CRANberries

Tue, 27 Sep 2022

New package OrdCD with initial version 1.0.0
Package: OrdCD
Title: Ordinal Causal Discovery
Version: 1.0.0
Date: 2022-09-23
Description: Algorithms for ordinal causal discovery. This package aims to enable users to discover causality for observational ordinal categorical data with greedy and exhaustive search. See Ni, Y., & Mallick, B. (2022) <https://proceedings.mlr.press/v180/ni22a/ni22a.pdf> "Ordinal Causal Discovery. Proceedings of the 38th Conference on Uncertainty in Artificial Intelligence, (UAI 2022), PMLR 180:1530–1540".
License: MIT + file LICENSE
Encoding: UTF-8
Imports: gRbase, MASS, bnlearn, igraph, stats
URL: https://github.com/nySTAT/OCD
BugReports: https://github.com/nySTAT/OCD/issues
NeedsCompilation: no
Packaged: 2022-09-27 02:50:05 UTC; yangn
Author: Yang Ni [aut, cre]
Maintainer: Yang Ni <yni@stat.tamu.edu>
Repository: CRAN
Date/Publication: 2022-09-27 10:30:02 UTC

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New package OptimalSurrogate with initial version 1.0
Package: OptimalSurrogate
Title: Model Free Approach to Quantifying Surrogacy
Version: 1.0
Description: Identifies an optimal transformation of a surrogate marker such that the proportion of treatment effect explained can be inferred based on the transformation of the surrogate and nonparametrically estimates two model-free quantities of this proportion. Details are described in Wang et al (2020) <doi:10.1093/biomet/asz065>.
License: GPL-3
Depends: R (>= 3.0)
Imports: splines, MASS, stats
NeedsCompilation: no
Packaged: 2022-09-27 00:03:52 UTC; parastlm
Author: Xuan Wang [aut], Layla Parast [aut, cre], Ming Yang [aut], Lu Tian [aut], Tianxi Cai [aut]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Repository: CRAN
Date/Publication: 2022-09-27 10:20:07 UTC

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New package less with initial version 0.1.0
Package: less
Title: Learning with Subset Stacking
Version: 0.1.0
Description: "Learning with Subset Stacking" is a supervised learning algorithm that is based on training many local estimators on subsets of a given dataset, and then passing their predictions to a global estimator. You can find the details about LESS in our manuscript at <arXiv:2112.06251>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: caret, e1071, FNN, MLmetrics, pracma, R6, randomForest, RANN, rpart, wordspace
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-27 10:19:15 UTC; ozerc
Author: Ilker Birbil [aut], Burhan Ozer Cavdar [aut, trl, cre]
Maintainer: Burhan Ozer Cavdar <bcavdar17@ku.edu.tr>
Repository: CRAN
Date/Publication: 2022-09-27 11:00:02 UTC

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New package getpublist with initial version 0.1.0
Package: getpublist
Title: Obtain a List of Publications from 'PubMed' and 'Google Scholar'
Version: 0.1.0
Maintainer: Xuefei Jia <xuefeij.ai@gmail.com>
Description: Use web scraping for 'PubMed'(<https://pubmed.ncbi.nlm.nih.gov>) and 'Google Scholar' profile page (for example <https://scholar.google.com/citations?user=lOOV8rwAAAAJ&hl=en>) to get all of the published information from the search page. Then placing it on a table.
License: GPL-3
Imports: dplyr, magrittr, rvest, stringr, tibble, tidyr, xml2
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-27 01:12:38 UTC; jiax
Author: Xuefei Jia [aut, ctb, cre]
Repository: CRAN
Date/Publication: 2022-09-27 10:20:02 UTC

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New package freebird with initial version 1.0
Package: freebird
Title: Estimation and Inference for High Dimensional Mediation and Surrogate Analysis
Version: 1.0
Description: Estimates and provides inference for quantities that assess high dimensional mediation and potential surrogate markers including the direct effect of treatment, indirect effect of treatment, and the proportion of treatment effect explained by a surrogate/mediator; details are described in Zhou et al (2022) <doi:10.1002/sim.9352> and Zhou et al (2020) <doi:10.1093/biomet/asaa016>. This package relies on the optimization software 'MOSEK', <https://www.mosek.com>.
Depends: R (>= 3.5.0), scalreg, Rmosek, Matrix
Imports: stats, MASS
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-09-27 00:47:45 UTC; parastlm
Author: Ruixuan Zhou [aut, cph], Dave Zhao [aut, cph], Layla Parast [cre]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Repository: CRAN
Date/Publication: 2022-09-27 10:20:05 UTC

