model approach to historical borrowing is discussed by Viele et al. (2013) <doi:10.1002/pst.1589>.
Version: 0.0.8
License: MIT + file LICENSE
URL: https://wlandau.github.io/historicalborrowlong/, https://github.com/wlandau/historicalborrowlong
BugReports: https://github.com/wlandau/historicalborrowlong/issues
Depends: R (>= 4.0.0)
Imports: clustermq, dplyr, ggplot2, MASS, Matrix, methods, posterior, Rcpp, RcppParallel, rlang, rstan (>= 2.26.0), rstantools, stats, tibble, tidyr, tidyselect, trialr, utils, withr, zoo
Suggests: knitr, markdown, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
Biarch: true
LinkingTo: BH, Rcpp, RcppEigen, RcppParallel, rstan (>= 2.26.0), StanHeaders (>= 2.26.0)
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2023-11-29 18:36:55 UTC; c240390
Author: William Michael Landau [aut, cre] , Albert Man [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-30 08:00:07 UTC

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New package geofacet with initial version 0.2.1
Package: geofacet
Title: 'ggplot2' Faceting Utilities for Geographical Data
Version: 0.2.1
Description: Provides geographical faceting functionality for 'ggplot2'. Geographical faceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.
Depends: R (>= 3.2)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2 (>= 3.2.1), gtable, graphics, rnaturalearth, sp, ggrepel, imguR, gridExtra, geogrid, methods, rlang
Suggests: sf, testthat, covr, lintr, knitr, rmarkdown
URL: https://github.com/hafen/geofacet
BugReports: https://github.com/hafen/geofacet/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-29 19:10:50 UTC; rhafen
Author: Ryan Hafen [aut, cre], Barret Schloerke [ctb]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-30 08:00:11 UTC

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Wed, 29 Nov 2023

New package HadIBDs with initial version 1.0.0
Package: HadIBDs
Title: Incomplete Block Designs using Hadamard Matrix (HadIBDs)
Version: 1.0.0
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Description: Hadamard matrix based statistical designs are of immense importance as the resultant designs carry various desirable characterizing properties. Constructing Partially Balanced Incomplete Block Designs (PBIBds) using Kronecker product of incidence matrices of Balanced Incomplete Block (BIB) and Partially Balanced Incomplete Block (PBIB) designs is much evident from literature. Here, we have constructed Incomplete Block Designs (IBDs) based on Hadamard matrices and Kronecker product of Hadamard matrices.
Suggests: MASS, utils
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-29 15:39:53 UTC; Ashutosh
Author: Mohd Harun [aut, ctb], Cini Varghese [aut, ctb], Ashutosh Dalal [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-29 19:10:06 UTC

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New package evapoRe with initial version 1.0.0
Package: evapoRe
Title: Evapotranspiration R Recipes
Version: 1.0.0
Description: An R-based application for exploratory data analysis of global EvapoTranspiration (ET) datasets. 'evapoRe' enables users to download, validate, visualize, and analyze multi-source ET data across various spatio-temporal scales. Also, the package offers calculation methods for estimating potential ET (PET), including temperature-based approaches described in : Oudin et al., (2005) <doi:10.1016/j.jhydrol.2004.08.026>. 'evapoRe' supports hydrological modeling, climate studies, agricultural research, and other data-driven fields by facilitating access to ET data and offering powerful analysis capabilities. Users can seamlessly integrate the package into their research applications and explore diverse ET data at different resolutions.
Depends: R (>= 4.0.0), pRecipe
Imports: methods, parallel, utils, data.table, doParallel, foreach, lubridate, raster
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/AkbarR1184/evapoRe
SystemRequirements: PROJ (>= 6, https://proj.org/download.html), GDAL (>= 3, https://gdal.org/download.html), NetCDF(>= 4, https://www.unidata.ucar.edu/software/netcdf/).
Suggests: rmarkdown, ggpubr, knitr, spelling, kableExtra, tibble, testthat (>= 3.0.0)
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-29 14:22:08 UTC; Admin
Author: Akbar Rahmati Ziveh [aut, cre] , Mijael Rodrigo Vargas Godoy [aut] , Vishal Thakur [ctb] , Yannis Markonis [aut, ths]
Maintainer: Akbar Rahmati Ziveh <rahmati_ziveh@fzp.czu.cz>
Repository: CRAN
Date/Publication: 2023-11-29 19:10:02 UTC

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New package pexm with initial version 1.1.3
Package: pexm
Title: Loading a JAGS Module for the Piecewise Exponential Distribution
Version: 1.1.3
Description: Load the Just Another Gibbs Sampling (JAGS) module 'pexm'. The module provides the tools to work with the Piecewise Exponential (PE) distribution in a Bayesian model with the corresponding Markov Chain Monte Carlo algorithm (Gibbs Sampling) implemented via JAGS. Details about the module implementation can be found in Mayrink et al. (2021) <doi:10.18637/jss.v100.i08>.
Depends: coda, rjags
Imports: msm
Encoding: UTF-8
License: GPL-3
URL: https://github.com/vdinizm/pexm
BugReports: https://github.com/vdinizm/pexm/issues
NeedsCompilation: yes
Suggests: testthat
Packaged: 2023-11-29 12:41:45 UTC; vinicius
Author: Vinicius Mayrink [aut, cre] , Joao Duarte [aut], Fabio Demarqui [ctb]
Maintainer: Vinicius Mayrink <vdinizm@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-29 18:50:02 UTC

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New package nexus with initial version 0.1.0
Package: nexus
Title: Sourcing Archaeological Materials by Chemical Composition
Version: 0.1.0
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Description: Exploration and analysis of compositional data in the framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package provides tools for chemical fingerprinting and source tracking of ancient materials.
License: GPL (>= 3)
URL: https://packages.tesselle.org/nexus/, https://github.com/tesselle/nexus
BugReports: https://github.com/tesselle/nexus/issues
Depends: R (>= 3.5)
Imports: arkhe (>= 1.4.0), dimensio (>= 0.5.0), graphics, grDevices, isopleuros (>= 1.0.0), methods, MASS, stats, utils
Suggests: cluster, folio, igraph, knitr, rmarkdown, rsvg, svglite, tinysnapshot, tinytest
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-29 08:32:56 UTC; nicolas
Author: Nicolas Frerebeau [aut, cre] , Anne Philippe [aut] , Brice Lebrun [ctb] , Universite Bordeaux Montaigne [fnd], CNRS [fnd]
Repository: CRAN
Date/Publication: 2023-11-29 18:40:02 UTC

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New package KINSIMU with initial version 0.1.1
Package: KINSIMU
Title: Panel Evaluation in Forensic Kinship Analysis
Version: 0.1.1
Date: 2023-11-20
Maintainer: Guanju Ma <mache124@126.com>
Description: Evaluate specific panels in different aspects: i) Simulation tools related to pedigree researches; ii) calculation for systemic effectiveness indicators, such as probability of exclusion (PE).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: utils
NeedsCompilation: no
Packaged: 2023-11-29 14:13:46 UTC; Ma Guanju
Author: Guanju Ma [aut, cre], Shujin Li [ctb]
Repository: CRAN
Date/Publication: 2023-11-29 19:00:06 UTC

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New package bexy with initial version 0.1.2
Package: bexy
Title: Visualize and Parse the Output of 'BeXY'
Version: 0.1.2
Maintainer: Madleina Caduff <madleina.caduff@unifr.ch>
Description: Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (<https://bitbucket.org/wegmannlab/bexy>), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.
License: GPL-2
Encoding: UTF-8
Imports: TeachingDemos,Ternary
NeedsCompilation: no
Packaged: 2023-11-29 13:17:00 UTC; madleina
Author: Madleina Caduff [aut, cre], Raphael Eckel [ctb], Christoph Leuenberger [ctb], Daniel Wegmann [aut]
Repository: CRAN
Date/Publication: 2023-11-29 19:00:02 UTC

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New package dsims with initial version 1.0.4
Package: dsims
Depends: dssd (>= 0.2.2)
Imports: mrds, Distance, sf, ggplot2, purrr, dplyr, mgcv, methods, rstudioapi, gridExtra, rlang
Suggests: testthat, parallel, pbapply, knitr, lwgeom, rmarkdown
VignetteBuilder: knitr
Title: Distance Sampling Simulations
Version: 1.0.4
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Description: Performs distance sampling simulations. 'dsims' repeatedly generates instances of a user defined population within a given survey region. It then generates realisations of a survey design and simulates the detection process. The data are then analysed so that the results can be compared for accuracy and precision across all replications. This process allows users to optimise survey designs for their specific set of survey conditions. The effects of uncertainty in population distribution or parameters can be investigated under a number of simulations so that users can be confident that they have achieved a robust survey design before deploying vessels into the field. The distance sampling designs used in this package from 'dssd' are detailed in Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008, ISBN-13: 978-0199225873). General distance sampling methods are detailed in Introduction to Distance Sampling: Estimating Abundance of Biological Populations, Buckland et. al. (2004 [...truncated...]
License: GPL (>= 2)
Language: en-GB
URL: https://github.com/DistanceDevelopment/dsims
BugReports: https://github.com/DistanceDevelopment/dsims/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-24 13:46:36 UTC; lhm
Author: Laura Marshall [aut, cre], Thomas Len [ctb]
Repository: CRAN
Date/Publication: 2023-11-29 14:10:02 UTC

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New package ivo.table with initial version 0.1
Package: ivo.table
Title: Pretty Contingency Tables and Frequency Tables
Version: 0.1
Description: Nicely formatted frequency tables and contingency tables (cross-tables), that can easily be exported to HTML or 'Office' documents, including 'Excel'. Designed to work with pipes.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, flextable, openxlsx, checkmate, officer, purrr, stringr, tidyr
NeedsCompilation: no
Packaged: 2023-11-29 07:53:41 UTC; mans
Author: Mans Thulin [aut, cre], Kajsa Grind [aut], Stefan Furne [aut]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Repository: CRAN
Date/Publication: 2023-11-29 14:00:02 UTC

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New package HDMAADMM with initial version 0.0.1
Package: HDMAADMM
Title: ADMM for High-Dimensional Mediation Models
Version: 0.0.1
Date: 2023-12-01
Maintainer: Pei-Shan Yen <peishan0824@gmail.com>
Description: We use the Alternating Direction Method of Multipliers (ADMM) for parameter estimation in high-dimensional, single-modality mediation models. To improve the sensitivity and specificity of estimated mediation effects, we offer the sure independence screening (SIS) function for dimension reduction. The available penalty options include Lasso, Elastic Net, Pathway Lasso, and Network-constrained Penalty. The methods employed in the package are based on Boyd, S., Parikh, N., Chu, E., Peleato, B., & Eckstein, J. (2011). <doi:10.1561/2200000016>, Fan, J., & Lv, J. (2008) <doi:10.1111/j.1467-9868.2008.00674.x>, Li, C., & Li, H. (2008) <doi:10.1093/bioinformatics/btn081>, Tibshirani, R. (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>, Zhao, Y., & Luo, X. (2022) <doi:10.4310/21-sii673>, and Zou, H., & Hastie, T. (2005) <doi:10.1111/j.1467-9868.2005.00503.x>.
License: MIT + file LICENSE
Depends: R (>= 4.0.0)
Imports: Rcpp (>= 1.0.0), dqrng, RcppEigen
LinkingTo: Rcpp, RcppEigen
Suggests: roxygen2
Encoding: UTF-8
URL: https://github.com/psyen0824/HDMAADMM
BugReports: https://github.com/psyen0824/HDMAADMM/issues
NeedsCompilation: yes
Packaged: 2023-11-29 01:24:52 UTC; peish
Author: Pei-Shan Yen [aut, cre] , Ching-Chuan Chen [aut]
Repository: CRAN
Date/Publication: 2023-11-29 14:00:16 UTC

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New package countts with initial version 0.1.0
Package: countts
Title: Thomson Sampling for Zero-Inflated Count Outcomes
Version: 0.1.0
Description: A specialized tool is designed for assessing contextual bandit algorithms, particularly those aimed at handling overdispersed and zero-inflated count data. It offers a simulated testing environment that includes various models like Poisson, Overdispersed Poisson, Zero-inflated Poisson, and Zero-inflated Overdispersed Poisson. The package is capable of executing five specific algorithms: Linear Thompson sampling with log transformation on the outcome, Thompson sampling Poisson, Thompson sampling Negative Binomial, Thompson sampling Zero-inflated Poisson, and Thompson sampling Zero-inflated Negative Binomial. Additionally, it can generate regret plots to evaluate the performance of contextual bandit algorithms. This package is based on the algorithms by Liu et al. (2023) <arXiv:2311.14359>.
Maintainer: Tanujit Chakraborty <tanujitisi@gmail.com>
License: GPL (>= 2)
Encoding: UTF-8
Imports: MASS, parallel, fastDummies, matrixStats, ggplot2, stats
NeedsCompilation: no
Packaged: 2023-11-29 04:15:35 UTC; mad-s
Author: Xueqing Liu [aut], Nina Deliu [aut], Tanujit Chakraborty [aut, cre, cph] , Lauren Bell [aut], Bibhas Chakraborty [aut]
Repository: CRAN
Date/Publication: 2023-11-29 14:00:10 UTC

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New package admtools with initial version 0.0.1
Package: admtools
Title: Estimate and Manipulate Age-Depth Models
Version: 0.0.1
Description: Estimate age-depth models from stratigraphic and sedimentological data, and transform data between the time and stratigraphic domain.
URL: https://github.com/MindTheGap-ERC/admtools
BugReports: https://github.com/MindTheGap-ERC/admtools/issues
License: Apache License (== 2.0)
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-29 07:08:12 UTC; hohma004
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Repository: CRAN
Date/Publication: 2023-11-29 14:00:13 UTC

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Tue, 28 Nov 2023

New package picClip with initial version 0.1.0
Package: picClip
Title: Paste Box Input for 'Shiny'
Version: 0.1.0
Author: Matt Deppe
Maintainer: Matt Deppe <deppemj@gmail.com>
Description: Provides a 'Shiny' input widget, pasteBoxInput, that allows users to paste images directly into a 'Shiny' application. The pasted images are captured as Base64 encoded strings and can be used within the application for various purposes, such as display or further processing. This package is particularly useful for applications that require easy and quick image uploads without the need for traditional file selection dialog boxes.
License: GPL-3
URL: https://github.com/deppemj/picClip
Encoding: UTF-8
Imports: shiny, base64enc, stringr, htmltools, testthat
NeedsCompilation: no
Packaged: 2023-11-28 17:27:17 UTC; deppe
Repository: CRAN
Date/Publication: 2023-11-28 18:10:05 UTC

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New package phyloraster with initial version 2.0.1
Package: phyloraster
Title: Evolutionary Diversity Metrics for Raster Data
Version: 2.0.1
Description: Phylogenetic Diversity (PD, Faith 1992), Evolutionary Distinctiveness (ED, Isaac et al. 2007), Phylogenetic Endemism (PE, Rosauer et al. 2009; Laffan et al. 2016), and Weighted Endemism (WE, Laffan et al. 2016) for presence-absence raster. Faith, D. P. (1992) <doi:10.1016/0006-3207(92)91201-3> Isaac, N. J. et al. (2007) <doi:10.1371/journal.pone.0000296> Laffan, S. W. et al. (2016) <doi:10.1111/2041-210X.12513> Rosauer, D. et al. (2009) <doi:10.1111/j.1365-294X.2009.04311.x>.
License: GPL (>= 3)
URL: https://gabferreira.github.io/phyloraster/
Depends: R (>= 2.10)
Imports: ape, methods, phylobase, SESraster, stats, terra
Suggests: knitr, maps, rmarkdown, testthat (>= 2.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-27 22:18:16 UTC; gabriela
Author: Gabriela Alves-Ferreira [aut, cre, cph] , Flavio M. M. Mota [aut] , Neander Marcel Heming [aut]
Maintainer: Gabriela Alves-Ferreira <gabriela-alves77@hotmail.com>
Repository: CRAN
Date/Publication: 2023-11-28 17:40:05 UTC

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New package nuggets with initial version 1.0.0
Package: nuggets
Title: Extensible Data Pattern Searching Framework
Version: 1.0.0
Maintainer: Michal Burda <michal.burda@osu.cz>
Description: Extensible framework for subgroup discovery (Atzmueller (2015) <doi:10.1002/widm.1144>), contrast patterns (Chen (2022) <doi:10.48550/arXiv.2209.13556>), emerging patterns (Dong (1999) <doi:10.1145/312129.312191>) and association rules (Agrawal (1994) <https://www.vldb.org/conf/1994/P487.PDF>). Both crisp (binary) and fuzzy data are supported. It generates conditions in the form of elementary conjunctions, evaluates them on a dataset and checks the induced sub-data for interesting statistical properties. Currently, the package searches for implicative association rules and conditional correlations (Hájek (1978) <doi:10.1007/978-3-642-66943-9>). A user-defined function may be defined to evaluate on each generated condition to search for custom patterns.
License: GPL (>= 3)
Encoding: UTF-8
Language: en-US
Imports: cli, methods, Rcpp, rlang, stats, tibble, tidyr, tidyselect
LinkingTo: Rcpp, testthat
SystemRequirements: C++17
Suggests: testthat (>= 3.0.0), xml2
NeedsCompilation: yes
Packaged: 2023-11-28 05:48:07 UTC; michal
Author: Michal Burda [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-28 17:50:02 UTC