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New package correspondenceTables with initial version 0.7.4
Package: correspondenceTables
Title: Creating Correspondence Tables Between Two Statistical Classifications
Date: 2022-09-25
Version: 0.7.4
Description: A candidate correspondence table between two classifications can be created when there are correspondence tables leading from the first classification to the second one via intermediate 'pivot' classifications. The correspondence table between two statistical classifications can be updated when one of the classifications gets updated to a new version.
License: EUPL
Encoding: UTF-8
Imports: data.table
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
URL: https://github.com/eurostat/correspondenceTables
BugReports: https://github.com/eurostat/correspondenceTables/issues
Maintainer: Matyas Meszaros <matyas.meszaros@ec.europa.eu>
Packaged: 2022-09-27 08:43:52 UTC; mmeszaros
Author: Vasilis Chasiotis [aut] , Photis Stavropoulos [aut] , Martin Karlberg [aut], Matyas Meszaros [cre]
Repository: CRAN
Date/Publication: 2022-09-27 10:50:02 UTC

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New package ContRespPP with initial version 0.4.1
Package: ContRespPP
Title: Predictive Probability for a Continuous Response with an ANOVA Structure
Version: 0.4.1
Description: A Bayesian approach to using predictive probability in an ANOVA construct with a continuous normal response, when threshold values must be obtained for the question of interest to be evaluated as successful (Sieck and Christensen (2021) <doi:10.1002/qre.2802>). The Bayesian Mission Mean (BMM) is used to evaluate a question of interest (that is, a mean that randomly selects combination of factor levels based on their probability of occurring instead of averaging over the factor levels, as in the grand mean). Under this construct, in contrast to a Gibbs sampler (or Metropolis-within-Gibbs sampler), a two-stage sampling method is required. The nested sampler determines the conditional posterior distribution of the model parameters, given Y, and the outside sampler determines the marginal posterior distribution of Y (also commonly called the predictive distribution for Y). This approach provides a sample from the joint posterior distribution of Y and the model parameters, while also [...truncated...]
URL: https://github.com/jcliff89/ContRespPP
BugReports: https://github.com/jcliff89/ContRespPP/issues
License: CC0
Encoding: UTF-8
LazyData: true
Imports: stats
Suggests: rjags, coda, knitr, devtools, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-09-26 21:58:05 UTC; jcliff
Author: Victoria Sieck [aut, cre] , Joshua Clifford [aut] , Fletcher Christensen [aut]
Maintainer: Victoria Sieck <vcarrillo314@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-27 10:20:10 UTC

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New package pompp with initial version 0.1.0
Package: pompp
Title: Presence-Only for Marked Point Process
Version: 0.1.0
Description: Inspired by Moreira and Gamerman (2022) <doi:10.1214/21-AOAS1569>, this methodology expands the idea by including Marks in the point process. Using efficient 'C++' code, the estimation is possible and made faster with 'OpenMP' <https://www.openmp.org/> enabled computers.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 2.14.0)
LinkingTo: Rcpp, RcppEigen, RcppProgress
Imports: Rcpp, coda, geoR, parallel, methods, graphics, stats, tools
Suggests: bayesplot, ggplot2, MASS
NeedsCompilation: yes
Packaged: 2022-09-26 20:30:08 UTC; anthorg
Author: Guido Alberti Moreira [cre, aut]
Maintainer: Guido Alberti Moreira <guidoalber@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-27 09:20:02 UTC

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New package FDboost with initial version 1.1-1
Package: FDboost
Title: Boosting Functional Regression Models
Version: 1.1-1
Date: 2022-09-08
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Description: Regression models for functional data, i.e., scalar-on-function, function-on-scalar and function-on-function regression models, are fitted by a component-wise gradient boosting algorithm. For a manual on how to use 'FDboost', see Brockhaus, Ruegamer, Greven (2017) <doi:10.18637/jss.v094.i10>.
Depends: R (>= 3.5.0), mboost (>= 2.9-0)
Imports: methods, graphics, grDevices, utils, stats, Matrix, gamboostLSS (>= 2.0-0), stabs, mgcv, MASS, zoo
Suggests: fda, fields, ggplot2, maps, mapdata, knitr, refund, testthat
License: GPL-2
Packaged: 2022-09-26 20:18:38 UTC; david
Encoding: UTF-8
BugReports: https://github.com/boost-R/FDboost/issues
URL: https://github.com/boost-R/FDboost
VignetteBuilder: knitr
NeedsCompilation: no
Author: Sarah Brockhaus [aut], David Ruegamer [aut, cre], Almond Stoecker [aut], Torsten Hothorn [ctb], with contributions by many others [ctb]
Repository: CRAN
Date/Publication: 2022-09-27 09:20:05 UTC

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New package squat with initial version 0.0.1
Package: squat
Title: Statistics for Quaternion Temporal Data
Version: 0.0.1
Description: An implementation of statistical tools for the analysis of unit quaternion time series. It relies on pre-existing quaternion data structure provided by the 'Eigen' C++ library.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, fdacluster
Imports: cli, dtw, fdacluster, funData, furrr, ggplot2, ggrepel, MFPCA, pbapply, purrr, Rcpp, roahd, scales, tibble, tidyr
Depends: R (>= 4.1.0)
Suggests: covr, gghighlight, testthat (>= 3.0.0), vdiffr, withr
URL: https://lmjl-alea.github.io/squat/
NeedsCompilation: yes
Packaged: 2022-09-26 19:04:50 UTC; stamm-a
Author: Lise Bellanger [aut], Pierre Drouin [aut], Aymeric Stamm [aut, cre] , Benjamin Martineau [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@math.cnrs.fr>
Repository: CRAN
Date/Publication: 2022-09-27 09:00:02 UTC

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New package shinyXYpad with initial version 0.2.0
Package: shinyXYpad
Title: XY Controller for 'Shiny'
Version: 0.2.0
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Description: Provides an XY pad input for the 'Shiny' framework. An XY pad is like a bivariate slider. It allows to pick up a pair of numbers.
License: GPL-3
Encoding: UTF-8
Imports: shiny
URL: https://github.com/stla/shinyXYpad
BugReports: https://github.com/stla/shinyXYpad/issues
NeedsCompilation: no
Packaged: 2022-09-26 14:24:37 UTC; stla
Author: Stephane Laurent [aut, cre], Anthony Terrien [cph]
Repository: CRAN
Date/Publication: 2022-09-27 08:10:02 UTC

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New package oceCens with initial version 0.1.1
Package: oceCens
Title: Ordered Composite Endpoints with Censoring
Version: 0.1.1
Description: Estimates win ratio or Mann-Whitney parameter for two group comparisons using ordered composite endpoints with right censoring as described in Follmann, Fay, Hamasaki, and Evans (2020)<doi:10.1002/sim.7890>.
License: GPL-3
Depends: R (>= 3.5.0), survival
Suggests: testthat (>= 3.0.0),knitr, rmarkdown
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-26 13:31:46 UTC; faym
Author: Michael P. Fay [aut, cre], Dean Follmann [aut]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Repository: CRAN
Date/Publication: 2022-09-27 08:10:05 UTC

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New package eixport with initial version 0.5.4
Package: eixport
Title: Export Emissions to Atmospheric Models
Version: 0.5.4
Date: 2022-09-26
Description: Emissions are the mass of pollutants released into the atmosphere. Air quality models need emissions data, with spatial and temporal distribution, to represent air pollutant concentrations. This package, 'eixport', creates inputs for the air quality models 'WRF-Chem' Grell et al (2005) <doi:10.1016/j.atmosenv.2005.04.027>, 'MUNICH' Kim et al (2018) <doi:10.5194/gmd-11-611-2018> , 'BRAMS-SPM' Freitas et al (2005) <doi:10.1016/j.atmosenv.2005.07.017> and 'RLINE' Snyder et al (2013) <doi:10.1016/j.atmosenv.2013.05.074>. See the 'eixport' website (<https://atmoschem.github.io/eixport/>) for more information, documentations and examples. More details in Ibarra-Espinosa et al (2018) <doi:10.21105/joss.00607>.
License: MIT + file LICENSE
URL: https://atmoschem.github.io/eixport/
BugReports: https://github.com/atmoschem/eixport/issues/
Depends: R (>= 3.5.0)
Imports: sf, ncdf4, raster, sp, methods, cptcity, utils, parallel, data.table, rgdal
Encoding: UTF-8
LazyData: no
Suggests: testthat, covr, lwgeom, units, knitr, rmarkdown, vein
NeedsCompilation: no
Packaged: 2022-09-26 15:32:50 UTC; sergio
Author: Sergio Ibarra-Espinosa [aut, cre] , Daniel Schuch [aut] , Edmilson Freitas [ths] , Umur Dinc [ctb]
Maintainer: Sergio Ibarra-Espinosa <zergioibarra@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-27 08:20:02 UTC

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New package dogesr with initial version 0.1.0
Package: dogesr
Title: Work with the Doges/Dogaresse Dataset
Version: 0.1.0
Author: Juan Julian Merelo-Guervos
Maintainer: Juan Julian Merelo-Guervos <jjmerelo@gmail.com>
Description: Work with data on Venetian doges and dogaresse, and use it for social network analysis.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Suggests: testthat (>= 3.0.0)
Imports: dplyr
NeedsCompilation: no
Packaged: 2022-09-26 16:35:14 UTC; jmerelo
Repository: CRAN
Date/Publication: 2022-09-27 08:30:02 UTC