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New package causalOT with initial version 1.0
Package: causalOT
Title: Optimal Transport Weights for Causal Inference
Version: 1.0
Date: 2023-11-23
Author: Eric Dunipace [aut, cre]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Description: Uses optimal transport distances to find probabilistic matching estimators for causal inference. These methods are described in Dunipace, Eric (2021) <arXiv:2109.01991>. The package will build the weights, estimate treatment effects, and calculate confidence intervals via the methods described in the paper. The package also supports several other methods as described in the help files.
License: GPL (== 3.0)
Imports: CBPS, ggplot2, lbfgsb3c, loo, Matrix (>= 1.5-0), matrixStats, methods, osqp, R6 (>= 2.4.1), Rcpp (>= 1.0.3), rlang, sandwich, torch, utils
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), torch
Suggests: data.table (>= 1.12.8), testthat (>= 2.1.0), knitr, reticulate, rkeops, rmarkdown, V8, withr
Biarch: true
Depends: R (>= 3.5.0)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-11-27 22:18:06 UTC; eifer
Repository: CRAN
Date/Publication: 2023-11-28 17:50:18 UTC

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New package BiostatsUHNplus with initial version 0.0.8
Package: BiostatsUHNplus
Title: Nested Data Summary and Adverse Events
Version: 0.0.8
Description: Miscellaneous code snippets and functions with pipes and multiple package dependencies used for summarizing nested data and adverse events.
License: MIT + file LICENSE
Depends: R (>= 4.2)
Imports: afex, cowplot, dplyr, forcats, ggh4x, ggplot2, ggstance, lifecycle, MCMCglmm, modeest, openxlsx, plyr, purrr, reportRmd, rlang, rstatix, stats, stringr, tibble, utils
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-27 20:56:58 UTC; t109810uhn
Author: Lisa Avery [aut] , Zeynep Baskurt [aut], Osvaldo Espin-Garcia [aut], Katrina Hueniken [aut], Katherine Lajkosz [aut] , Xuan Li [aut], Tyler Pittman [cre, aut] , Anna Santiago [aut] , Jessica Weiss [aut], Wei Xu [aut]
Maintainer: Tyler Pittman <tyler.pittman@uhn.ca>
Repository: CRAN
Date/Publication: 2023-11-28 17:30:09 UTC

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New package ARDECO with initial version 0.1.0
Package: ARDECO
Title: 'ARDECO' Dataset
Version: 0.1.0
Author: European Commission
Maintainer: European Commission <carmelo.attardo@ec.europa.eu>
Description: A set of functions to access the 'ARDECO' (Annual Regional Database of the European Commission) data directly from the official ARDECO public repository through the exploitation of the 'ARDECO' APIs. The APIs are completely transparent to the user and the provided functions provide a direct access to the 'ARDECO' data. The 'ARDECO' database is a collection of variables related to demography, employment, labour market, domestic product, capital formation. Each variable can be exposed in one or more units of measure as well as refers to total values plus economic sectors. The description of the 'ARDECO' database can be found at the following URL <https://urban.jrc.ec.europa.eu/ardeco>.
Depends: R (>= 4.2.0),
Imports: httr, ghql, rjstat, jsonlite, dplyr
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-28 09:37:35 UTC; attar
Repository: CRAN
Date/Publication: 2023-11-28 17:50:23 UTC

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New package aloom with initial version 0.1.0
Package: aloom
Title: All Leave-One-Out Models
Version: 0.1.0
Description: Creates all leave-one-out models and produces predictions for test samples.
Imports: glmnet, randomForest, stats
License: GPL-2
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-11-27 21:45:59 UTC; damjan
Author: Damjan Krstajic [aut, cre]
Maintainer: Damjan Krstajic <Damjan.Krstajic@rcc.org.rs>
Repository: CRAN
Date/Publication: 2023-11-28 17:40:08 UTC

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New package rlibkriging with initial version 0.8-0.1
Package: rlibkriging
Title: Kriging Models using the 'libKriging' Library
Version: 0.8-0.1
Date: 2023-11-21
Maintainer: Yann Richet <yann.richet@irsn.fr>
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should provide most standard Kriging / Gaussian process regression features (like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages). 'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson, 'lbfgsb_cpp' is a 'C++' port around 'lbfgsb' library (BSD-3 license) by Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization, and HDF5 features coming from HDF Group (see HDF5_LICENSE file) possibly provided by Rhdf5lib by Mike Smith (Artistic-2.0 license).
License: Apache License (>= 2)
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 4.2)
Imports: Rcpp (>= 0.12.11), methods, DiceKriging
Suggests: testthat, RobustGaSP, utils, DiceDesign, foreach
SystemRequirements: GNU make, cmake (>= 3.2.0), gcc, gfortran, HDF5
URL: https://github.com/libKriging
NeedsCompilation: yes
Packaged: 2023-11-21 20:42:14 UTC; richet
Author: Yann Richet [aut, cre] , Pascal Have [aut], Yves Deville [aut], Conrad Sanderson [ctb], Ciyou Zhu [ctb], Richard Byrd [ctb], Jorge Nocedal [ctb], Jose Luis Morales [ctb], Mike Smith [ctb]
Repository: CRAN
Date/Publication: 2023-11-28 12:10:03 UTC

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Mon, 27 Nov 2023

New package FDRsamplesize2 with initial version 0.1.0
Package: FDRsamplesize2
Title: Computing Power and Sample Size for the False Discovery Rate in Multiple Applications
Version: 0.1.0
Maintainer: Yonghui Ni <Yonghui.Ni@STJUDE.ORG>
Description: Defines a collection of functions to compute average power and sample size for studies that use the false discovery rate as the final measure of statistical significance. A three-rectangle approximation method of a p-value histogram is proposed to derive a formula to compute the statistical power for analyses that involve the FDR. The methodology paper of this package is under review.
Encoding: UTF-8
License: MIT + file LICENSE
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-11-27 17:49:21 UTC; yni54
Author: Yonghui Ni [aut, cre], Stanley Pounds [aut]
Repository: CRAN
Date/Publication: 2023-11-27 19:10:05 UTC

More information about FDRsamplesize2 at CRAN
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New package spatialising with initial version 0.6.0
Package: spatialising
Title: Ising Model for Spatial Data
Version: 0.6.0
Description: Performs simulations of binary spatial raster data using the Ising model (Ising (1925) <doi:10.1007/BF02980577>; Onsager (1944) <doi:10.1103/PhysRev.65.117>). It allows to set a few parameters that represent internal and external pressures, and the number of simulations (Stepinski and Nowosad (2023) <doi:10.1098/rsos.231005>).
License: MIT + file LICENSE
Encoding: UTF-8
Imports: comat, Rcpp, terra
URL: https://github.com/Nowosad/spatialising
BugReports: https://github.com/Nowosad/spatialising/issues
Suggests: covr, knitr, rmarkdown, optimization, testthat (>= 3.0.0)
Depends: R (>= 2.10)
LazyData: false
LinkingTo: Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-11-26 20:07:45 UTC; jn
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-27 17:10:02 UTC

More information about spatialising at CRAN
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New package rosmium with initial version 0.1.0
Package: rosmium
Title: Bindings for 'Osmium Tool'
Version: 0.1.0
Description: Allows one to use 'Osmium Tool' (<https://osmcode.org/osmium-tool/>) from R. 'Osmium' is a multipurpose command line tool that enables one to manipulate and analyze OpenStreetMap files through several different commands. Currently, this package does not aim to offer functions that cover the entire 'Osmium' API, instead making available functions that wrap only a very limited set of its features.
License: MIT + file LICENSE
URL: https://ipeagit.github.io/rosmium/, https://github.com/ipeaGIT/rosmium
BugReports: https://github.com/ipeaGIT/rosmium/issues
Imports: checkmate, geojsonsf, processx, sf, utils
Suggests: ggplot2, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-27 14:53:17 UTC; dhersz
Author: Daniel Herszenhut [aut, cre]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-27 17:30:02 UTC

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New package rnndescent with initial version 0.1.1
Package: rnndescent
Title: Nearest Neighbor Descent Method for Approximate Nearest Neighbors
Version: 0.1.1
Description: The Nearest Neighbor Descent method for finding approximate nearest neighbors by Dong and co-workers (2010) <doi:10.1145/1963405.1963487>. Based on the 'Python' package 'PyNNDescent' <https://github.com/lmcinnes/pynndescent>.
License: GPL (>= 3)
URL: https://jlmelville.github.io/rnndescent/, https://github.com/jlmelville/rnndescent
BugReports: https://github.com/jlmelville/rnndescent/issues
Imports: dqrng, Matrix (>= 1.3-0), methods, Rcpp
Suggests: covr, knitr, rmarkdown, testthat
LinkingTo: BH, dqrng, Rcpp, sitmo
VignetteBuilder: knitr
Encoding: UTF-8
SystemRequirements: C++17
NeedsCompilation: yes
Packaged: 2023-11-26 15:46:05 UTC; jlmel
Author: James Melville [aut, cre, cph], Vitalie Spinu [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-27 17:10:05 UTC

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New package MJMbamlss with initial version 0.1.0
Package: MJMbamlss
Title: Multivariate Joint Models with 'bamlss'
Version: 0.1.0
Description: Multivariate joint models of longitudinal and time-to-event data based on functional principal components implemented with 'bamlss'. Implementation for Volkmann, Umlauf, Greven (2023) <arXiv:2311.06409>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5), mgcv, bamlss
LinkingTo: Rcpp, RcppEigen
Imports: stats, funData, statmod, mvtnorm, zoo, coda, gamm4, Matrix, refund, utils, fdapace, sparseFLMM, MFPCA, foreach
Suggests: testthat (>= 3.0.0), splines, tidyverse
NeedsCompilation: yes
Packaged: 2023-11-27 15:29:07 UTC; alex
Author: Nikolaus Umlauf [aut] , Alexander Volkmann [aut, cre]
Maintainer: Alexander Volkmann <alexander.volkmann@hu-berlin.de>
Repository: CRAN
Date/Publication: 2023-11-27 17:30:05 UTC

More information about MJMbamlss at CRAN
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New package dartR.captive with initial version 0.75
Package: dartR.captive
Title: Analysing 'SNP' Data to Support Captive Breeding
Version: 0.75
Date: 2023-11-27
Description: Functions are provided that facilitate the analysis of SNP (single nucleotide polymorphism) data to answer questions regarding captive breeding and relatedness between individuals. 'dartR.captive' is part of the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.
Encoding: UTF-8
Depends: R (>= 3.5), adegenet (>= 2.0.0), dartR.base, dartR.data
Imports: methods, utils, crayon, ggplot2, patchwork, stringr
Suggests: SIBER, gplots, fields, igraph, reshape2, rrBLUP, scales, spelling
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2023-11-27 01:11:27 UTC; s425824
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb], Eric Archer [ctb]
URL: https://green-striped-gecko.github.io/dartR/
BugReports: https://groups.google.com/g/dartr?pli=1
Language: en-US
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2023-11-27 17:10:09 UTC

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New package cwbtools with initial version 0.3.9
Package: cwbtools
Title: Tools to Create, Modify and Manage 'CWB' Corpora
Version: 0.3.9
Date: 2023-11-20
Description: The 'Corpus Workbench' ('CWB', <https://cwb.sourceforge.io/>) offers a classic and mature approach for working with large, linguistically and structurally annotated corpora. The 'CWB' is memory efficient and its design makes running queries fast, see Evert (2011) <https://eprints.lancs.ac.uk/id/eprint/62721>. The 'cwbtools' package offers pure 'R' tools to create indexed corpus files as well as high-level wrappers for the original 'C' implementation of 'CWB' as exposed by the 'RcppCWB' package (<https://CRAN.R-project.org/package=RcppCWB>). Additional functionality to add and modify annotations of corpora from within 'R' makes working with 'CWB' indexed corpora much more flexible and convenient. The 'cwbtools' package in combination with the 'R' packages 'RcppCWB' (<https://CRAN.R-project.org/package=RcppCWB>) and 'polmineR' (<https://CRAN.R-project.org/package=polmineR>) offers a lightweight infrastructure to support the combination of quantitative and qu [...truncated...]
Imports: data.table, R6, xml2, stringi, curl, RcppCWB (>= 0.5.2), pbapply, methods, tools, cli, jsonlite, httr, rstudioapi, zen4R (>= 0.9), lifecycle, fs
Suggests: tm (>= 0.7.3), knitr, markdown, tokenizers (>= 0.2.1), tidytext, SnowballC, janeaustenr, testthat, rmarkdown, aws.s3
VignetteBuilder: knitr
License: GPL-3
Language: en-US
Encoding: UTF-8
URL: https://github.com/PolMine/cwbtools
BugReports: https://github.com/PolMine/cwbtools/issues
NeedsCompilation: no
Packaged: 2023-11-27 14:56:14 UTC; andreasblatte
Author: Andreas Blaette [aut, cre], Christoph Leonhardt [aut]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Repository: CRAN
Date/Publication: 2023-11-27 15:30:05 UTC

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New package multipanelfigure with initial version 2.1.5
Package: multipanelfigure
Title: Infrastructure to Assemble Multi-Panel Figures (from Grobs)
Version: 2.1.5
Date: 2023-11-26
Author: Johannes Graumann [cre, aut], Richard Cotton [aut]
Maintainer: Johannes Graumann <johannes.graumann@uni-marburg.de>
Description: Tools to create a layout for figures made of multiple panels, and to fill the panels with base, 'lattice', 'ggplot2' and 'ComplexHeatmap' plots, grobs, as well as content from all image formats supported by 'ImageMagick' (accessed through 'magick').
Imports: assertive.base (>= 0.0-7), assertive.files (>= 0.0-2), assertive.numbers (>= 0.0-2), ggplot2 (>= 2.2.1), grid, gridGraphics (>= 0.3-0), gtable (>= 0.2.0), magick (>= 1.9), magrittr (>= 1.5), stats, stringi (>= 1.2.3), utils
Suggests: ComplexHeatmap (>= 1.17.1), grDevices, lattice (>= 0.20-35), roxygen2 (>= 6.0.1), VennDiagram (>= 1.6.20), knitr, rmarkdown, markdown
License: GPL (>= 3)
LazyData: TRUE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-26 21:17:27 UTC; rstudio
Repository: CRAN
Date/Publication: 2023-11-27 14:30:02 UTC

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New package flippant with initial version 1.5.4
Package: flippant
Title: Dithionite Scramblase Assay Analysis
Description: The lipid scrambling activity of protein extracts and purified scramblases is often determined using a fluorescence-based assay involving many manual steps. flippant offers an integrated solution for the analysis and publication-grade graphical presentation of dithionite scramblase assays, as well as a platform for review, dissemination and extension of the strategies it employs. The package's name derives from a play on the fact that lipid scrambling is also sometimes referred to as 'flipping'. The package is originally published as Cotton, R.J., Ploier, B., Goren, M.A., Menon, A.K., and Graumann, J. (2017). "flippant–An R package for the automated analysis of fluorescence-based scramblase assays." BMC Bioinformatics 18, 146. <DOI:10.1186/s12859-017-1542-y>.
Version: 1.5.4
Author: Johannes Graumann [cre, aut], Richard Cotton [aut]
Maintainer: Johannes Graumann <johannes.graumann@uni-marburg.de>
Depends: R (>= 3.5.0), ggplot2 (>= 2.2.1)
Suggests: bookdown, devtools, microbenchmark, multipanelfigure, pander, roxygen2, tools
Imports: assertive.base (>= 0.0-7), assertive.files (>= 0.0-2), assertive.numbers (>= 0.0-2), data.table (>= 1.11.4), magrittr (>= 1.5), minpack.lm (>= 1.2-1), plyr (>= 1.8.4), pracma (>= 2.3.3), stringi (>= 1.2.3), utils, withr (>= 2.1.2)
License: GPL (>= 3)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-26 21:52:27 UTC; rstudio
Repository: CRAN
Date/Publication: 2023-11-27 14:50:02 UTC

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Sun, 26 Nov 2023

New package simEd with initial version 2.0.1
Package: simEd
Title: Simulation Education
Version: 2.0.1
Imports: graphics, grDevices, methods, stats, utils, shape
Depends: rstream
Suggests: magick
Description: Contains various functions to be used for simulation education, including simple Monte Carlo simulation functions, queueing simulation functions, variate generation functions capable of producing independent streams and antithetic variates, functions for illustrating random variate generation for various discrete and continuous distributions, and functions to compute time-persistent statistics. Also contains functions for visualizing: event-driven details of a single-server queue model; a Lehmer random number generator; variate generation via acceptance-rejection; and of generating a non-homogeneous Poisson process via thinning. Also contains two queueing data sets (one fabricated, one real-world) to facilitate input modeling. More details on the use of these functions can be found in Lawson and Leemis (2015) <doi:10.1109/WSC.2017.8248124>, in Kudlay, Lawson, and Leemis (2020) <doi:10.1109/WSC48552.2020.9384010>, and in Lawson and Leemis (2021) <doi:10.1109/WSC52266.2 [...truncated...]
License: MIT + file LICENSE
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-26 13:08:36 UTC; blawson
Author: Barry Lawson [aut, cre, cph], Larry Leemis [aut], Vadim Kudlay [aut]
Maintainer: Barry Lawson <blawson@bates.edu>
Repository: CRAN
Date/Publication: 2023-11-26 23:20:13 UTC