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New package Blaunet with initial version 2.2.1
Package: Blaunet
Version: 2.2.1
Title: Calculate and Analyze Blau Statuses for Measuring Social Distance
Depends: R (>= 3.0.0)
Imports: digest, gWidgets2, gWidgets2tcltk, plot3D, plot3Drgl, rgl, network, sna, ergm, statnet.common, haven, foreign
Description: Calculate and analyze Blau statuses for quantifying social distance between individuals belonging to organizations. Relational (network) data can be incorporated for additional analyses. This project is supported by Defense Threat Reduction Agency (DTRA) Grant HDTRA-10-1-0043.
License: GPL-3
License_restricts_use: no
URL: https://www.facebook.com/groups/425015561030239/
Packaged: 2022-09-26 13:29:05 UTC; cheng
Repository: CRAN
Date/Publication: 2022-09-27 08:10:08 UTC
NeedsCompilation: no
Author: Cheng Wang [aut, cre], Michael Genkin [aut], George Berry [aut], Liyuan Chen [aut], Matthew Brashears [aut]
Maintainer: Cheng Wang <chengwang@wayne.edu>

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Mon, 26 Sep 2022

New package highs with initial version 0.1-4
Package: highs
Title: 'HiGHS' Optimization Solver
Version: 0.1-4
Description: R interface to 'HiGHS', an optimization solver for solving mixed integer optimization problems with quadratic or linear objective and linear constraints.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.7), checkmate
SystemRequirements: Bash, PkgConfig, CMAKE (>=3.16), C++11
URL: https://gitlab.com/roigrp/solver/highs
BugReports: https://gitlab.com/roigrp/solver/highs/-/issues
Suggests: tinytest
Biarch: FALSE
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2022-09-26 05:27:41 UTC; florian
Author: Florian Schwendinger [aut, cre], Dirk Schumacher [aut], Julian Hall [cph], Ivet Galabova [cph], Leona Gottwald [cph], Michael Feldmeier [cph]
Maintainer: Florian Schwendinger <florianschwendinger@gmx.at>
Repository: CRAN
Date/Publication: 2022-09-26 20:40:02 UTC

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New package tmod with initial version 0.50.11
Package: tmod
Title: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics
Version: 0.50.11
Maintainer: January Weiner <january.weiner@gmail.com>
Description: Methods and feature set definitions for feature or gene set enrichment analysis in transcriptional and metabolic profiling data. Package includes tests for enrichment based on ranked lists of features, functions for visualisation and multivariate functional analysis. See Zyla et al (2019) <doi:10.1093/bioinformatics/btz447>.
License: GPL (>= 2.0)
Depends: R (>= 2.10)
LazyData: false
VignetteBuilder: knitr
Imports: beeswarm,tagcloud,XML,methods,plotwidgets,RColorBrewer,gplots,tibble,pheatmap,ggplot2,tidyr,purrr,rlang,tidyselect,ggrepel
Suggests: testthat,knitr,rmarkdown,dplyr,pander,pca3d,cowplot
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-26 13:03:08 UTC; january
Author: January Weiner [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-26 13:30:01 UTC

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New package scTEP with initial version 0.1.0
Package: scTEP
Title: Single-Cell Trajectory Inference using Ensemble Pseudotimes
Version: 0.1.0
Maintainer: Yifan Zhang <yfzhang@nevada.unr.edu>
Description: A single-cell trajectory inference method using 'Autoencoder' and Minimum Spanning Tree (MST) from high dimensional 'scRNA-Seq' data. The software run clustering methods six times using 'scDHA' with the number of clusters set from 6 to 10. Then, the 'scTEP' calculates pseudotime based on multiple clustering results. Lastly, the 'scTEP' generates trajectory using MST algorithm and fine-tunes it according to the pseudotime of clusters.
License: LGPL
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Depends: R (>= 3.6.0)
Imports: stats, dplyr, igraph, scDHA, foreach, BiocGenerics, Matrix, SummarizedExperiment, doParallel, ggsci, psych, tibble, rlang, SingleCellExperiment
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-25 20:14:33 UTC; yifanzhang
Author: Yifan Zhang [aut, cre], Duc Tran [aut], Tin Nguyen [fnd], Sergiu M. Dascalu [fnd], Frederick C. Harris, Jr. [fnd]
Repository: CRAN
Date/Publication: 2022-09-26 13:10:02 UTC

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New package rtika with initial version 2.4.1
Package: rtika
Title: R Interface to 'Apache Tika'
Version: 2.4.1
Maintainer: Sasha Goodman <goodmansasha@gmail.com>
Imports: curl, sys (>= 2.1), stats, utils, digest, backports
Suggests: jsonlite, xml2, testthat, knitr, rmarkdown, covr, magrittr
License: Apache License 2.0 | file LICENSE
SystemRequirements: Java (>=8)
Description: Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Depends: R (>= 3.5.0)
Encoding: UTF-8
URL: https://docs.ropensci.org/rtika/, https://github.com/ropensci/rtika/
BugReports: https://github.com/ropensci/rtika/issues/
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-26 00:06:39 UTC; sashagoodman
Author: Sasha Goodman [aut, cre], The Apache Software Foundation [aut, cph], Julia Silge [rev] , David Gohel [rev]
Repository: CRAN
Date/Publication: 2022-09-26 13:30:05 UTC