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New package accrual with initial version 1.4
Package: accrual
Title: Bayesian Accrual Prediction
Version: 1.4
Date: 2023-11-23
Maintainer: Junhao Liu <liujunhao2008@gmail.com>
Depends: R(>= 3.1.3), tcltk2
Imports: fgui, SMPracticals
Description: Participant recruitment for medical research is challenging. Slow accrual leads to delays in research. Accrual monitoring during the process of recruitment is critical. Researchers need reliable tools to manage the accrual rate. We developed a Bayesian method that integrates the researcher's experience with previous trials and data from the current study, providing reliable predictions on accrual rate for clinical studies. For more details and background on these methodologies, see the publications of Byron, Stephen and Susan (2008) <doi:10.1002/sim.3128>, and Yu et al. (2015) <doi:10.1002/sim.6359>. In this R package, Bayesian accrual prediction functions are presented, which can be easily used by statisticians and clinical researchers.
License: GPL-2
Encoding: UTF-8
LazyLoad: true
NeedsCompilation: no
Packaged: 2023-11-26 18:08:02 UTC; disne
Author: Junhao Liu [aut, cre] , Yu Jiang [aut] , Cen Wu [aut], Steve Simon [aut], Matthew S. Mayo [aut], Rama Raghavan [aut], Byron J. Gajewski [aut]
Repository: CRAN
Date/Publication: 2023-11-26 23:20:19 UTC

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Sat, 25 Nov 2023

New package frailtypack with initial version 3.5.1
Package: frailtypack
Version: 3.5.1
Date: 2023-11-23
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Depends: R (>= 2.10.0), survival, boot, MASS, survC1, doBy
Imports: statmod, nlme, shiny, rootSolve, splines
LazyLoad: no
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested fra [...truncated...]
License: GPL (>= 2.0)
URL: https://virginie1rondeau.wixsite.com/virginierondeau/software-frailtypack https://frailtypack-pkg.shinyapps.io/shiny_frailtypack/
Suggests: knitr, testthat, rmarkdown, markdown
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2023-11-25 05:20:02 UTC
Packaged: 2023-11-24 14:09:42 UTC; Romain
NeedsCompilation: yes
Author: Virginie Rondeau [aut, cre] , Juan R. Gonzalez [aut], Yassin Mazroui [aut], Audrey Mauguen [aut], Amadou Diakite [aut], Alexandre Laurent [aut], Myriam Lopez [aut], Agnieszka Krol [aut], Casimir L. Sofeu [aut], Julien Dumerc [aut], Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>

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Fri, 24 Nov 2023

New package froth with initial version 1.0.0
Package: froth
Title: Emulate a 'Forth' Programming Environment
Version: 1.0.0
Description: Emulates a 'Forth' programming environment with added features to interface between R and 'Forth'. Implements most of the functionality described in the original "Starting Forth" textbook <https://www.forth.com/starting-forth/>.
Depends: R (>= 4.3.0)
Imports: methods
Suggests: markdown, knitr
License: GPL-3
ByteCompile: true
Encoding: UTF-8
NeedsCompilation: yes
URL: https://www.ahl27.com/froth/
BugReports: https://github.com/ahl27/froth/issues/new/choose
VignetteBuilder: knitr
Packaged: 2023-11-24 15:30:54 UTC; aidan
Author: Aidan Lakshman [aut, cre]
Maintainer: Aidan Lakshman <ahl27@pitt.edu>
Repository: CRAN
Date/Publication: 2023-11-24 17:10:02 UTC

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New package orbweaver with initial version 0.0.3
Package: orbweaver
Title: Fast and Efficient Graph Data Structures
Version: 0.0.3
Description: Empower your data analysis with 'orbweaver', an R package designed for effortless construction and analysis of graph data structures. With 'orbweaver', you can seamlessly build and manipulate graph structures, leveraging its high-performance methods for filtering, joining, and mutating data within the R environment. Drawing inspiration from the efficiency of the 'data.table' package, 'orbweaver' ensures that mutations and changes to the graph are performed in place, streamlining your workflow for optimal productivity.
URL: https://github.com/ixpantia/orbweaver
BugReports: https://github.com/ixpantia/orbweaver/issues
License: MIT + file LICENSE
Encoding: UTF-8
SystemRequirements: Cargo (Rust's package manager), rustc
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2023-11-24 14:24:06 UTC; andres
Author: ixpantia, SRL [cph], Andres Quintero [aut, cre], The authors of the dependency Rust crates [ctb]
Maintainer: Andres Quintero <andres@ixpantia.com>
Repository: CRAN
Date/Publication: 2023-11-24 17:00:02 UTC

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New package curvir with initial version 0.1.1
Package: curvir
Title: Specify Reserve Demand Curves
Version: 0.1.1
Maintainer: Nikolaos Kourentzes <nikolaos@kourentzes.com>
Description: Automatic specification and estimation of reserve demand curves for central bank operations. The package can help to choose the best demand curve and identify additional explanatory variables. Various plot and predict options are included. For more details, see Chen et al. (2023) <https://www.imf.org/en/Publications/WP/Issues/2023/09/01/Modeling-the-Reserve-Demand-to-Facilitate-Central-Bank-Operations-538754>.
Imports: RColorBrewer, abind, cvTools, pbapply, pso, mgcv, qgam, quantregForest, randomForest
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-24 13:53:07 UTC; Nikos
Author: Nikolaos Kourentzes [aut, cre], Zhuohui Chen [aut], Romain Veyrune [aut]
Repository: CRAN
Date/Publication: 2023-11-24 17:00:05 UTC

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New package treats with initial version 1.0
Package: treats
Title: Trees and Traits Simulations
Version: 1.0
Date: 2023-11-24
Description: A modular package for simulating phylogenetic trees and species traits jointly. Trees can be simulated using modular birth-death parameters (e.g. changing starting parameters or algorithm rules). Traits can be simulated in any way designed by the user. The growth of the tree and the traits can influence each other through modifiers objects providing rules for affecting each other. Finally, events can be created to modify both the tree and the traits under specific conditions.
Depends: R (>= 4.0.0), ape, dispRity, stats
Imports: graphics, MASS, methods, utils, rgl,
Suggests: testthat, knitr
License: GPL-3
URL: https://github.com/TGuillerme/treats
NeedsCompilation: yes
Packaged: 2023-11-24 10:24:44 UTC; tguillerme
Author: Thomas Guillerme [aut, cre, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>
Repository: CRAN
Date/Publication: 2023-11-24 13:40:02 UTC

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New package StormR with initial version 0.1.1
Package: StormR
Title: Analyzing the Behaviour of Wind Generated by Tropical Storms and Cyclones
Maintainer: Thomas Arsouze <thomas.arsouze@cirad.fr>
Version: 0.1.1
URL: https://umr-amap.github.io/StormR/
BugReports: https://github.com/umr-amap/StormR/issues/new/choose
Description: Set of functions to quantify and map the behaviour of winds generated by tropical storms and cyclones in space and time. It includes functions to compute and analyze fields such as the maximum sustained wind field, power dissipation index and duration of exposure to winds above a given threshold. It also includes functions to map the trajectories as well as characteristics of the storms.
License: GPL (>= 3)
Depends: R (>= 2.10)
Imports: graphics, maps, methods, ncdf4, rworldmap, sf, stringr, terra, utils, zoo
Suggests: knitr, rmarkdown, rworldxtra, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-23 14:27:27 UTC; arsouze
Author: Baptiste Delaporte [aut], Thomas Ibanez [aut] , Gunnar Keppel [aut] , Swen Jullien [aut] , Christophe Menkes [aut] , Thomas Arsouze [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-24 13:40:06 UTC

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New package sqlcaser with initial version 0.2.0
Package: sqlcaser
Title: 'SQL' Case Statement Generator
Version: 0.2.0
Date: 2023-11-21
Description: Includes built-in methods for generating long 'SQL' CASE statements, and other 'SQL' statements that may otherwise be arduous to construct by hand. The generated statement can easily be concatenated to string literals to form queries to 'SQL'-like databases, such as when using the 'RODBC' package. The current methods include casewhen() for building CASE statements, inlist() for building IN statements, and updatetable() for building UPDATE statements.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-23 17:36:37 UTC; leoso
Author: Leoson Hoay [aut, cre]
Maintainer: Leoson Hoay <leoson.public@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-24 13:20:02 UTC

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New package multipleDL with initial version 1.0.0
Package: multipleDL
Version: 1.0.0
Date: 2023-11-17
Title: Addressing Detection Limits by Cumulative Probability Models (CPMs)
Description: Build CPMs (cumulative probability models, also known as cumulative link models) to account for detection limits (both single and multiple detection limits) in response variables. Conditional quantiles and conditional CDFs can be calculated based on fitted models. The package implements methods described in Tian, Y., Li, C., Tu, S., James, N. T., Harrell, F. E., & Shepherd, B. E. (2022). "Addressing Detection Limits with Semiparametric Cumulative Probability Models". <arXiv:2207.02815>.
License: GPL (>= 2)
Encoding: UTF-8
Biarch: true
Depends: R (>= 3.4.0)
Imports: methods, stats, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.1.1), SparseM
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: 2023-11-23 17:40:43 UTC; yuqitian
Author: Yuqi Tian [aut, cre], Chun Li [aut], Shengxin Tu [aut], Nathan James [aut], Frank Harrell [aut], Bryan Shepherd [aut]
Maintainer: Yuqi Tian <yuqitian35@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-24 13:20:05 UTC

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New package MCDA with initial version 0.1.0
Package: MCDA
Version: 0.1.0
Title: Support for the Multicriteria Decision Aiding Process
Author: Patrick Meyer, Sebastien Bigaret, Richard Hodgett, Alexandru-Liviu Olteanu, David Palma, Aritad Alan Choicharoon
Maintainer: David Palma <d.palma@leeds.ac.uk>
Description: Support for the analyst in a Multicriteria Decision Aiding (MCDA) process with algorithms, preference elicitation and data visualisation functions. Sébastien Bigaret, Richard Hodgett, Patrick Meyer, Tatyana Mironova, Alexandru Olteanu (2017) Supporting the multi-criteria decision aiding process : R and the MCDA package, Euro Journal On Decision Processes, Volume 5, Issue 1 - 4, pages 169 - 194 <doi:10.1007/s40070-017-0064-1>.
Imports: Rglpk, glpkAPI, RColorBrewer, combinat, triangle, plyr, ggplot2
License: EUPL (>= 1.1)
Encoding: UTF-8
URL: https://github.com/paterijk/MCDA
NeedsCompilation: no
Suggests: testthat (>= 3.0.0)
Packaged: 2023-11-22 17:59:32 UTC; david
Repository: CRAN
Date/Publication: 2023-11-24 09:20:13 UTC

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Thu, 23 Nov 2023

New package shinyInvoice with initial version 0.0.1
Package: shinyInvoice
Title: Shiny App - Generate a Pdf Invoice with 'Rmarkdown'
Version: 0.0.1
Date: 2023-11-23
Description: Generate an invoice containing a header with invoice number and businesses details. The invoice table contains any of: salary, one-liner costs, grouped costs. Under the table signature and bank account details appear. Pages are numbered when more than one. Source .json and .Rmd files are editable in the app. This package includes functions for getting exchange rates between currencies based on 'quantmod' (Ryan and Ulrich, 2023 <https://CRAN.R-project.org/package=quantmod>).
Depends: R (>= 3.5)
Imports: tibble, dplyr, quantmod, rlang, stringr, shiny
Suggests: fs, jsonlite, lubridate, pillar, readr, rhino, rjson, shinyAce, tinytex, rmarkdown
License: GPL (>= 2)
Encoding: UTF-8
SystemRequirements: pandoc (>= 2.0)
URL: https://github.com/fernandoroa/invoice-public
BugReports: https://github.com/fernandoroa/invoice-public/issues
NeedsCompilation: no
Packaged: 2023-11-23 12:03:11 UTC; fernando
Author: Fernando Roa [aut, cre]
Maintainer: Fernando Roa <froao@ufg.br>
Repository: CRAN
Date/Publication: 2023-11-23 16:20:02 UTC

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New package revert with initial version 0.0.1
Package: revert
Title: Reversion Mutation Identifier for Sequencing Data
Version: 0.0.1
Date: 2023-11-03
Author: Hui Xiao [aut, cre], Adam Mills [aut], John Alexander [ctb], Stephen Pettitt [aut], Syed Haider [aut]
Maintainer: Hui Xiao <hui.xiao@icr.ac.uk>
Description: A tool for detecting reversions for a given pathogenic mutation from next-generation DNA sequencing data. It analyses reads aligned to the locus of the pathogenic mutation and reports reversion events where secondary mutations have restored or undone the deleterious effect of the original pathogenic mutation, e.g., secondary indels complement to a frameshift pathogenic mutation converting the orignal frameshift mutation into inframe mutaions, deletions or SNVs that replaced the original pathogenic mutation restoring the open reading frame, SNVs changing the stop codon caused by the original nonsense SNV into an amino acid, etc.
SystemRequirements: R >= 4.1.0, SAMtools >= 1.11
License: GPL-2
Suggests: knitr, rmarkdown, futile.logger
Imports: IRanges, GenomicRanges, Biostrings, Rsamtools, BSgenome, BSgenome.Hsapiens.UCSC.hg38
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-23 15:35:55 UTC; hxiao
Repository: CRAN
Date/Publication: 2023-11-23 16:20:05 UTC

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New package metaRange with initial version 1.0.0
Package: metaRange
Title: Framework to Build Mechanistic and Metabolic Constrained Species Distribution Models
Version: 1.0.0
Description: Build spatially and temporally explicit process-based species distribution models, that can include an arbitrary number of environmental factors, species and processes including metabolic constraints and species interactions. The focus of the package is simulating populations of one or multiple species in a grid-based landscape and studying the meta-population dynamics and emergent patterns that arise from the interaction of species under complex environmental conditions. It provides functions for common ecological processes such as negative exponential, kernel-based dispersal (see Nathan et al. (2012) <doi:10.1093/acprof:oso/9780199608898.003.0015>), calculation of the environmental suitability based on cardinal values ( Yin et al. (1995) <doi:10.1016/0168-1923(95)02236-Q>, simplified by Yan and Hunt (1999) <doi:10.1006/anbo.1999.0955> see eq: 4), reproduction in form of an Ricker model (see Ricker (1954) <doi:10.1139/f54-039> and Cabral and Schurr (2010) <d [...truncated...]
License: GPL-3
Copyright: see inst/COPYRIGHTS
URL: https://metaRange.github.io/metaRange/
BugReports: https://github.com/metaRange/metaRange/issues
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 1.0.10), terra, R6, checkmate, grDevices, graphics, utils
Suggests: knitr, rmarkdown, tinytest
VignetteBuilder: knitr
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2023-11-23 10:45:55 UTC; srfall
Author: Stefan Fallert [aut, cre, cph] , Lea Li [aut, cph] , Juliano Sarmento Cabral [aut, cph, ths] , Tyler Morgan-Wall [ctb, cph] , Bavarian Ministry of Science and Arts [fnd], Deutsche Bundesstiftung Umwelt [fnd]
Maintainer: Stefan Fallert <srfallert@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-23 16:10:02 UTC

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New package scrapeR with initial version 0.1.7
Package: scrapeR
Title: These Functions Fetch and Extract Text Content from Specified Web Pages
Version: 0.1.7
Description: The 'scrapeR' package utilizes functions that fetch and extract text content from specified web pages. It handles HTTP errors and parses HTML efficiently. The package can handle hundreds of websites at a time using the scrapeR_in_batches() command.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: httr, rvest, utils, magrittr
NeedsCompilation: no
Packaged: 2023-11-22 14:46:17 UTC; mathieu.dubeau
Author: Mathieu Dubeau [aut, cre, cph]
Maintainer: Mathieu Dubeau <mdubeau20@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-23 16:00:02 UTC

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New package PubChemR with initial version 0.99-1
Package: PubChemR
Title: Interface to the 'PubChem' Database for Chemical Data Retrieval
Version: 0.99-1
Description: Provides an R interface to the 'PubChem' database, which is a repository for chemical information and a resource for finding chemical and biological data. The package simplifies the process of retrieving and handling chemical compound information from 'PubChem'. Users can search for compounds, retrieve standard chemical information, download data in various formats, and query the database using the 'PubChem' Power User Gateway (PUG) 'RESTful' API <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest>. The package aims to facilitate the integration of chemical data in bioinformatics and cheminformatics workflows.
License: GPL (>= 2)
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
Imports: dplyr, httr, RJSONIO, RCurl, tibble, tidyr, utils, magrittr, stringr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-23 09:50:56 UTC; selcukkorkmaz
Author: Selcuk Korkmaz [aut, cre] , Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-23 16:00:06 UTC

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New package clusterCrit with initial version 1.3.0
Package: clusterCrit
Version: 1.3.0
License: GPL (>= 2)
Description: Package providing functions for computing a collection of clustering validation or quality criteria and partition comparison indices.
Title: Clustering Indices
Date: 2023-11-21
Suggests: RUnit, rbenchmark
URL: https://gitlab.com/iagogv/clusterCrit
BugReports: https://gitlab.com/iagogv/clusterCrit/-/issues
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2023-11-21 23:09:51 UTC; iago
Author: Iago Gine-Vazquez [cre] , Bernard Desgraupes [aut]
Maintainer: Iago Gine-Vazquez <iago.gin-vaz@protonmail.com>
Repository: CRAN
Date/Publication: 2023-11-23 16:00:05 UTC

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New package reactable.extras with initial version 0.2.0
Package: reactable.extras
Title: Extra Features for 'reactable' Package
Version: 0.2.0
Description: Enhanced functionality for 'reactable' in 'shiny' applications, offering interactive and dynamic data table capabilities with ease. With 'reactable.extras', easily integrate a range of functions and components to enrich your 'shiny' apps and facilitate user-friendly data exploration.
License: LGPL-3
URL: https://appsilon.github.io/reactable.extras/, https://github.com/Appsilon/reactable.extras
BugReports: https://github.com/Appsilon/reactable.extras/issues
Depends: R (>= 4.1.0)
Imports: checkmate, dplyr, htmltools, purrr (>= 1.0.0), reactable (>= 0.4.0), rjson, rlang, shiny
Suggests: covr, lintr, mockery, rcmdcheck, shinytest2, spelling, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2023-11-23 08:16:47 UTC; kuba
Author: Recle Vibal [aut, cre], Ivan Hrychaniuk [aut], Andres Quintero [aut], Pedro Silva [aut], Eduardo Almeida [ctb], Appsilon Sp. z o.o. [cph]
Maintainer: Recle Vibal <opensource+recle@appsilon.com>
Repository: CRAN
Date/Publication: 2023-11-23 12:50:02 UTC

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New package AssocBin with initial version 0.1-0
Package: AssocBin
Version: 0.1-0
Encoding: UTF-8
Title: Measuring Association with Recursive Binning
Description: An iterative implementation of a recursive binary partitioning algorithm to measure pairwise dependence with a modular design that allows user specification of the splitting logic and stop criteria. Helper functions provide suggested versions of both and support visualization and the computation of summary statistics on final binnings. For a complete description of the functionality and algorithm, see Salahub and Oldford (2023) <arxiv:2311.08561>.
Maintainer: Chris Salahub <chris.salahub@uwaterloo.ca>
Depends: R (>= 4.3.0)
Imports:
Suggests: knitr, rmarkdown
Enhances:
License: GPL (>= 3)
NeedsCompilation: no
Repository: CRAN
VignetteBuilder: knitr
Packaged: 2023-11-23 00:11:52 UTC; Chris
Author: Chris Salahub [aut, cre]
Date/Publication: 2023-11-23 12:50:05 UTC

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New package RTSA with initial version 0.2.2
Package: RTSA
Title: 'Trial Sequential Analysis' for Error Control and Inference in Sequential Meta-Analyses
Version: 0.2.2
Description: Frequentist sequential meta-analysis based on 'Trial Sequential Analysis' (TSA) in programmed in Java by the Copenhagen Trial Unit (CTU). The primary function is the calculation of group sequential designs for meta-analysis to be used for planning and analysis of both prospective and retrospective sequential meta-analyses to preserve type-I-error control under sequential testing. 'RTSA' includes tools for sample size and trial size calculation for meta-analysis and core meta-analyses methods such as fixed-effect and random-effects models and forest plots. TSA is described in Wetterslev et. al (2008) <doi:10.1016/j.jclinepi.2007.03.013>. The methods for deriving the group sequential designs are based on Jennison and Turnbull (1999, ISBN:9780849303166).
License: GPL (>= 2)
URL: https://github.com/AnneLyng/RTSA
BugReports: https://github.com/AnneLyng/RTSA/issues
Imports: stats, metafor, ggplot2, scales, Rcpp (>= 0.11.0)
LinkingTo: Rcpp
Encoding: UTF-8
Depends: R (>= 3.5.0)
LazyData: true
Suggests: gsDesign, CompQuadForm, dplyr, kableExtra, rmarkdown, knitr, bookdown, gridExtra, testthat (>= 3.0.0)
VignetteBuilder: knitr, bookdown
NeedsCompilation: yes
Packaged: 2023-11-22 15:32:59 UTC; anne
Author: Anne Lyngholm Soerensen [aut, cre, trl], Markus Harboe Olsen [aut, ctr], Theis Lange [ctr], Christian Gluud [ctr]
Maintainer: Anne Lyngholm Soerensen <lynganne@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-23 08:50:10 UTC

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New package Racmacs with initial version 1.2.8
Package: Racmacs
Title: Antigenic Cartography Macros
Version: 1.2.8
Date: 2023-11-22
Description: A toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.
Depends: R (>= 4.0)
Imports: Rcpp, jsonlite, ks, brotli, shiny, shinyFiles, shinyjs, htmlwidgets, ggplot2 (>= 3.0.0), htmltools, rmarchingcubes, shape, ellipsis, MASS, magrittr, igraph, dplyr, vctrs, rlang
Suggests: testthat, r3js, knitr, rmarkdown, rstudioapi, plotly, geometry, readxl, stringr, tibble, tidyr, base64enc, lifecycle, MCMCpack, spelling
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, RcppEnsmallen, rapidjsonr
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://acorg.github.io/Racmacs/, https://github.com/acorg/Racmacs/
BugReports: https://github.com/acorg/Racmacs/issues
License: AGPL-3
Language: en-GB
NeedsCompilation: yes
Packaged: 2023-11-22 18:09:50 UTC; cambridge
Author: Sam Wilks [aut, cre]
Maintainer: Sam Wilks <sw463@cam.ac.uk>
Repository: CRAN
Date/Publication: 2023-11-23 09:00:07 UTC

More information about Racmacs at CRAN
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New package letsR with initial version 5.0
Package: letsR
Title: Data Handling and Analysis in Macroecology
Version: 5.0
Date: 2023-11-22
Description: Handling, processing, and analyzing geographic data on species' distributions and environmental variables. Read Vilela & Villalobos (2015) <doi:10.1111/2041-210X.12401> for details.
License: GPL-2
Imports: geosphere, sf
Depends: R (>= 3.1.0), terra, grDevices, graphics, methods, stats
Suggests: testthat, devtools, knitr, rmarkdown, dplyr, kableExtra, ggplot2
LazyData: true
URL: https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12401, https://github.com/macroecology/letsR, https://brunovilela.github.io/letsR/
BugReports: https://github.com/macroecology/letsR/issues
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-22 20:22:10 UTC; brunovilela
Author: Bruno Vilela [aut, cre] , Fabricio Villalobos [aut]
Maintainer: Bruno Vilela <bvilela.bv@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-23 09:00:02 UTC

More information about letsR at CRAN
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New package granovaGG with initial version 1.4.1
Package: granovaGG
Version: 1.4.1
Date: 2023-11-22
Title: Graphical Analysis of Variance Using ggplot2
Description: Create what we call Elemental Graphics for display of anova results. The term elemental derives from the fact that each function is aimed at construction of graphical displays that afford direct visualizations of data with respect to the fundamental questions that drive the particular anova methods. This package represents a modification of the original granova package; the key change is to use 'ggplot2', Hadley Wickham's package based on Grammar of Graphics concepts (due to Wilkinson). The main function is granovagg.1w() (a graphic for one way ANOVA); two other functions (granovagg.ds() and granovagg.contr()) are to construct graphics for dependent sample analyses and contrast-based analyses respectively. (The function granova.2w(), which entails dynamic displays of data, is not currently part of 'granovaGG'.) The 'granovaGG' functions are to display data for any number of groups, regardless of their sizes (however, very large data sets or numbers of groups can be problematic). For gr [...truncated...]
URL: https://github.com/briandk/granovaGG
BugReports: https://github.com/briandk/granovaGG/issues
License: MIT + file LICENSE
Depends: R (>= 2.14.0),
Imports: dplyr, ggplot2 (>= 0.9.2), magrittr, RColorBrewer, tibble, tidyr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-22 22:46:24 UTC; briandk
Author: Brian A. Danielak [aut, cre, cph] , Robert M. Pruzek [aut], William E. J. Doane [ctb] , James E. Helmreich [ctb], Jason Bryer [ctb]
Maintainer: Brian A. Danielak <briandanielak+granovagg@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-23 08:00:02 UTC

More information about granovaGG at CRAN
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Wed, 22 Nov 2023

New package HyMETT with initial version 1.1.2
Package: HyMETT
Title: Hydrologic Model Evaluation and Time-Series Tools
Version: 1.1.2
Date: 2023-11-21
Description: Facilitates the analysis and evaluation of hydrologic model output and time-series data with functions focused on comparison of modeled (simulated) and observed data, period-of-record statistics, and trends.
URL: https://code.usgs.gov/hymett/hymett
BugReports: https://code.usgs.gov/hymett/hymett/-/issues
Depends: R (>= 3.6.0)
Imports: checkmate, dplyr, EnvStats, lmomco, lubridate, plyr, rlang, stats, tibble, zoo
Suggests: knitr, rmarkdown, roxygen2, testthat
License: CC0
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
BuildVignettes: true
Copyright: This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey, an agency of the U.S. Department of Interior. For more information, see the official USGS copyright policy at http://www.usgs.gov/visual-id/credit_usgs.html#copyright
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-21 21:01:29 UTC; cpenn
Author: Colin Penn [aut, cre] , Caelan Simeone [aut] , Sara Levin [aut] , Samuel Saxe [aut] , Sydney Foks [aut] , Robert Dudley [dtc] , Glenn Hodgkins [dtc] , Timothy Hodson [aut] , Thomas Over [dtc] , Amy Russell [dtc]
Maintainer: Colin Penn <cpenn@usgs.gov>
Repository: CRAN
Date/Publication: 2023-11-22 19:20:02 UTC

More information about HyMETT at CRAN
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New package gen3sis with initial version 1.5.11
Package: gen3sis
Title: General Engine for Eco-Evolutionary Simulations
Version: 1.5.11
Date: 2023-11-21
Description: Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 0.12.16), Matrix, methods, utils, raster, gdistance, stringr, tools, grDevices
Suggests: knitr, markdown, testthat (>= 2.1.0), rmarkdown, formatR
LinkingTo: Rcpp, BH
URL: https://github.com/project-Gen3sis/R-package
BugReports: https://github.com/project-Gen3sis/R-package/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-11-21 13:40:32 UTC; benjamin
Author: ETH Zuerich [cph], Oskar Hagen [aut, cre] , Benjamin Flueck [aut] , Fabian Fopp [aut] , Juliano S. Cabral [aut] , Florian Hartig [aut] , Mikael Pontarp [aut] , Charles Novaes de Santana [ctb] , Thiago F. Rangel [aut] , Theo Gaboriau [ctb] , Loic Pellis [...truncated...]
Maintainer: Oskar Hagen <oskar@hagen.bio>
Repository: CRAN
Date/Publication: 2023-11-22 15:20:06 UTC

More information about gen3sis at CRAN
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New package PoolBal with initial version 0.1-0
Package: PoolBal
Version: 0.1-0
Encoding: UTF-8
Title: Balancing Central and Marginal Rejection of Pooled p-Values
Description: When using pooled p-values to adjust for multiple testing, there is an inherent balance that must be struck between rejection based on weak evidence spread among many tests and strong evidence in a few, explored in Salahub and Olford (2023) <arXiv:2310.16600>. This package provides functionality to compute marginal and central rejection levels and the centrality quotient for p-value pooling functions and provides implementations of the chi-squared quantile pooled p-value (described in Salahub and Oldford (2023)) and a proposal from Heard and Rubin-Delanchy (2018) <doi:10.1093/biomet/asx076> to control the quotient's value.
Author: Chris Salahub [aut, cre]
Maintainer: Chris Salahub <chris.salahub@uwaterloo.ca>
Depends: R (>= 4.3.0)
Imports: methods
Suggests:
Enhances:
License: GPL (>= 3)
NeedsCompilation: no
Repository: CRAN
Packaged: 2023-11-21 22:30:01 UTC; Chris
Date/Publication: 2023-11-22 10:10:02 UTC

More information about PoolBal at CRAN
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New package GrFA with initial version 0.1.0
Package: GrFA
Title: Group Factor Analysis
Date: 2023-10-22
Version: 0.1.0
Author: Jiaqi Hu [cre, aut], Xueqin Wang [aut]
Maintainer: Jiaqi Hu <hujiaqi@mail.ustc.edu.cn>
Description: Several group factor analysis algorithms are implemented, including Canonical Correlation-based Estimation by Choi et al. (2021) <doi:10.1016/j.jeconom.2021.09.008> , Generalised Canonical Correlation Estimation by Lin and Shin (2022) <doi:10.2139/ssrn.4295429>, Circularly Projected Estimation by Chen (2022) <doi:10.1080/07350015.2022.2051520>, and the approach we recently proposed, named Weighted Projection Estimation.
Imports: mvtnorm
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-22 03:28:29 UTC; hujiaqi
Repository: CRAN
Date/Publication: 2023-11-22 10:20:02 UTC

More information about GrFA at CRAN
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New package StateLevelForest with initial version 0.1.0
Package: StateLevelForest
Title: Historical State-Level Forest Cover Data in the United States
Version: 0.1.0
Description: Provides a unique dataset of historical forest cover across all states in the United States, spanning from 1907 to 2017, along with 1630 as a reference year. This dataset is important for understanding environmental changes and land use trends over time. It includes functionality for easy access of the data.
License: CC BY 4.0
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Suggests: knitr, rmarkdown, dplyr, ggplot2, scales
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-21 20:11:14 UTC; gatesdupont
Author: Gates Dupont [aut, cre]
Maintainer: Gates Dupont <gatesdupont@princeton.edu>
Repository: CRAN
Date/Publication: 2023-11-22 10:00:09 UTC

More information about StateLevelForest at CRAN
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New package rexpokit with initial version 0.26.6.14
Package: rexpokit
Title: R Wrappers for EXPOKIT; Other Matrix Functions
Version: 0.26.6.14
Date: 2023-11-22
Author: Nicholas J. Matzke [aut, cre, cph], Roger B. Sidje [aut, cph], Drew Schmidt [aut]
Maintainer: Nicholas J. Matzke <nickmatzke.ncse@gmail.com>
Depends: R (>= 3.0.2)
Imports: stats, Rcpp (>= 0.11.0)
LinkingTo: Rcpp (>= 0.11.0)
Copyright: See /inst/LAPACK_LICENSE.txt for code in /src.
Description: Wraps some of the matrix exponentiation utilities from EXPOKIT (<http://www.maths.uq.edu.au/expokit/>), a FORTRAN library that is widely recommended for matrix exponentiation (Sidje RB, 1998. "Expokit: A Software Package for Computing Matrix Exponentials." ACM Trans. Math. Softw. 24(1): 130-156). EXPOKIT includes functions for exponentiating both small, dense matrices, and large, sparse matrices (in sparse matrices, most of the cells have value 0). Rapid matrix exponentiation is useful in phylogenetics when we have a large number of states (as we do when we are inferring the history of transitions between the possible geographic ranges of a species), but is probably useful in other ways as well. NOTE: In case FORTRAN checks temporarily get rexpokit archived on CRAN, see archived binaries at GitHub in: nmatzke/Matzke_R_binaries (binaries install without compilation of source code).
URL: http://phylo.wikidot.com/rexpokit
License: GPL (>= 2)
LazyLoad: yes
ByteCompile: yes
Packaged: 2023-11-21 22:53:42 UTC; nmat471
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2023-11-22 09:20:05 UTC

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New package public.ctn0094extra with initial version 1.0.4
Package: public.ctn0094extra
Title: Helper Files for the CTN-0094 Relational Database
Version: 1.0.4
Date: 2023-11-21
Description: Engineered features and "helper" functions ancillary to the 'public.ctn0094data' package, extending this package for ease of use (see <https://CRAN.R-project.org/package=public.ctn0094data>). This 'public.ctn0094data' package contains harmonized datasets from some of the National Institute of Drug Abuse's Clinical Trials Network (NIDA's CTN) projects. Specifically, the CTN-0094 project is to harmonize and de-identify clinical trials data from the CTN-0027, CTN-0030, and CTN-51 studies for opioid use disorder. This current version is built from 'public.ctn0094data' v. 1.0.6.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
LazyData: true
Depends: R (>= 2.10), public.ctn0094data
Imports: dplyr, magrittr, purrr, tibble, tidyr, utils
Suggests: knitr, kableExtra, rmarkdown, scales, stringr
VignetteBuilder: knitr
URL: https://ctn-0094.github.io/public.ctn0094extra/
BugReports: https://github.com/CTN-0094/public.ctn0094extra/issues
NeedsCompilation: no
Packaged: 2023-11-21 21:21:53 UTC; gabrielodom
Author: Gabriel Odom [aut, cre] , Raymond Balise [aut]
Maintainer: Gabriel Odom <gabriel.j.odom@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-22 10:00:02 UTC

More information about public.ctn0094extra at CRAN
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New package fr with initial version 0.5.0
Package: fr
Title: Frictionless Standards
Version: 0.5.0
Description: A "tabular-data-resource" (<https://specs.frictionlessdata.io/tabular-data-resource/>) is a simple format to describe a singular tabular data resource such as a CSV file. It includes support both for metadata such as author and title and a schema to describe the data, for example the types of the fields/columns in the data. Create a tabular-data-resource by providing a data.frame and specifying metadata. Write and read tabular-data-resources to and from disk.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: cli, purrr, vroom, S7 (>= 0.1.1), tibble, tidyselect, yaml, dplyr, rlang
Suggests: testthat (>= 3.0.0), withr, fs, knitr, rmarkdown
URL: https://github.com/cole-brokamp/fr, https://cole-brokamp.github.io/fr/
BugReports: https://github.com/cole-brokamp/fr/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-21 21:18:50 UTC; cole
Author: Cole Brokamp [aut, cre, cph]
Maintainer: Cole Brokamp <cole@colebrokamp.com>
Repository: CRAN
Date/Publication: 2023-11-22 10:00:05 UTC