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New package NMcalc with initial version 0.0.1
Package: NMcalc
Title: Basic Calculations for PK/PD Modeling
Version: 0.0.1
Maintainer: Philip Delff <philip@delff.dk>
Description: Essentials for PK/PD (pharmacokinetics/pharmacodynamics) such as area under the curve, (geometric) coefficient of variation, and other calculations that are not part of base R. This is not a noncompartmental analysis (NCA) package.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, data.table
Suggests: ggplot2
NeedsCompilation: no
Packaged: 2022-09-25 21:01:37 UTC; philip
Author: Philip Delff [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-26 13:10:05 UTC

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New package watson with initial version 0.0.1
Package: watson
Title: Fitting and Simulating Mixtures of Watson Distributions
Version: 0.0.1
Maintainer: Lukas Sablica <lsablica@wu.ac.at>
Description: Tools for fitting and simulating mixtures of Watson distributions. The random sampling scheme of the package offers two sampling algorithms that are based of the results of Sablica, Hornik and Leydold (2022) <https://research.wu.ac.at/en/publications/random-sampling-from-the-watson-distribution>. What is more, the package offers a smart tool to combine these two methods, and based on the selected parameters, it approximates the relative sampling speed for both methods and picks the faster one. In addition, the package offers a fitting function for the mixtures of Watson distribution, that uses the expectation-maximization (EM) algorithm. Special features are the possibility to use multiple variants of the E-step and M-step, sparse matrices for the data representation and state of the art methods for numerical evaluation of needed special functions using the results of Sablica and Hornik (2022) <https://www.ams.org/journals/mcom/2022-91-334/S0025-5718-2021-03690-X/>.
License: GPL-3
Encoding: UTF-8
Imports: Rcpp (>= 0.12.18), Tinflex (>= 1.8)
LinkingTo: Rcpp, RcppArmadillo, Tinflex
Depends: R (>= 3.1.0)
NeedsCompilation: yes
Packaged: 2022-09-23 21:51:58 UTC; sablica
Author: Lukas Sablica [aut, cre] , Kurt Hornik [aut] , Josef Leydold [aut], Gerard Jungman [ctb, cph] , Brian Gough [ctb, cph]
Repository: CRAN
Date/Publication: 2022-09-26 12:20:02 UTC

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New package survout with initial version 0.1.0
Package: survout
Title: Excel Conversion of R Surival Analysis Output
Version: 0.1.0
Author: Xuefei Jia
Maintainer: Xuefei Jia <xuefeij.ai@gmail.com>
Description: Simple and quick method of exporting the most often used survival analysis results to an Excel sheet.
License: GPL-3
Imports: cmprsk, dplyr, openxlsx, stats, survival, tibble
Suggests: covr, MASS, reshape2, testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-25 19:50:44 UTC; jiax
Repository: CRAN
Date/Publication: 2022-09-26 12:50:02 UTC

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New package rempsyc with initial version 0.0.9
Package: rempsyc
Title: Convenience Functions for Psychology
Version: 0.0.9
Date: 2022-09-24
Description: Make your workflow faster and easier. Easily customizable plots (via 'ggplot2'), nice APA tables (following the style of the *American Psychological Association*) exportable to Word (via 'flextable'), easily run statistical tests or check assumptions, and automatize various other tasks.
License: GPL (>= 3)
URL: https://rempsyc.remi-theriault.com
BugReports: https://github.com/rempsyc/rempsyc/issues
Depends: R (>= 3.5)
Imports: boot, car, dplyr (>= 1.0.4), effectsize, flextable (>= 0.7.1), ggplot2, ggrepel, ggsignif, lmtest, methods, qqplotr, rlang
Suggests: bootES, broom, correlation, datawizard (>= 0.5.0), emmeans, ftExtra, ggpubr, interactions, knitr, markdown, openxlsx, openxlsx2, patchwork, performance (>= 0.9.1), psych, report (>= 0.5.1), rmarkdown, see, testthat (>= 3.0.0), VennDiagram
VignetteBuilder: knitr
Additional_repositories: https://janmarvin.r-universe.dev
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-25 13:23:24 UTC; rempsyc
Author: Remi Theriault [aut, cre]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Repository: CRAN
Date/Publication: 2022-09-26 13:00:02 UTC

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New package hce with initial version 0.0.2
Package: hce
Title: Design and Analysis of Hierarchical Composite Endpoints
Version: 0.0.2
Description: Simulate and analyze hierarchical composite endpoints. Win odds is the main analysis method. See Gasparyan SB et al (2022) <doi:10.1007/s43441-022-00420-1>).
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: base, stats
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-23 17:28:31 UTC; ktpz678
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-26 12:10:12 UTC

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New package EEMDlstm with initial version 0.1.0
Package: EEMDlstm
Title: EEMD Based LSTM Model for Time Series Forecasting
Version: 0.1.0
Maintainer: Kapil Choudhary <kapiliasri@gmail.com>
Description: Forecasting univariate time series with ensemble empirical mode decomposition (EEMD) with long short-term memory (LSTM). For method details see Jaiswal, R. et al. (2022). <doi:10.1007/s00521-021-06621-3>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: keras, tensorflow, reticulate, tsutils, BiocGenerics, utils, graphics, magrittr,Rlibeemd, TSdeeplearning
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-09-24 01:11:19 UTC; kapil
Author: Kapil Choudhary [aut, cre], Girish Kumar Jha [aut, ths, ctb], Ronit Jaiswal [ctb], Rajeev Ranjan Kumar [ctb]
Repository: CRAN
Date/Publication: 2022-09-26 12:30:02 UTC

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New package coefa with initial version 1.0.1
Package: coefa
Title: Meta Analysis of Factor Analysis Based on CO-Occurrence Matrices
Version: 1.0.1
Description: Provide a series of functions to conduct a meta analysis of factor analysis based on co-occurrence matrices. The tool can be used to solve the factor structure (i.e. inner structure of a construct, or scale) debate in several disciplines, such as psychology, psychiatry, management, education so on. References: Shafer (2005) <doi:10.1037/1040-3590.17.3.324>; Shafer (2006) <doi:10.1002/jclp.20213>; Loeber and Schmaling (1985) <doi:10.1007/BF00910652>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: TRUE
Depends: openxlsx, psych, R (>= 2.10)
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
Imports: purrr
Date: 2022-9-15
Author: Xijian Zheng [aut, cre], Huiyong Fan [aut]
Maintainer: Xijian Zheng <psydreammer@foxmail.com>
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2022-09-25 16:52:30 UTC; F
Repository: CRAN
Date/Publication: 2022-09-26 12:40:02 UTC

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New package TDApplied with initial version 0.1.2
Package: TDApplied
Title: Machine Learning and Inference for Topological Data Analysis
Version: 0.1.2
Author: Shael Brown [aut, cre], Dr. Reza Farivar [aut, fnd]
Maintainer: Shael Brown <shaelebrown@gmail.com>
Description: Topological data analysis is a powerful tool for finding non-linear global structure in whole datasets. 'TDApplied' aims to bridge topological data analysis with data, statistical and machine learning practitioners so that more analyses may benefit from the power of topological data analysis. The main tool of topological data analysis is persistent homology, which computes a shape descriptor of a dataset, called a persistence diagram. There are three goals of this package: (1) convert persistence diagrams computed using the two main R packages for topological data analysis into a data frame, (2) implement fast versions of both distance and kernel calculations for pairs of persistence diagrams, and (3) provide methods for machine learning and inference for persistence diagrams which scale well.
Depends: R (>= 3.2.2)
Imports: parallel, doParallel, foreach, clue, rdist, parallelly, kernlab, iterators, methods, stats, utils
License: GPL-3
URL: https://github.com/shaelebrown/TDApplied
BugReports: https://github.com/shaelebrown/TDApplied/issues
Encoding: UTF-8
NeedsCompilation: yes
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TDA, TDAstats
VignetteBuilder: knitr
Packaged: 2022-09-25 18:00:50 UTC; jibaccount
Repository: CRAN
Date/Publication: 2022-09-26 07:10:02 UTC

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New package Rsomoclu with initial version 1.7.6
Package: Rsomoclu
Version: 1.7.6
Date: 2022-09-20
Title: Somoclu
Imports: kohonen
Suggests:
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal . Details refer to (Peter Wittek, et al (2017)) <doi:10.18637/jss.v078.i09>.
URL: https://peterwittek.github.io/somoclu/
BugReports: https://github.com/peterwittek/somoclu/issues
License: GPL-3
Packaged: 2022-09-25 05:08:58 UTC; sgao
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
NeedsCompilation: yes
Repository: CRAN
SystemRequirements: C++11
LinkingTo: Rcpp
LazyData: true
Date/Publication: 2022-09-26 07:10:07 UTC