More information about fr at CRAN
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New package DiffNet with initial version 1.0.2
Package: DiffNet
Title: Identifying Significant Node Scores using Network Diffusion Algorithm
Version: 1.0.2
Description: Designed for network analysis, leveraging the personalized PageRank algorithm to calculate node scores in a given graph. This innovative approach allows users to uncover the importance of nodes based on a customized perspective, making it particularly useful in fields like bioinformatics, social network analysis, and more.
License: GPL (>= 3)
Encoding: UTF-8
Depends: igraph, assertthat
Imports: MASS, parallel
NeedsCompilation: no
Packaged: 2023-11-21 18:14:58 UTC; faren
Author: Farzaneh Firoozbakht [aut, cre, cph]
Maintainer: Farzaneh Firoozbakht <faren.firoozbakht@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-22 09:20:15 UTC

More information about DiffNet at CRAN
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Tue, 21 Nov 2023

New package lehdr with initial version 1.1.2
Package: lehdr
Title: Grab Longitudinal Employer-Household Dynamics (LEHD) Flat Files
Version: 1.1.2
Maintainer: Jamaal Green <jamaal.green@gmail.com>
Description: Designed to query Longitudinal Employer-Household Dynamics (LEHD) workplace/residential association and origin-destination flat files and optionally aggregate Census block-level data to block group, tract, county, or state. Data comes from the LODES FTP server <https://lehd.ces.census.gov/data/lodes/LODES8/>.
Depends: R (>= 4.0.0)
License: MIT + file LICENSE
Encoding: UTF-8
Imports: readr, rlang, stringr, glue, httr, dplyr
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, devtools, pacman
VignetteBuilder: knitr
URL: https://github.com/jamgreen/lehdr/
BugReports: https://github.com/jamgreen/lehdr/issues/
NeedsCompilation: no
Packaged: 2023-11-20 16:36:00 UTC; jamaalgreen
Author: Jamaal Green [cre, aut], Liming Wang [aut], Dillon Mahmoudi [aut], Matthew Rogers [ctb], Kyle Walker [ctb]
Repository: CRAN
Date/Publication: 2023-11-21 22:30:02 UTC

More information about lehdr at CRAN
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New package smof with initial version 1.0
Package: smof
Title: Scoring Methodology for Ordered Factors
Version: 1.0
Date: 2023-11-21
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Depends: R (>= 4.0.0)
Suggests: ggplot2, survival
Description: Starting from a given object representing a fitted model (within a certain set of model classes) whose linear predictor includes some ordered factor(s) among the explanatory variables, a new model is constructed and fitted where each named factor is replaced by a single numeric score, suitably chosen so that the new variable produces a fit comparable with the standard methodology based on a set of polynomial contrasts. Reference: Azzalini (2023) <doi:10.1002/sta4.624>.
License: GPL-2 | GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-21 07:21:07 UTC; aa
Author: Adelchi Azzalini [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-21 18:20:02 UTC

More information about smof at CRAN
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New package SharkDemography with initial version 1.1.0
Package: SharkDemography
Title: Shark Demographic Analyses Using Leslie Matrix Models
Version: 1.1.0
Maintainer: Jonathan Smart <jonsmartphd@gmail.com>
Description: Run Leslie Matrix models using Monte Carlo simulations for any specified shark species. This package was developed during the publication of Smart, JJ, White, WT, Baje, L, et al. (2020) "Can multi-species shark longline fisheries be managed sustainably using size limits? Theoretically, yes. Realistically, no".J Appl Ecol. 2020; 57; 1847–1860. <doi:10.1111/1365-2664.13659>.
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3)
Imports: MASS, interp, dplyr, tidyr, readr, popbio, iterators, parallel, doFuture, doParallel, foreach, magrittr
License: GPL (>= 3)
Suggests: knitr, rmarkdown
URL: https://github.com/jonathansmart/SharkDemography
BugReports: https://github.com/jonathansmart/SharkDemography/issues
NeedsCompilation: no
Packaged: 2023-11-21 00:00:54 UTC; smartj
Author: Jonathan Smart [aut, cre, ctb, cph]
Repository: CRAN
Date/Publication: 2023-11-21 18:10:05 UTC

More information about SharkDemography at CRAN
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New package scfetch with initial version 0.5.0
Package: scfetch
Title: Access and Format Single-Cell RNA-Seq Datasets from Public Resources
Version: 0.5.0
Maintainer: Yabing Song <songyb0519@gmail.com>
Description: The goal of 'scfetch' is to access and format single-cell RNA-seq datasets. It can be used to download single-cell RNA-seq datasets from widely used public resources, including GEO <https://www.ncbi.nlm.nih.gov/geo/>, Zenodo <https://zenodo.org/>, CELLxGENE <https://cellxgene.cziscience.com/>, Human Cell Atlas <https://www.humancellatlas.org/>, PanglaoDB <https://panglaodb.se/index.html> and UCSC Cell Browser <https://cells.ucsc.edu/>. And, it can also be used to perform object conversion between SeuratObject <https://satijalab.org/seurat/>, loom <http://loompy.org/>, h5ad <https://scanpy.readthedocs.io/en/stable/>, SingleCellExperiment <https://bioconductor.org/packages/release/bioc/html/scran.html>, CellDataSet <http://cole-trapnell-lab.github.io/monocle-release/> and cell_data_set <https://cole-trapnell-lab.github.io/monocle3/>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: Biobase, curl, data.table, dplyr, GEOquery, jsonlite, magrittr, Matrix, openxlsx, parallel, pbapply, purrr, rPanglaoDB, reticulate, Seurat, tibble, tools, utils, SingleCellExperiment, SummarizedExperiment, scater, LoomExperiment, httr, rlang, tidyr, methods
Suggests: knitr, rmarkdown, scRNAseq, BiocStyle, htmltools, sceasy, SeuratDisk, SeuratWrappers, zellkonverter, GEOfastq
VignetteBuilder: knitr
Additional_repositories: https://showteeth.github.io/drat/
URL: https://github.com/showteeth/scfetch
BugReports: https://github.com/showteeth/scfetch/issues
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2023-11-21 09:18:20 UTC; soyabean
Author: Yabing Song [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-21 18:20:05 UTC

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New package result with initial version 0.1.0
Package: result
Title: Result Type for Safely Handling Operations that can Succeed or Fail
Version: 0.1.0
Description: Allows wrapping values in success() and failure() types to capture the result of operations, along with any status codes. Risky expressions can be wrapped in as_result() and functions wrapped in result() to catch errors and assign the relevant result types. Monadic functions can be bound together as pipelines or transaction scripts using then_try(), to gracefully handle errors at any step.
Encoding: UTF-8
License: MIT + file LICENSE
Suggests: testthat (>= 3.0.0)
URL: https://github.com/soumyaray/result
BugReports: https://github.com/soumyaray/result/issues
NeedsCompilation: no
Packaged: 2023-11-21 14:44:56 UTC; soumyaray
Author: Soumya Ray [aut, cre, cph]
Maintainer: Soumya Ray <soumya.ray@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-21 18:40:02 UTC

More information about result at CRAN
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New package Mhorseshoe with initial version 0.1.0
Package: Mhorseshoe
Title: Approximate Algorithm for Horseshoe Prior
Version: 0.1.0
Description: Provides an approximate algorithm for the horseshoe estimator used in Bayesian linear models. By implementing a sampler with high computational cost in the 'Rcpp' package and using an approximate algorithm that reduces matrix calculation complexity, parameter estimation speed for high-dimensional sparse data is faster. The approximate algorithm is described in Johndrow et al. (2020) <https://www.jmlr.org/papers/v21/19-536.html>.
Encoding: UTF-8
Imports: stats, Rcpp (>= 1.0.11)
LinkingTo: Rcpp
License: MIT + file LICENSE
Suggests: knitr, rmarkdown, ggplot2, horseshoe
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-11-21 12:12:09 UTC; rkdal
Author: Kang Mingi [aut, cre], Lee Kyoungjae [aut]
Maintainer: Kang Mingi <leehuimin115@g.skku.edu>
Repository: CRAN
Date/Publication: 2023-11-21 18:30:02 UTC

More information about Mhorseshoe at CRAN
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New package marradistrees with initial version 1.0
Package: marradistrees
Title: Plots a Tree-Like Representation of a Numerical Variable (Marradi's Tree)
Version: 1.0
Date: 2023-11-21
Maintainer: Massimo Cannas <massimo.cannas@unica.it>
Description: Provides a single function plotting Marradi's trees: a graphical representation of a numerical variable for comparing the variable mean and standard deviation across subgroups. See A. Marradi "L'analisi monovariata" (1993, ISBN: 9788820496876).
License: GPL-3
NeedsCompilation: no
Packaged: 2023-11-21 12:13:44 UTC; massimo
Author: Massimo Cannas [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-21 18:50:02 UTC

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New package gpkg with initial version 0.0.7
Package: gpkg
Title: Utilities for the Open Geospatial Consortium 'GeoPackage' Format
Version: 0.0.7
Maintainer: Andrew Brown <brown.andrewg@gmail.com>
Description: Build Open Geospatial Consortium 'GeoPackage' files (<https://www.geopackage.org/>). 'GDAL' utilities for reading and writing spatial data are provided by the 'terra' package. Additional 'GeoPackage' and 'SQLite' features for attributes and tabular data are implemented with the 'RSQLite' package.
URL: https://humus.rocks/gpkg/, https://github.com/brownag/gpkg
BugReports: https://github.com/brownag/gpkg/issues
Imports: utils, methods, DBI
Suggests: RSQLite, terra (>= 1.6), tinytest, dplyr, dbplyr
License: CC0
Depends: R (>= 3.1.0)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-21 06:45:05 UTC; andrew
Author: Andrew Brown [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-21 18:20:09 UTC

More information about gpkg at CRAN
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New package dartR.popgen with initial version 0.32
Package: dartR.popgen
Title: Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis
Version: 0.32
Date: 2023-11-21
Description: Facilitates the analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. 'dartR.popgen' provides a suit of functions to analyse such data in a population genetics context. It provides several functions to calculate population genetic metrics and to study population structure. Quite a few functions need additional software to be able to run (gl.run.structure(), gl.blast(), gl.LDNe()). You find detailed description in the help pages how to download and link the packages so the function can run the software. 'dartR.popgen' is part of the the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.
Encoding: UTF-8
Depends: R (>= 3.5), adegenet (>= 2.0.0), dartR.base, dartR.data
Imports: methods, utils, MASS, dplyr, patchwork, crayon, ggplot2, data.table, stringr
Suggests: SIBER, expm, fields, gplots, gridExtra, igraph, iterpc, label.switching, leaflet, plyr, proxy, purrr, qvalue, raster, reshape2, scales, snpStats, tidyr, viridis, zoo, gsubfn, sp
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2023-11-20 23:51:05 UTC; s425824
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb], Eric Archer [ctb]
URL: https://green-striped-gecko.github.io/dartR/
BugReports: https://groups.google.com/g/dartr?pli=1
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2023-11-21 18:10:02 UTC

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New package cfr with initial version 0.1.0
Package: cfr
Title: Estimate Disease Severity and Case Ascertainment
Version: 0.1.0
Description: Estimate the severity of a disease and ascertainment of cases, as discussed in Nishiura et al. (2009) <doi:10.1371/journal.pone.0006852>.
License: MIT + file LICENSE
URL: https://github.com/epiverse-trace/cfr, https://epiverse-trace.github.io/cfr/
BugReports: https://github.com/epiverse-trace/cfr/issues
Encoding: UTF-8
Imports: checkmate, stats
Suggests: dplyr, tidyr, purrr, scales, forcats, ggplot2, testthat (>= 3.0.0), knitr, bookdown, spelling, incidence2, data.table, distributional, distcrete
Depends: R (>= 3.5.0)
LazyData: true
VignetteBuilder: knitr
Language: en-GB
NeedsCompilation: no
Packaged: 2023-11-21 14:50:15 UTC; lshpg6
Author: Pratik R. Gupte [aut, cre, cph] , Adam Kucharski [aut, cph] , Tim Russell [aut, cph] , Joshua W. Lambert [rev] , Hugo Gruson [rev] , Tim Taylor [rev] , James M. Azam [rev] , Abdoelnaser M. Degoot [rev] , Sebastian Funk [rev]
Maintainer: Pratik R. Gupte <pratik.gupte@lshtm.ac.uk>
Repository: CRAN
Date/Publication: 2023-11-21 18:40:05 UTC

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New package BayesGrowth with initial version 1.0.0
Package: BayesGrowth
Title: Estimate Fish Growth Using MCMC Analysis
Date: 2023-11-13
Version: 1.0.0
Maintainer: Jonathan Smart <jonsmartphd@gmail.com>
Description: Estimate fish length-at-age models using MCMC analysis with 'rstan' models. This package allows a multimodel approach to growth fitting to be applied to length-at-age data and is supported by further analyses to determine model selection and result presentation. The core methods of this package are presented in Smart and Grammer (2021) "Modernising fish and shark growth curves with Bayesian length-at-age models". PLOS ONE 16(2): e0246734 <doi:10.1371/journal.pone.0246734>.
License: GPL-3
URL: https://github.com/jonathansmart/BayesGrowth
BugReports: https://github.com/jonathansmart/BayesGrowth/issues
Depends: R (>= 3.4.0)
SystemRequirements: GNU make
Imports: AquaticLifeHistory, bayesplot, dplyr, ggplot2, loo, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.3.1.1), stats, tibble, tidybayes
Suggests: knitr, rmarkdown,
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
Biarch: true
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)
NeedsCompilation: yes
Packaged: 2023-11-21 01:04:11 UTC; smartj
Author: Jonathan Smart [aut, cre, ctb, cph]
Repository: CRAN
Date/Publication: 2023-11-21 18:10:08 UTC

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New package TSLSTMplus with initial version 1.0.0
Package: TSLSTMplus
Title: Long-Short Term Memory for Time-Series Forecasting, Enhanced
Version: 1.0.0
Author: Jaime Pizarroso Gonzalo [aut, ctb, cre], Antonio Munoz San Roque [aut]
Maintainer: Jaime Pizarroso Gonzalo <jpizarroso@comillas.edu>
Description: The LSTM (Long Short-Term Memory) model is a Recurrent Neural Network (RNN) based architecture that is widely used for time series forecasting. Customizable configurations for the model are allowed, improving the capabilities and usability of this model compared to other packages. This package is based on 'keras' and 'tensorflow' modules and the algorithm of Paul and Garai (2021) <doi:10.1007/s00500-021-06087-4>.
License: GPL-3
Encoding: UTF-8
Imports: keras, tensorflow, tsutils, stats
NeedsCompilation: no
Date: 2023-11-19
Packaged: 2023-11-20 19:20:11 UTC; jaime
Repository: CRAN
Date/Publication: 2023-11-21 18:00:02 UTC

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New package NoviceDeveloperResources with initial version 1.0
Package: NoviceDeveloperResources
Version: 1.0
Date: 2023-11-10
Title: Resources to Assist Novice Developers
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Depends: R (>= 4.2.0)
Imports: utils, devtools
Description: Assist novice developers when preparing a single package or a set of integrated packages to submit to CRAN. Automate the following individual or batch processing: check local source packages; build local .tar.gz source files; install packages from local .tar.gz files; detect conflicts between function names in the environment.
License: GPL (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-11-20 21:24:34 UTC; barryzeeberg
Author: Barry Zeeberg [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-21 18:00:05 UTC

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New package RCPA with initial version 0.1.2
Package: RCPA
Title: Consensus Pathway Analysis
Version: 0.1.2
Description: Provides a set of functions to perform pathway analysis and meta analysis from multiple gene expression datasets, as well as visualization of the results. The package is a wrapper of the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu, Z. (2012) <https://CRAN.R-project.org/package=CePa>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0), tidyr, dplyr, ggplot2, utils, stats
Imports: AnnotationDbi, SummarizedExperiment, BiocManager, Biobase, DESeq2, GEOquery, edgeR, limma, stringr(>= 1.5.0), ggnewscale, ggrepel, graph, httr, rlang, ggpattern, scales, RobustRankAggreg, methods, jsonlite, IRdisplay
Suggests: knitr, rmarkdown, markdown, testthat (>= 3.0.0), ROntoTools, RCyjs, fgsea, BrowserViz, GSA, CePa, meta, png, ggvenn, RCurl, XML, S4Vectors, devtools, hgu133plus2.db, org.Hs.eg.db, oligo
VignetteBuilder: knitr, rmarkdown
BugReports: https://github.com/tinnlab/RCPA/issues
NeedsCompilation: no
Packaged: 2023-11-20 23:36:28 UTC; hanguyen
Author: Ha Nguyen [aut, cre], Zeynab Maghsoudi [aut], Phi Hung Bya [aut], Tin Nguyen [fnd]
Maintainer: Ha Nguyen <hvn0006@auburn.edu>
Repository: CRAN
Date/Publication: 2023-11-21 16:10:03 UTC