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Sun, 25 Sep 2022

New package wflo with initial version 1.7
Package: wflo
Title: Data Set and Helper Functions for Wind Farm Layout Optimization Problems
Version: 1.7
Date: 2022-09-22
Description: Provides a convenient data set, a set of helper functions, and a benchmark function for economically (profit) driven wind farm layout optimization. This enables researchers in the field of the NP-hard (non-deterministic polynomial-time hard) problem of wind farm layout optimization to focus on their optimization methodology contribution and also provides a realistic benchmark setting for comparability among contributions. See Croonenbroeck, Carsten & Hennecke, David (2020) <doi:10.1016/j.energy.2020.119244>.
Depends: R (>= 3.5.0)
Imports: plotrix, progress, emstreeR, raster, sp
Suggests: MASS, nloptr, pso, rgenoud, rgdal, snow, doSNOW, foreach, parallel
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-24 19:14:41 UTC; ccroo
Author: Carsten Croonenbroeck [aut, cre], David Hennecke [ctb]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Repository: CRAN
Date/Publication: 2022-09-25 22:40:02 UTC

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New package popEpi with initial version 0.4.10
Package: popEpi
Title: Functions for Epidemiological Analysis using Population Data
Version: 0.4.10
Author: Joonas Miettinen [cre, aut] , Matti Rantanen [aut], Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>
Description: Enables computation of epidemiological statistics, including those where counts or mortality rates of the reference population are used. Currently supported: excess hazard models (Dickman, Sloggett, Hills, and Hakulinen (2012) <doi:10.1002/sim.1597>), rates, mean survival times, relative/net survival (in particular the Ederer II (Ederer and Heise (1959)) and Pohar Perme (Pohar Perme, Stare, and Esteve (2012) <doi:10.1111/j.1541-0420.2011.01640.x>) estimators), and standardized incidence and mortality ratios, all of which can be easily adjusted for by covariates such as age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.
License: GPL-3
URL: https://github.com/FinnishCancerRegistry/popEpi
BugReports: https://github.com/FinnishCancerRegistry/popEpi/issues
Depends: R (>= 3.2.0)
Imports: data.table (>= 1.10.4), Epi (>= 2.0), splines, survival
Suggests: covr, date, knitr, mstate, relsurv, rmarkdown, roxygen2, testthat
VignetteBuilder: knitr
ByteCompile: true
Encoding: UTF-8
Language: en-GB
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-16 07:49:50 UTC; joonas.miettinen
Repository: CRAN
Date/Publication: 2022-09-25 16:40:02 UTC

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New package bfsMaps with initial version 0.9.7
Package: bfsMaps
Title: Plot Maps from Switzerland by Swiss Federal Statistical Office
Version: 0.9.7
Date: 2022-09-20
Description: At the Swiss Federal Statistical Office (SFSO), spatial maps of Switzerland are available free of charge as 'Cartographic bases for small-scale thematic mapping'. This package contains convenience functions to import ESRI (Environmental Systems Research Institute) shape files using the package 'rgdal' and to plot them easily and quickly without having to worry too much about the technical details. It contains utilities to combine multiple areas to one single polygon and to find neighbours for single regions. For any point on a map, a special locator can be used to determine to which municipality, district or canton it belongs.
Depends: base, stats, R (>= 4.0.0), sp, DescTools
Imports: graphics, grDevices, spdep, maptools, rgdal, rlang, methods, rgeos
Suggests: R.rsp
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
URL: https://github.com/AndriSignorell/bfsMaps/
BugReports: https://github.com/AndriSignorell/bfsMaps/issues
Encoding: UTF-8
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2022-09-20 16:47:51 UTC; andri
Author: Andri Signorell [aut, cre], Juerg Guggenbuehl [ctb], Jeffery S. Evans [ctb]
Maintainer: Andri Signorell <andri@signorell.net>
Repository: CRAN
Date/Publication: 2022-09-25 16:40:10 UTC

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New package colorDF with initial version 0.1.5
Package: colorDF
Title: Colorful Data Frames in R Terminal
Version: 0.1.5
Description: Colorful Data Frames in the terminal. The new class does change the behaviour of any of the objects, but adds a style definition and a print method. Using ANSI escape codes, it colors the terminal output of data frames. Some column types (such as p-values and identifiers) are automatically recognized.
URL: https://january3.github.io/colorDF/, https://github.com/january3/colorDF/
Depends: R (>= 2.10)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: purrr,crayon
Suggests: knitr, rmarkdown, fansi, htmltools, data.table, testthat (>= 2.1.0), tibble, dplyr, tidyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-23 19:54:41 UTC; january
Author: January Weiner [aut, cre]
Maintainer: January Weiner <january.weiner@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-25 10:30:02 UTC