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New package WhatsR with initial version 1.0.2
Package: WhatsR
Title: Parsing, Anonymizing and Visualizing Exported 'WhatsApp' Chat Logs
Version: 1.0.2
Date: 2023-11-17
Author: Julian Kohne <julian.kohne@gesis.org>
Maintainer: Julian Kohne <julian.kohne@gesis.org>
Description: Imports 'WhatsApp' chat logs and parses them into a usable dataframe object. The parser works on chats exported from Android or iOS phones and on Linux, macOS and Windows. The parser has multiple options for extracting smileys and emojis from the messages, extracting URLs and domains from the messages, extracting names and types of sent media files from the messages, extracting timestamps from messages, extracting and anonymizing author names from messages. Can be used to create anonymized versions of data.
License: GPL-3
Imports: stringi, qdapRegex, readr, tokenizers, stringr, data.table, ggplot2, anytime, mgsub, stats, qdap, ggwordcloud, dplyr, ragg, checkmate, visNetwork, lubridate, methods
Encoding: UTF-8
Suggests: extrafont, tm, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-11-21 14:26:52 UTC; juko
Repository: CRAN
Date/Publication: 2023-11-21 15:00:02 UTC

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New package SpatMCA with initial version 1.0.4
Package: SpatMCA
Title: Regularized Spatial Maximum Covariance Analysis
Version: 1.0.4
URL: https://github.com/egpivo/SpatMCA
BugReports: https://github.com/egpivo/SpatMCA/issues
Description: Provide regularized maximum covariance analysis incorporating smoothness, sparseness and orthogonality of couple patterns by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D (Wang and Huang, 2017 <doi:10.1002/env.2481>).
License: GPL-3
Depends: R (>= 3.4.0)
Imports: Rcpp, RcppParallel (>= 0.11.2), MASS, ggplot2, scales
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
Suggests: testthat (>= 2.1.0), RColorBrewer, plot3D, pracma, spTimer, fields, maps, covr, V8
SystemRequirements: GNU make
NeedsCompilation: yes
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Encoding: UTF-8
Packaged: 2023-11-20 23:14:19 UTC; joseph
Author: Wen-Ting Wang [aut, cre] , Hsin-Cheng Huang [aut]
Repository: CRAN
Date/Publication: 2023-11-21 14:10:12 UTC

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New package pepr with initial version 0.5.0
Package: pepr
Title: Reading Portable Encapsulated Projects
Version: 0.5.0
Date: 2023-11-16
Maintainer: Nathan Sheffield <nathan@code.databio.org>
Description: A PEP, or Portable Encapsulated Project, is a dataset that subscribes to the PEP structure for organizing metadata. It is written using a simple YAML + CSV format, it is your one-stop solution to metadata management across data analysis environments. This package reads this standardized project configuration structure into R. Described in Sheffield et al. (2021) <doi:10.1093/gigascience/giab077>.
Imports: yaml, stringr, pryr, data.table, methods, RCurl
Suggests: knitr, testthat, rmarkdown, curl
VignetteBuilder: knitr
License: BSD_2_clause + file LICENSE
BugReports: https://github.com/pepkit/pepr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-21 12:55:04 UTC; nsheff
Author: Nathan Sheffield [aut, cph, cre], Michal Stolarczyk [aut]
Repository: CRAN
Date/Publication: 2023-11-21 14:10:06 UTC

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New package MultBiplotR with initial version 23.11.0
Package: MultBiplotR
Title: Multivariate Analysis Using Biplots in R
Version: 23.11.0
Date: 2023-11-16
Author: Jose Luis Vicente-Villardon, Laura Vicente-Gonzalez, Elisa Frutos-Bernal
Maintainer: Jose Luis Vicente Villardon <villardon@usal.es>
Description: Several multivariate techniques from a biplot perspective. It is the translation (with many improvements) into R of the previous package developed in 'Matlab'. The package contains some of the main developments of my team during the last 30 years together with some more standard techniques. Package includes: Classical Biplots, HJ-Biplot, Canonical Biplots, MANOVA Biplots, Correspondence Analysis, Canonical Correspondence Analysis, Canonical STATIS-ACT, Logistic Biplots for binary and ordinal data, Multidimensional Unfolding, External Biplots for Principal Coordinates Analysis or Multidimensional Scaling, among many others. References can be found in the help of each procedure.
License: GPL (>= 2)
Encoding: UTF-8
Repository: CRAN
Depends: R (>= 4.0.0)
Suggests:
Imports: MASS, scales, geometry, deldir, mirt, GPArotation, Hmisc, car, dunn.test, gplots, lattice, polycor, dae, xtable, mvtnorm, psych, ThreeWay, knitr
LazyData: yes
Archs: i386, x64
NeedsCompilation: no
Packaged: 2023-11-20 11:36:24 UTC; joseluis
Date/Publication: 2023-11-21 15:00:06 UTC

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New package clustermq with initial version 0.9.1
Package: clustermq
Title: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM, PBS/Torque)
Version: 0.9.1
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Description: Evaluate arbitrary function calls using workers on HPC schedulers in single line of code. All processing is done on the network without accessing the file system. Remote schedulers are supported via SSH.
URL: https://mschubert.github.io/clustermq/
BugReports: https://github.com/mschubert/clustermq/issues
SystemRequirements: ZeroMQ (libzmq) >= 4.3.0 (optional; otherwise bundled)
Depends: R (>= 3.6.2)
LinkingTo: Rcpp
Imports: methods, narray, progress, R6, Rcpp, utils
License: Apache License (== 2.0) | file LICENSE
Encoding: UTF-8
Suggests: callr, devtools, dplyr, foreach, iterators, knitr, parallel, rmarkdown, roxygen2 (>= 5.0.0), testthat, tools
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-11-15 14:31:44 UTC; mschu
Author: Michael Schubert [aut, cre, cph] , ZeroMQ authors [aut, cph]
Repository: CRAN
Date/Publication: 2023-11-21 14:10:09 UTC

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New package mapmisc with initial version 2.0.3
Package: mapmisc
Title: Utilities for Producing Maps
Version: 2.0.3
Date: 2023-11-20
Depends: terra, R (>= 3.5.0)
Imports: methods, grDevices, stats, utils, graphics, geosphere
Suggests: RColorBrewer, geonames, classInt, knitr
Enhances: XML, RCurl
Description: Provides a minimal, light-weight set of tools for producing nice looking maps in R, with support for map projections. See Brown (2016) <doi:10.32614/RJ-2016-005>.
License: GPL
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-20 17:21:15 UTC; patrick
Author: Patrick Brown [aut, cre, cph]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Repository: CRAN
Date/Publication: 2023-11-21 11:30:07 UTC

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New package bivariatemaps with initial version 1.2
Package: bivariatemaps
Title: Creates Bivariate Maps
Version: 1.2
Description: Contains functions to plot bivariate maps and to generate grids from shapefiles based on area coverage. For more info, see: Hidasi-Neto, J (2015) <https://rfunctions.blogspot.com/2015/03/bivariate-maps-bivariatemap-function.html>, Hidasi-Neto, J (2014) <https://rfunctions.blogspot.com/2014/12/gridfilter-intersect-grid-with-shape.html>.
License: GPL-3
Encoding: UTF-8
Imports: classInt, terra, base, graphics, stats
NeedsCompilation: no
Packaged: 2023-11-21 03:18:50 UTC; heavy
Author: Jose Hidasi-Neto [aut, cre]
Maintainer: Jose Hidasi-Neto <hidasineto@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-21 11:40:02 UTC

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New package rSPARCS with initial version 0.1.1
Package: rSPARCS
Title: Sites, Population, and Records Cleaning Skills
Version: 0.1.1
Maintainer: Wangjian Zhang <zhangwj227@mail.sysu.edu.cn>
Description: Data cleaning including 1) generating datasets for time-series and case-crossover analyses based on raw hospital records, 2) linking individuals to an areal map, 3) picking out cases living within a buffer of certain size surrounding a site, etc. For more information, please refer to Zhang W,etc. (2018) <doi:10.1016/j.envpol.2018.08.030>.
License: GPL-3
Encoding: UTF-8
Imports: data.table,sf,geosphere,tigris,raster,sp,plyr,dplyr,methods
NeedsCompilation: no
Packaged: 2023-11-21 02:14:21 UTC; wzhan
Author: Wangjian Zhang [aut, cre], Zhicheng Du [aut], Xinlei Deng [aut], Ziqiang Lin [aut], Bo Ye [aut], Jijin Yao [aut], Yanan Jin [aut], Wayne Lawrence [aut]
Repository: CRAN
Date/Publication: 2023-11-21 08:20:02 UTC

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New package ggstats with initial version 0.5.1
Package: ggstats
Title: Extension to 'ggplot2' for Plotting Stats
Version: 0.5.1
Description: Provides new statistics, new geometries and new positions for 'ggplot2' and a suite of functions to facilitate the creation of statistical plots.
License: GPL (>= 3)
URL: https://larmarange.github.io/ggstats/, https://github.com/larmarange/ggstats
BugReports: https://github.com/larmarange/ggstats/issues
Imports: broom.helpers (>= 1.14.0), cli, dplyr, forcats, ggplot2 (>= 3.4.0), lifecycle, magrittr, patchwork, purrr, rlang, scales, stats, stringr, tidyr
Suggests: betareg, broom, emmeans, glue, knitr, labelled (>= 2.11.0), reshape, rmarkdown, nnet, parameters, pscl, testthat (>= 3.0.0), spelling, survey, survival, vdiffr
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-21 07:02:14 UTC; josep
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Repository: CRAN
Date/Publication: 2023-11-21 08:10:02 UTC

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New package semidist with initial version 0.1.0
Package: semidist
Title: Measure Dependence Between Categorical and Continuous Variables
Version: 0.1.0
Date: 2023-11-19
Description: Semi-distance and mean-variance (MV) index are proposed to measure the dependence between a categorical random variable and a continuous variable. Test of independence and feature screening for classification problems can be implemented via the two dependence measures. For the details of the methods, see Zhong et al. (2023) <doi:10.1080/01621459.2023.2284988>; Cui and Zhong (2019) <doi:10.1016/j.csda.2019.05.004>; Cui, Li and Zhong (2015) <doi:10.1080/01621459.2014.920256>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: energy, FNN, furrr, purrr, Rcpp, stats
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat (>= 3.0.0)
URL: https://github.com/wzhong41/semidist
BugReports: https://github.com/wzhong41/semidist/issues
NeedsCompilation: yes
Packaged: 2023-11-20 19:43:13 UTC; Chain
Author: Wei Zhong [aut], Zhuoxi Li [aut, cre, cph], Wenwen Guo [aut], Hengjian Cui [aut], Runze Li [aut]
Maintainer: Zhuoxi Li <chainchei@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-21 06:50:02 UTC

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New package PNDSIBGE with initial version 0.1.0
Package: PNDSIBGE
Title: Downloading, Reading and Analyzing PNDS Microdata - Package in Development
Version: 0.1.0
Description: Provides tools for downloading, reading and analyzing the PNDS, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Depends: R (>= 3.2.0)
Imports: dplyr, httr, magrittr, projmgr, RCurl, readr, readxl, survey, tibble, timeDate, utils
Suggests: convey, SIPDIBGE, srvyr
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
BugReports: https://github.com/Gabriel-Assuncao/PNDSIBGE/issues
Packaged: 2023-11-20 16:40:22 UTC; gabriel.assuncao
Repository: CRAN
Date/Publication: 2023-11-21 06:50:06 UTC

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Mon, 20 Nov 2023

New package unhcrthemes with initial version 0.6.1
Package: unhcrthemes
Title: UNHCR 'ggplot2' Theme and Colour Palettes
Version: 0.6.1
Description: A 'ggplot2' theme and color palettes following the United Nations High Commissioner for Refugees (UNHCR) Data Visualization Guidelines recommendations.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/unhcr-dataviz/unhcrthemes, https://unhcr-dataviz.github.io/unhcrthemes/
BugReports: https://github.com/unhcr-dataviz/unhcrthemes/issues
Depends: R (>= 3.5)
Imports: ggplot2, scales, ggtext, ggrepel, systemfonts, extrafont
Suggests: rmarkdown, knitr, colorspace, ragg, refugees, tidyverse, treemapify, ggstream, dplyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-20 13:42:50 UTC; cvidonne
Author: Cedric Vidonne [aut, cre], Ahmadou Dicko [aut], UNHCR [cph]
Maintainer: Cedric Vidonne <cedric@vidonne.me>
Repository: CRAN
Date/Publication: 2023-11-20 19:40:03 UTC

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New package odbr with initial version 0.1.0
Package: odbr
Title: Download Data from Brazil's Origin Destination Surveys
Version: 0.1.0
Description: Download data from Brazil's Origin Destination Surveys. The package covers both data from household travel surveys, dictionaries of variables, and the spatial geometries of surveys conducted in different years and across various urban areas in Brazil. For some cities, the package will include enhanced versions of the data sets with variables "harmonized" across different years.
License: GPL (>= 3)
Depends: R (>= 2.10)
Imports: data.table, fs, haven, piggyback, R.utils, sf, usethis
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.2.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
Language: en-US
NeedsCompilation: no
Packaged: 2023-11-20 13:43:07 UTC; hsvab
Author: Haydee Svab [aut, cre], Beatriz Milz [aut] , Diego Rabatone Oliveira [aut], Rafael H. M. Pereira [aut]
Maintainer: Haydee Svab <hsvab@hsvab.eng.br>
Repository: CRAN
Date/Publication: 2023-11-20 19:40:06 UTC

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New package ggScatRidges with initial version 0.1.0
Package: ggScatRidges
Title: Scatter Plot Combined with Ridgelines in 'ggplot2'
Version: 0.1.0
Date: 2023-11-20
Maintainer: Matthieu Bourgery <matthieu.bourgery@gmail.com>
Imports: ggplot2, cowplot, ggpubr, ggridges, viridis, hrbrthemes
Description: The function combines a scatter plot with ridgelines to better visualise the distribution between sample groups. The plot is created with 'ggplot2'.
License: GPL-3
URL: https://github.com/matbou85/ggScatRidges,
BugReports: https://github.com/matbou85/ggScatRidges/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-20 13:07:38 UTC; matbou
Author: Matthieu Bourgery [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-20 19:40:09 UTC

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New package FlexVarJM with initial version 0.1.0
Package: FlexVarJM
Title: Estimate Joint Models with Subject-Specific Variance
Version: 0.1.0
Description: Estimation of mixed models including a subject-specific variance which can be time and covariate dependent. In the joint model framework, the package handles left truncation and allows a flexible dependence structure between the competing events and the longitudinal marker. The estimation is performed under the frequentist framework, using the Marquardt-Levenberg algorithm. (Courcoul, Tzourio, Woodward, Barbieri, Jacqmin-Gadda (2023) <arXiv:2306.16785>).
License: GPL (>= 3)
Encoding: UTF-8
Imports: ggplot2, lcmm, marqLevAlg, mvtnorm, randtoolbox, Rcpp, stats, survminer, utils
Depends: R (>= 3.5.0), splines, survival
URL: https://github.com/LeonieCourcoul/FlexVarJM
BugReports: https://github.com/LeonieCourcoul/FlexVarJM/issues
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2023-11-20 12:07:33 UTC; lc14
Author: Leonie Courcoul [aut, cre], Antoine Barbieri [aut], Helene Jacqmin-Gadda [aut]
Maintainer: Leonie Courcoul <leonie.courcoul@u-bordeaux.fr>
Repository: CRAN
Date/Publication: 2023-11-20 19:40:12 UTC

More information about FlexVarJM at CRAN
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New package dartR.sim with initial version 0.70
Package: dartR.sim
Title: Computer Simulations of 'SNP' Data
Version: 0.70
Description: Allows to simulate SNP data using genlight objects. For example, it is straight forward to simulate a simple drift scenario with exchange of individuals between two populations or create a new genlight object based on allele frequencies of an existing genlight object.
Encoding: UTF-8
Depends: R (>= 3.5), adegenet (>= 2.0.0), dartR.base, dartR.data, ggplot2
Imports: shiny, fields, utils, methods, stringi, stringr, data.table, Rcpp, shinyBS, shinyjs, shinythemes, shinyWidgets, hierfstat, reshape2
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2023-11-20 06:56:23 UTC; mijangos
Author: Jose L. Mijangos [aut, cre], Bernd Gruber [aut], Arthur Georges [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb]
URL: https://green-striped-gecko.github.io/dartR/, https://github.com/green-striped-gecko/dartR.sim
BugReports: https://github.com/green-striped-gecko/dartR.sim/issues
Maintainer: Jose L. Mijangos <luis.mijangos@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-20 19:30:02 UTC

More information about dartR.sim at CRAN
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New package bpca with initial version 1.3-6
Package: bpca
Version: 1.3-6
Date: 2023-10-20
Title: Biplot of Multivariate Data Based on Principal Components Analysis
Author: Jose C. Faria [aut, cre], Ivan B. Allaman [aut], Clarice G. B. Demetrio [aut]
Maintainer: Jose C. Faria <joseclaudio.faria@gmail.com>
Depends: R (>= 2.6.0), scatterplot3d, rgl
Imports: xtable
Description: Implements biplot (2d and 3d) of multivariate data based on principal components analysis and diagnostic tools of the quality of the reduction.
License: GPL (>= 2)
Encoding: UTF-8
LazyLoad: yes
LazyData: yes
NeedsCompilation: no
Packaged: 2023-11-20 10:27:42 UTC; jcfaria
Repository: CRAN
Date/Publication: 2023-11-20 15:20:02 UTC

More information about bpca at CRAN
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New package hydflood with initial version 0.5.7
Package: hydflood
Title: Flood Extents and Durations along the Rivers Elbe and Rhine
Version: 0.5.7
Date: 2023-11-17
Description: Raster based flood modelling internally using 'hyd1d', an R package to interpolate 1d water level and gauging data. The package computes flood extent and durations through strategies originally developed for 'INFORM', an 'ArcGIS'-based hydro-ecological modelling framework. It does not provide a full, physical hydraulic modelling algorithm, but a simplified, near real time 'GIS' approach for flood extent and duration modelling. Computationally demanding annual flood durations have been computed already and data products were published by Weber (2022) <doi:10.1594/PANGAEA.948042>.
Depends: R (>= 4.0.0), sf, terra, raster, hyd1d
Imports: stats, Rdpack, grDevices
Suggests: knitr, rmarkdown, devtools, pkgdown, roxygen2, testthat, plot3D, plotrix, shiny, shinyjs, shiny.i18n, leaflet, leaflet.extras, leaflet.esri, pangaear, rgrass, stringr
License: GPL-2
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
BugReports: https://github.com/bafg-bund/hydflood/issues/
URL: https://hydflood.bafg.de, https://github.com/bafg-bund/hydflood
NeedsCompilation: no
Packaged: 2023-11-17 13:26:20 UTC; WeberA
Author: Arnd Weber [aut, cre] , Stephan Rosenzweig [ctb], Benjamin Eberhardt [ctb]
Maintainer: Arnd Weber <arnd.weber@bafg.de>
Repository: CRAN
Date/Publication: 2023-11-20 08:00:02 UTC

More information about hydflood at CRAN
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Sun, 19 Nov 2023

New package stratastats with initial version 0.1
Package: stratastats
Title: Stratified Analysis of 2x2 Contingency Tables
Version: 0.1
Description: Offers a comprehensive approach for analysing stratified 2x2 contingency tables. It facilitates the calculation of odds ratios, 95% confidence intervals, and conducts chi-squared tests, Cochran-Mantel-Haenszel tests, and Breslow-Day-Tarone tests. The package is particularly useful in fields like epidemiology and social sciences where stratified analysis is essential. The package also provides interpretative insights into the results, aiding in the understanding of complex statistical outcomes.
Depends: R (>= 4.0.0)
Imports: abind (>= 1.4.0), gt (>= 0.8.0), stats (>= 4.0.0)
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-19 11:04:39 UTC; gianmarcoalberti
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-19 16:00:02 UTC

More information about stratastats at CRAN
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New package REFA with initial version 0.1.0
Package: REFA
Title: Robust Exponential Factor Analysis
Date: 2023-11-01
Version: 0.1.0
Author: Jiaqi Hu [cre, aut], Xueqin Wang [aut]
Maintainer: Jiaqi Hu <hujiaqi@mail.ustc.edu.cn>
Description: A robust alternative to the traditional principal component estimator is proposed within the framework of factor models, known as Robust Exponential Factor Analysis, specifically designed for the modeling of high-dimensional datasets with heavy-tailed distributions. The algorithm estimates the latent factors and the loading by minimizing the exponential squared loss function. To determine the appropriate number of factors, we propose a modified rank minimization technique, which has been shown to significantly enhance finite-sample performance.
Imports: mvtnorm
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-18 03:28:45 UTC; hujiaqi
Repository: CRAN
Date/Publication: 2023-11-19 15:20:05 UTC

More information about REFA at CRAN
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New package PowerSDI with initial version 0.1.3
Package: PowerSDI
Title: Calculate Standardised Drought Indices Using NASA POWER Data
Version: 0.1.3
Description: A set of functions designed to calculate the standardised precipitation and standardised precipitation evapotranspiration indices using NASA POWER data as described in Blain et al. (2023) <doi:10.2139/ssrn.4442843>. These indices are calculated using a reference data source. The functions verify if the indices' estimates meet the assumption of normality and how well NASA POWER estimates represent real-world data. Indices are calculated in a routine mode. Potential evapotranspiration amounts and the difference between rainfall and potential evapotranspiration are also calculated. The functions adopt a basic time scale that splits each month into four periods. Days 1 to 7, days 8 to 14, days 15 to 21, and days 22 to 28, 29, 30, or 31, where 'TS=4' corresponds to a 1-month length moving window (calculated 4 times per month) and 'TS=48' corresponds to a 12-month length moving window (calculated 4 times per month).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1.0)
Imports: graphics, lmom, lubridate, nasapower, stats
URL: https://github.com/gabrielblain/PowerSDI
BugReports: https://github.com/gabrielblain/PowerSDI/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), vcr (>= 0.6.0), vdiffr (>= 1.0.0)
VignetteBuilder: knitr
Language: en-GB
NeedsCompilation: no
Packaged: 2023-11-18 12:58:52 UTC; Gabriel
Author: Gabriel Constantino Blain [aut, cre] , Graciela R. Sobierajski [aut] , Leticia L. Martins [aut] , Adam H. Sparks [aut]
Maintainer: Gabriel Constantino Blain <gabriel.blain@sp.gov.br>
Repository: CRAN
Date/Publication: 2023-11-19 15:30:02 UTC

More information about PowerSDI at CRAN
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New package HVT with initial version 23.11.1
Package: HVT
Date: 2023-11-17
Title: Constructing Hierarchical Voronoi Tessellations and Overlay Heatmaps for Data Analysis
Version: 23.11.1
Description: Facilitates building topology preserving maps for rich multivariate data. See <https://en.wikipedia.org/wiki/Voronoi_diagram> for more information. Credits to Mu Sigma for their continuous support throughout the development of the package.
License: Apache License 2.0
Encoding: UTF-8
Imports: MASS, deldir, grDevices, splancs, sp, conf.design, Hmisc, stats, dplyr, purrr, magrittr, polyclip, ggplot2, tidyr, scales, cluster, reshape2, plyr, data.table
Depends: R (>= 3.6.0)
BugReports: https://github.com/Mu-Sigma/HVT/issues
URL: https://github.com/Mu-Sigma/HVT
Suggests: knitr, rmarkdown, testthat, geozoo, kableExtra, plotly, DT, gridExtra, gtable, htmlwidgets, installr, skimr, tibble, devtools, tidyverse, DataExplorer, htmltools, corrplot, gganimate
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-18 10:35:22 UTC; gopi
Author: Zubin Dowlaty [aut], Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>
Repository: CRAN
Date/Publication: 2023-11-19 15:20:12 UTC

More information about HVT at CRAN
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New package HDCD with initial version 1.0
Package: HDCD
Title: High-Dimensional Changepoint Detection
Version: 1.0
Date: 2023-11-17
Maintainer: Per August Jarval Moen <pamoen@math.uio.no>
Description: Efficient implementations of the following multiple changepoint detection algorithms: Efficient Sparsity Adaptive Change-point estimator by Moen, Glad and Tveten (2023) <arXiv:2306.04702> , Informative Sparse Projection for Estimating Changepoints by Wang and Samworth (2017) <doi:10.1111/rssb.12243>, and the method of Pilliat et al (2023) <doi:10.1214/23-EJS2126>.
License: GPL-3
Encoding: UTF-8
Imports: mclust, Rdpack
NeedsCompilation: yes
Packaged: 2023-11-18 13:48:21 UTC; peraugust
Author: Per August Jarval Moen [cre, aut]
Repository: CRAN
Date/Publication: 2023-11-19 15:30:06 UTC

More information about HDCD at CRAN
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New package oHMMed with initial version 1.0.1
Package: oHMMed
Title: HMMs with Ordered Hidden States and Emission Densities
Version: 1.0.1
Description: Inference using a class of Hidden Markov models (HMMs) called 'oHMMed'(ordered HMM with emission densities <doi:10.1101/2023.06.26.546495>): The 'oHMMed' algorithms identify the number of comparably homogeneous regions within observed sequences with autocorrelation patterns. These are modelled as discrete hidden states; the observed data points are then realisations of continuous probability distributions with state-specific means that enable ordering of these distributions. The observed sequence is labelled according to the hidden states, permitting only neighbouring states that are also neighbours within the ordering of their associated distributions. The parameters that characterise these state-specific distributions are then inferred. Relevant for application to genomic sequences, time series, or any other sequence data with serial autocorrelation.
License: GPL-3
URL: https://github.com/LynetteCaitlin/oHMMed, https://lynettecaitlin.github.io/oHMMed/
BugReports: https://github.com/LynetteCaitlin/oHMMed/issues
Depends: R (>= 3.5.0)
Imports: cvms, ggmcmc, ggplot2, gridExtra, mistr, scales, stats, vcd
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-18 21:13:31 UTC; michal
Author: Michal Majka [aut, cre] , Lynette Caitlin Mikula [aut] , Claus Vogl [aut]
Maintainer: Michal Majka <michalmajka@hotmail.com>
Repository: CRAN
Date/Publication: 2023-11-19 07:50:02 UTC

More information about oHMMed at CRAN
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Sat, 18 Nov 2023

New package datplot with initial version 1.1.1
Package: datplot
Title: Preparation of Object Dating Ranges for Density Plots (Aoristic Analysis)
Version: 1.1.1
Maintainer: Lisa Steinmann <lisa.steinmann@rub.de>
Description: Converting date ranges into dating 'steps' eases the visualization of changes in e.g. pottery consumption, style and other variables over time. This package provides tools to process and prepare data for visualization and employs the concept of aoristic analysis.
License: GPL (>= 3)
URL: https://github.com/lsteinmann/datplot, https://lsteinmann.github.io/datplot/
BugReports: https://github.com/lsteinmann/datplot/issues
Depends: R (>= 3.3)
Suggests: covr, devtools, dplyr, forcats, ggplot2, ggridges, knitr, reshape2, rmarkdown, stringr, testthat
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-18 13:59:29 UTC; l_steinmann
Author: Lisa Steinmann [aut, cre, cph] , Barbora Weissova [ctb]
Repository: CRAN
Date/Publication: 2023-11-18 23:50:07 UTC

More information about datplot at CRAN
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New package SFSI with initial version 1.3.1
Package: SFSI
Title: Sparse Family and Selection Index
Version: 1.3.1
Date: 2023-11-17
Description: Here we provide tools for the estimation of coefficients in penalized regressions when the (co)variance matrix of predictors and the covariance vector between predictors and response, are provided. These methods are extended to the context of a Selection Index (commonly used for breeding value prediction). The approaches offer opportunities such as the integration of high-throughput traits in genetic evaluations ('Lopez-Cruz et al., 2020') <doi:10.1038/s41598-020-65011-2> and solutions for training set optimization in Genomic Prediction ('Lopez-Cruz & de los Campos, 2021') <doi:10.1093/genetics/iyab030>.
LazyLoad: true
Depends: R (>= 3.6.0), ggplot2
Imports: stats, scales, tensorEVD, parallel, reshape2, viridis, igraph
Suggests: BGLR, knitr, rmarkdown
VignetteBuilder: rmarkdown
Encoding: UTF-8
License: GPL-3
NeedsCompilation: yes
Packaged: 2023-11-17 22:48:13 UTC; marco
Author: Marco Lopez-Cruz [aut, cre], Gustavo de los Campos [aut], Paulino Perez-Rodriguez [ctb]
Maintainer: Marco Lopez-Cruz <maraloc@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-18 07:00:03 UTC

More information about SFSI at CRAN
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Fri, 17 Nov 2023

New package spatialEco with initial version 2.0-2
Package: spatialEco
Title: Spatial Analysis and Modelling Utilities
Version: 2.0-2
Date: 2023-11-17
Description: Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.
Depends: R (>= 4.2)
Imports: sf, terra
Suggests: spatstat.geom (>= 3.0-3), spatstat.explore, spdep, ks, cluster, readr, RCurl, RANN, rms, yaImpute, mgcv, zyp, SpatialPack (>= 0.3), MASS, caret, dplyr, earth, Matrix, gstat, spatstat.data, methods, units, sp, stringr, lwgeom, geodata
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
License: GPL-3
URL: https://github.com/jeffreyevans/spatialEco, https://jeffreyevans.github.io/spatialEco/
BugReports: https://github.com/jeffreyevans/spatialEco/issues
NeedsCompilation: no
Repository: CRAN
LazyData: true
Encoding: UTF-8
Packaged: 2023-11-17 21:27:53 UTC; jeffrey_evans
Author: Jeffrey S. Evans [aut, cre] , Melanie A. Murphy [ctb], Karthik Ram [ctb]
Date/Publication: 2023-11-17 22:40:02 UTC

More information about spatialEco at CRAN
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New package fdth with initial version 1.3-0
Package: fdth
Version: 1.3-0
Date: 2023-11-17
Title: Frequency Distribution Tables, Histograms and Polygons
Author: J. C. Faria [aut, cre], I. B. Allaman [aut], E. G. Jelihovschi [aut]
Maintainer: J. C. Faria <joseclaudio.faria@gmail.com>
Depends: R (>= 2.6.0)
Imports: xtable
Description: Perform frequency distribution tables, associated histograms and polygons from vector, data.frame and matrix objects for numerical and categorical variables.
License: GPL (>= 2)
URL: https://github.com/jcfaria/fdth
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-17 22:02:23 UTC; jcfaria
Repository: CRAN
Date/Publication: 2023-11-17 23:00:02 UTC

More information about fdth at CRAN
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New package ScRNAIMM with initial version 0.1
Package: ScRNAIMM
Title: Performing Single-Cell RNA-Seq Imputation by Using Mean/Median Imputation
Version: 0.1
Maintainer: Mohamed Soudy <Mohmedsoudy2009@gmail.com>
Description: Performing single-cell imputation in a way that preserves the biological variations in the data. The package clusters the input data to do imputation for each cluster, and do a distribution check using the Anderson-Darling normality test to impute dropouts using mean or median (Yazici, B., & Yolacan, S. (2007) <DOI:10.1080/10629360600678310>).
License: GPL-3
Encoding: UTF-8
Imports: magrittr, dplyr, nortest, mclust, scDHA
NeedsCompilation: no
Packaged: 2023-11-17 14:25:50 UTC; Soudy
Author: Mohamed Soudy [aut, cre], Sascha Jung [aut], Antonio DEL SOL [aut]
Repository: CRAN
Date/Publication: 2023-11-17 20:10:10 UTC

More information about ScRNAIMM at CRAN
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New package PANPRSnext with initial version 1.2.0
Package: PANPRSnext
Title: Building PRS Models Based on Summary Statistics of GWAs
Version: 1.2.0
Description: Shrinkage estimator for polygenic risk prediction (PRS) models based on summary statistics of genome-wide association (GWA) studies. Based upon the methods and original 'PANPRS' package as found in: Chen, Chatterjee, Landi, and Shi (2020) <doi:10.1080/01621459.2020.1764849>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10), gtools
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
NeedsCompilation: yes
Packaged: 2023-11-17 21:24:51 UTC; Katherine
Author: Katherine Luo [aut, cre], Garcia Espin Osvaldo [aut]
Maintainer: Katherine Luo <hluo224@uwo.ca>
Repository: CRAN
Date/Publication: 2023-11-17 20:20:14 UTC

More information about PANPRSnext at CRAN
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New package gspcr with initial version 0.9.4
Package: gspcr
Title: Generalized Supervised Principal Component Regression
Version: 0.9.4
Description: Generalization of supervised principal component regression (SPCR; Bair et al., 2006, <doi:10.1198/016214505000000628>) to support continuous, binary, and discrete variables as outcomes and predictors (inspired by the 'superpc' R package <https://cran.r-project.org/package=superpc>).
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, lmtest, patchwork, rmarkdown, superpc, testthat (>= 3.0.0)
Depends: R (>= 2.10)
LazyData: true
Imports: dplyr, FactoMineR, ggplot2, MASS, MLmetrics, nnet, PCAmixdata, reshape2, rlang
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-17 15:19:27 UTC; edoardo
Author: Edoardo Costantini [aut, cre]
Maintainer: Edoardo Costantini <costantini.edoardo@yahoo.com>
Repository: CRAN
Date/Publication: 2023-11-17 20:20:04 UTC

More information about gspcr at CRAN
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New package air with initial version 0.2.2
Package: air
Title: AI Assistant to Write and Understand R Code
Version: 0.2.2
Description: An R console utility that lets you ask R related questions to the 'OpenAI' large language model. It can answer 'how-to()' questions by providing code, and 'whatis()' questions by explaining what given code does. You must provision your own key for the 'OpenAI' API <https://platform.openai.com/docs/api-reference>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: httr, keyring, rjson
Suggests: testthat (>= 3.0.0), vcr (>= 0.6.0)
URL: https://github.com/soumyaray/air
BugReports: https://github.com/soumyaray/air/issues
NeedsCompilation: no
Packaged: 2023-11-17 15:03:35 UTC; soumyaray
Author: Soumya Ray [aut, cre, cph]
Maintainer: Soumya Ray <soumya.ray@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-17 20:10:07 UTC

More information about air at CRAN
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New package ulrb with initial version 0.1.3
Package: ulrb
Title: Unsupervised Learning Based Definition of Microbial Rare Biosphere
Version: 0.1.3
Maintainer: Francisco Pascoal <fpascoal1996@gmail.com>
Date: 2023-11-13
Description: A tool to define rare biosphere. 'ulrb' solves the problem of the definition of rarity by replacing human decision with an unsupervised machine learning algorithm (partitioning around medoids, or k-medoids). This algorithm works for any type of microbiome data, provided there is an abundance score for each phylogenetic unit. For validation of this method to several kinds of molecular data and environments, please see Pascoal et al, 2023 (in preparation). Preliminary data suggest this method also works well for non-microbiome data, if there is a species abundance table.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown, stringr, testthat (>= 3.0.0), vegan
Imports: cluster, dplyr, ggplot2, purrr, rlang, stats, tidyr, clusterSim, gridExtra
VignetteBuilder: knitr
URL: https://pascoalf.github.io/ulrb/
BugReports: https://github.com/pascoalf/ulrb/issues
NeedsCompilation: no
Packaged: 2023-11-17 09:30:19 UTC; fpascoal
Author: Francisco Pascoal [aut, cre] , Paula Branco [aut] , Luis Torgo [aut] , Rodrigo Costa [aut] , Catarina Magalhaes [aut]
Repository: CRAN
Date/Publication: 2023-11-17 19:50:02 UTC

More information about ulrb at CRAN
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New package semantic.assets with initial version 1.0.0
Package: semantic.assets
Title: Assets for 'shiny.semantic'
Version: 1.0.0
Description: Style sheets and JavaScript assets for 'shiny.semantic' package.
URL: https://github.com/Appsilon/semantic.assets
BugReports: https://github.com/Appsilon/semantic.assets/issues
License: LGPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-17 09:51:08 UTC; kuba
Author: Jakub Nowicki [aut, cre]
Maintainer: Jakub Nowicki <opensource+kuba@appsilon.com>
Repository: CRAN
Date/Publication: 2023-11-17 19:50:06 UTC

More information about semantic.assets at CRAN
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New package rllama with initial version 0.2.0
Package: rllama
Title: Access and Analyze Data from 'DeFiLlama'
Version: 0.2.0
Description: Provides an interface to access and analyze data from 'DeFiLlama'<https://defillama.com>. This package simplifies the process of fetching and manipulating 'DeFiLlama' data for further analysis and visualization.
License: MIT + file LICENSE
URL: https://github.com/AlexTwoR/rllama
BugReports: https://github.com/AlexTwoR/rllama/issues
Imports: data.table, httr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2023-11-17 12:43:42 UTC; alex
Author: Alexey Ivanov [aut, cre, cph]
Maintainer: Alexey Ivanov <twor.2r@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-17 20:00:02 UTC

More information about rllama at CRAN
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New package remstats with initial version 3.2.0
Package: remstats
Title: Computes Statistics for Relational Event History Data
Version: 3.2.0
Date: 2023-11-15
Maintainer: Marlyne Meijerink-Bosman <m.l.meijerink@tilburguniversity.edu>
Description: Computes a variety of statistics for relational event models. Relational event models enable researchers to investigate both exogenous and endogenous factors influencing the evolution of a time-ordered sequence of events. These models are categorized into tie-oriented models (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>), where the probability of a dyad interacting next is modeled in a single step, and actor-oriented models (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>), which first model the probability of a sender initiating an interaction and subsequently the probability of the sender's choice of receiver. The package is designed to compute a variety of statistics that summarize exogenous and endogenous influences on the event stream for both types of models.
License: GPL (>= 3)
URL: https://github.com/TilburgNetworkGroup/remstats
BugReports: https://github.com/TilburgNetworkGroup/remstats/issues
LazyData: true
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: Rcpp (>= 1.0.8.3), stats
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Suggests: graphics, tinytest, remify (>= 3.2.0), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-11-17 10:24:09 UTC; mlbosman
Author: Marlyne Meijerink-Bosman [aut, cre], Giuseppe Arena [ctb], Diana Karimova [ctb], Rumana Lakdawala [ctb], Mahdi Shafiee Kamalabad [ctb], Fabio Generoso Vieira [ctb], Roger Leenders [ctb], Joris Mulder [ctb]
Repository: CRAN
Date/Publication: 2023-11-17 19:50:10 UTC

More information about remstats at CRAN
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New package nlopt with initial version 0.1.1
Package: nlopt
Title: Call Optimization Solvers with .nl Files
Version: 0.1.1
Description: The purpose of this library is to to call different optimization solvers (such as Gonzalez Rodriguez et al. (2022) <doi:10.1007/s10898-022-01229-w>, Tawarmalani and Sahinidis (2005) <doi:10.1007/s10107-005-0581-8>, and Byrd et al. (2006) <doi:10.1007/0-387-30065-1_4>) to solve problems given by a standard nl file.
License: GPL-3
Language: en-US
Imports: stringr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-17 12:16:59 UTC; brais
Author: Brais Gonzalez-Rodriguez [aut, cre]
Maintainer: Brais Gonzalez-Rodriguez <braisgonzalez.rodriguez@usc.es>
Repository: CRAN
Date/Publication: 2023-11-17 20:00:05 UTC

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New package dssd with initial version 1.0.2
Package: dssd
Imports: sf, ggplot2, methods
Suggests: knitr, rmarkdown, tibble, covr, testthat
VignetteBuilder: knitr
Title: Distance Sampling Survey Design
Version: 1.0.2
Description: Creates survey designs for distance sampling surveys. These designs can be assessed for various effort and coverage statistics. Once the user is satisfied with the design characteristics they can generate a set of transects to use in their distance sampling survey. Many of the designs implemented in this R package were first made available in our 'Distance' for Windows software and are detailed in Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008, ISBN-13: 978-0199225873). Find out more about estimating animal/plant abundance with distance sampling at <http://distancesampling.org/>.
BugReports: https://github.com/DistanceDevelopment/dssd/issues
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-17 11:08:39 UTC; lhm
Author: Laura Marshall [aut, cre], Rexstad Eric [ctb]
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Repository: CRAN
Date/Publication: 2023-11-17 16:30:02 UTC

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New package ohun with initial version 1.0.1
Package: ohun
Title: Optimizing Acoustic Signal Detection
Version: 1.0.1
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Description: Facilitates the automatic detection of acoustic signals, providing functions to diagnose and optimize the performance of detection routines. Detections from other software can also be explored and optimized. Araya-Salas et al. (2022) <doi:10.1101/2022.12.13.520253>.
License: GPL (>= 2)
Encoding: UTF-8
URL: https://docs.ropensci.org/ohun/, https://github.com/ropensci/ohun/
BugReports: https://github.com/ropensci/ohun/issues/
VignetteBuilder: knitr
Language: en-US
Imports: tuneR, warbleR (>= 1.1.29), cli, methods, stats, utils, seewave (>= 2.0.1), fftw, rlang, sf, igraph, checkmate, ggplot2
Depends: R (>= 3.2.1)
Suggests: knitr, rmarkdown, testthat, viridis, Sim.DiffProc, vdiffr
NeedsCompilation: no
Packaged: 2023-11-15 14:17:41 UTC; m
Author: Marcelo Araya-Salas [aut, cre] , Alec L. Robitaille [rev] , Sam Lapp [rev]
Repository: CRAN
Date/Publication: 2023-11-17 11:30:02 UTC

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New package simRestore with initial version 1.1.4
Package: simRestore
Title: Simulate the Effect of Management Policies on Restoration Efforts
Version: 1.1.4
Description: Simulation methods to study the effect of management policies on efforts to restore populations back to their original genetic composition. Allows for single-scenario simulation and for optimization of specific chosen scenarios. Further information can be found in Hernandez, Janzen and Lavretsky (2023) <doi:10.1111/1755-0998.13892>.
License: GPL (>= 2)
Imports: Rcpp, shiny, subplex, tibble
Suggests: dplyr, ggplot2, knitr, magrittr, rmarkdown, shinyBS, shinythemes, shinyWidgets, testthat, tidyr, egg
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2023-11-16 19:05:55 UTC; thijsjanzen
Author: Thijs Janzen [aut, cre]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-17 09:50:02 UTC

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New package simStateSpace with initial version 1.0.1
Package: simStateSpace
Title: Simulate Data from State Space Models
Version: 1.0.1
Description: Provides a streamlined and user-friendly framework for simulating data in state space models, particularly when the number of subjects/units (n) exceeds one, a scenario commonly encountered in social and behavioral sciences. For an introduction to state space models in social and behavioral sciences, refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
URL: https://github.com/jeksterslab/simStateSpace, https://jeksterslab.github.io/simStateSpace/
BugReports: https://github.com/jeksterslab/simStateSpace/issues
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
Suggests: knitr, rmarkdown, testthat, Matrix
NeedsCompilation: yes
Packaged: 2023-11-16 22:48:30 UTC; root
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-17 08:30:02 UTC

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New package perARMA with initial version 1.7
Package: perARMA
Title: Periodic Time Series Analysis
Version: 1.7
Maintainer: Karolina Marek <karolina.marek10@gmail.com>
Description: Identification, model fitting and estimation for time series with periodic structure. Additionally, procedures for simulation of periodic processes and real data sets are included. Hurd, H. L., Miamee, A. G. (2007) <doi:10.1002/9780470182833> Box, G. E. P., Jenkins, G. M., Reinsel, G. (1994) <doi:10.1111/jtsa.12194> Brockwell, P. J., Davis, R. A. (1991, ISBN:978-1-4419-0319-8) Bretz, F., Hothorn, T., Westfall, P. (2010, ISBN: 9780429139543) Westfall, P. H., Young, S. S. (1993, ISBN:978-0-471-55761-6) Bloomfield, P., Hurd, H. L.,Lund, R. (1994) <doi:10.1111/j.1467-9892.1994.tb00181.x> Dehay, D., Hurd, H. L. (1994, ISBN:0-7803-1023-3) Vecchia, A. (1985) <doi:10.1080/00401706.1985.10488076> Vecchia, A. (1985) <doi:10.1111/j.1752-1688.1985.tb00167.x> Jones, R., Brelsford, W. (1967) <doi:10.1093/biomet/54.3-4.403> Makagon, A. (1999) <https://www.math.uni.wroc.pl/~pms/files/19.2/Article/19.2.5.pdf> Sakai, H. (1989) <doi:10.1111/j.1467-9892.1991.t [...truncated...]
License: GPL (>= 2.0)
LazyData: TRUE
Imports: corpcor, gnm, matlab, Matrix, signal, stats
NeedsCompilation: no
Packaged: 2023-11-16 21:43:34 UTC; karolina
Repository: CRAN
Date/Publication: 2023-11-17 08:20:02 UTC
Author: Anna Dudek [aut], Harry Hurd [aut], Wioletta Wojtowicz [aut], Karolina Marek [cre]

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New package miLAG with initial version 1.0.2
Package: miLAG
Title: Calculates Microbial Lag Duration (on the Population Level) from Provided Growth Curve Data
Version: 1.0.2
Date: 2023-11-14
Description: Microbial growth is often measured by growth curves i.e. a table of population sizes and times of measurements. This package allows to use such growth curve data to determine the duration of "microbial lag phase" i.e. the time needed for microbes to restart divisions. It implements the most commonly used methods to calculate the lag duration, these methods are discussed and described in Opalek et.al. 2022. Citation: "How to determine microbial lag phase duration?", M. Opalek, B. Smug, D. Wloch-Salamon (2022) <doi:10.1101/2022.11.16.516631>.
License: GPL-3
Depends: R (>= 4.3.0), dplyr (>= 1.0.8), ggplot2 (>= 3.4.1), testthat (>= 3.1.8), minpack.lm (>= 1.2.2), nlsMicrobio (>= 0.0.3)
Suggests: knitr, rmarkdown
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-17 08:13:24 UTC; bognasmug
Author: Bogna Smug [aut, cre]
Maintainer: Bogna Smug <bogna.smug@uj.edu.pl>
Repository: CRAN
Date/Publication: 2023-11-17 08:50:03 UTC

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New package factor256 with initial version 0.1.0
Package: factor256
Title: Use Raw Vectors to Minimize Memory Consumption of Factors
Version: 0.1.0
Description: Uses raw vectors to minimize memory consumption of categorical variables with fewer than 256 unique values. Useful for analysis of large datasets involving variables such as age, years, states, countries, or education levels.
License: GPL-2
Encoding: UTF-8
Imports: utils
Suggests: data.table, tinytest
NeedsCompilation: yes
Packaged: 2023-11-17 05:59:45 UTC; hughp
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-17 08:50:06 UTC

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New package AquaticLifeHistory with initial version 1.0.5
Package: AquaticLifeHistory
Title: Life History Analysis Tools
Version: 1.0.5
Date: 2023-11-09
Maintainer: Jonathan Smart <jonsmartphd@gmail.com>
Description: Estimate aquatic species life history using robust techniques. This package supports users undertaking two types of analysis: 1) Growth from length-at-age data, and 2) maturity analyses for length and/or age data. Maturity analyses are performed using generalised linear model approaches incorporating either a binomial or quasibinomial distribution. Growth modelling is performed using the multimodel approach presented by Smart et al. (2016) "Multimodel approaches in shark and ray growth studies: strengths, weaknesses and the future" <doi:10.1111/faf.12154>.
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3)
Imports: plyr, MASS, readr, broom, MuMIn, magrittr, rlist, minpack.lm, dplyr, tidyr, ggplot2
License: GPL-3
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/jonathansmart/AquaticLifeHistory
BugReports: https://github.com/jonathansmart/AquaticLifeHistory/issues
NeedsCompilation: no
Packaged: 2023-11-16 22:41:03 UTC; smartj
Author: Jonathan Smart [aut, cre, ctb]
Repository: CRAN
Date/Publication: 2023-11-17 08:33:58 UTC

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New package ANOFA with initial version 0.1.2
Package: ANOFA
Title: Analyses of Frequency Data
Version: 0.1.2
Date: 2023-11-16
Author: Denis Cousineau [aut, cre], Louis Laurencelle [ctb], Pier-Olivier Caron [ctb]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>
BugReports: https://github.com/dcousin3/ANOFA/issues/
URL: https://dcousin3.github.io/ANOFA/
Description: Analyses of frequencies can be performed using an alternative test based on the G statistic. The test has similar type-I error rates and power as the chi-square test. However, it is based on a total statistic that can be decomposed in an additive fashion into interaction effects, main effects, simple effects, contrast effects, etc., mimicking precisely the logic of ANOVA. We call this set of tools 'ANOFA' (Analysis of Frequency data) to highlight its similarities with ANOVA. This framework also renders plots of frequencies along with confidence intervals. Finally, effect sizes and planning statistical power are easily done under this framework. The ANOFA is a tool that assesses the significance of effects instead of the significance of parameters; as such, it is more intuitive to most researchers than alternative approaches based on generalized linear models. See Laurencelle and Cousineau (2023) <doi:10.20982/tqmp.19.2.p173>.
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
Depends: R (>= 3.5.0)
Imports: rrapply (>= 1.2.6), superb (>= 0.95.0), Rdpack (>= 0.7), ggplot2 (>= 3.1.0), stats, utils
Suggests: rmarkdown, testthat, knitr
NeedsCompilation: no
Packaged: 2023-11-16 22:33:44 UTC; Denis Cousineau
Repository: CRAN
Date/Publication: 2023-11-17 08:34:01 UTC

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Thu, 16 Nov 2023

New package GREENeR with initial version 0.1.3
Package: GREENeR
Title: Geospatial Regression Equation for European Nutrient Losses (GREEN)
Version: 0.1.3
Author: A. Udias [aut], B. Grizzetti [aut], O. Vigiak [aut], J. Gomez [aut], C. Alfaro [aut, cre], A. Aloe [aut]
Maintainer: C. Alfaro <c.alfarog@gmail.com>
Description: Tools and methods to apply the model Geospatial Regression Equation for European Nutrient losses (GREEN); Grizzetti et al. (2005) <doi:10.1016/j.jhydrol.2004.07.036>; Grizzetti et al. (2008); Grizzetti et al. (2012) <doi:10.1111/j.1365-2486.2011.02576.x>; Grizzetti et al. (2021) <doi:10.1016/j.gloenvcha.2021.102281>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: FME (>= 1.3.6.1), data.table (>= 1.13.6), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), graphics (>= 3.6.1), sf (>= 1.0-2), dplyr (>= 1.0.7), magrittr (>= 2.0.1), tmap (>= 3.3-2), gridExtra (>= 2.3), tidyselect (>= 1.1.0), classInt (>= 0.4-3), grDevices (>= 3.5), networkD3 (>= 0.4), parallelly (>= 1.30.0)
Depends: R (>= 3.5.0)
URL: https://github.com/calfarog/GREENeR
BugReports: https://github.com/calfarog/GREENeR/issues
Suggests: testthat, knitr, rmarkdown, codetools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-16 20:07:52 UTC; cesar.alfaro
Repository: CRAN
Date/Publication: 2023-11-16 23:03:53 UTC

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New package umx with initial version 4.19.0
Package: umx
Version: 4.19.0
Date: 2023-11-20
Title: Structural Equation Modeling and Twin Modeling in R
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
License: GPL-3
Language: en-US
Encoding: UTF-8
URL: https://github.com/tbates/umx#readme
Description: Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Depends: R (>= 4.1.0), OpenMx (>= 2.19.0),
Imports: cowplot, DiagrammeR, ggplot2, kableExtra, knitr, lavaan, MASS, Matrix, methods, MuMIn, mvtnorm, nlme, polycor, R2HTML, RCurl, scales, utils, xtable, gert, hrbrthemes, openxlsx, paran, psych, psychTools, foreign, pwr, rmarkdown
Suggests: cocor, devtools, rhub, spelling, testthat, parallel, GPArotation
Enhances: DiagrammeRsvg, rsvg
BugReports: https://github.com/tbates/umx/issues
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-16 21:36:59 UTC; tim
Author: Timothy C. Bates [aut, cre] , Nathan Gillespie [wit], Hermine Maes [ctb], Michael C. Neale [ctb], Joshua N. Pritikin [ctb], Luis De Araujo [ctb], Brenton Wiernik [ctb], Michael Zakharin [wit]
Repository: CRAN
Date/Publication: 2023-11-16 22:50:06 UTC

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