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New package adaptsmoFMRI with initial version 1.2
Package: adaptsmoFMRI
Title: Adaptive Smoothing of FMRI Data
Version: 1.2
Date: 2022-09-24
Description: Adaptive smoothing functions for estimating the blood oxygenation level dependent (BOLD) effect by using functional Magnetic Resonance Imaging (fMRI) data, based on adaptive Gauss Markov random fields, for real as well as simulated data. The implemented models make use of efficient Markov Chain Monte Carlo methods. Implemented methods are based on the research developed by A. Brezger, L. Fahrmeir, A. Hennerfeind (2007) <https://www.jstor.org/stable/4626770>.
License: GPL-2
Depends: R(>= 4.2.0)
Imports: methods, stats, spatstat, spatstat.geom, Matrix, coda, mvtnorm, MCMCpack, parallel
NeedsCompilation: no
Packaged: 2022-09-24 09:09:31 UTC; gordonmax
Author: Maximilian Hughes [aut, cre, ctb]
Maintainer: Maximilian Hughes <hughesgm@me.com>
Repository: CRAN
Date/Publication: 2022-09-25 10:30:05 UTC

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Sat, 24 Sep 2022

New package renderthis with initial version 0.2.0
Package: renderthis
Title: Render Slides to Different Formats
Version: 0.2.0
Description: Render slides to different formats, including 'html', 'pdf', 'png', 'gif', 'pptx', and 'mp4', as well as a 'social' output, a 'png' of the first slide re-sized for sharing on social media.
License: MIT + file LICENSE
URL: https://jhelvy.github.io/renderthis/, https://github.com/jhelvy/renderthis
BugReports: https://github.com/jhelvy/renderthis/issues
Depends: R (>= 3.4.0)
Imports: cli (>= 3.0.0), digest, fs, jsonlite, magick (>= 2.7.1), pagedown, progress, quarto, rmarkdown, withr, xaringan, zip
Suggests: av, chromote, knitr, lifecycle, officer, pdftools, testthat (>= 3.0.0), webshot2
Config/Needs/website: xaringanExtra
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-23 16:01:25 UTC; jhelvy
Author: John Helveston [aut, cre, cph] , Garrick Aden-Buie [aut] , Bryan Shalloway [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-24 05:40:11 UTC

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New package httk with initial version 2.2.1
Package: httk
Version: 2.2.1
Date: 2022-09-16
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals and species using chemical-specific in vitro data and physiological information. These tools allow incorporation of chemical toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE") into bioinformatics, as described by Pearce et al. (2017) (<doi:10.18637/jss.v079.i04>). Chemical-specific in vitro data characterizing toxicokinetics can be been obtained from relatively high-throughput experiments. The chemical-independent ("generic") physiologically-based ("PBTK") and empirical (for example, one compartment) "TK" models included here can be parameterized with in vitro data or in silico predictions which are provided for thousands of chemicals, multiple exposure routes, and various species. The models are systems of ordinary differential equations that are solved using compiled (C-based) code for speed. A Monte Carlo sampler is included for simulating human biological variability (Ring et al., 2017 <doi:1 [...truncated...]
Depends: R (>= 2.10)
Imports: deSolve, msm, data.table, survey, mvtnorm, truncnorm, stats, graphics, utils, magrittr, purrr, methods, Rdpack
Suggests: ggplot2, knitr, rmarkdown, R.rsp, GGally, gplots, scales, EnvStats, MASS, RColorBrewer, TeachingDemos, classInt, ks, stringr, reshape, reshape2, viridis, gmodels, colorspace, cowplot, ggrepel, dplyr, forcats, smatr, gridExtra, testthat
License: GPL-3
LazyData: true
LazyDataCompression: xz
Encoding: UTF-8
VignetteBuilder: knitr, R.rsp
URL: https://www.epa.gov/chemical-research/rapid-chemical-exposure-and-dose-research
BugReports: https://github.com/USEPA/CompTox-ExpoCast-httk
NeedsCompilation: yes
Packaged: 2022-09-22 15:57:35 UTC; jwambaug
Author: John Wambaugh [aut, cre] , Sarah Davidson [aut] , Robert Pearce [aut] , Caroline Ring [aut] , Greg Honda [aut] , Mark Sfeir [aut], Matt Linakis [aut] , Dustin Kapraun [aut] , Miyuki Breen [ctb] , Shannon Bell [ctb] , Xiaoqing Chang [ctb] , Todor Anto [...truncated...]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Copyright: This package is primarily developed by employees of the U.S. Federal government as part of their official duties and is therefore public domain.
Repository: CRAN
Date/Publication: 2022-09-24 05:40:14 UTC

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Fri, 23 Sep 2022

New package spcov with initial version 1.3
Package: spcov
Title: Sparse Estimation of a Covariance Matrix
Version: 1.3
Date: 2022-09-21
Author: Jacob Bien and Rob Tibshirani
Maintainer: Jacob Bien <jbien@usc.edu>
Description: Provides a covariance estimator for multivariate normal data that is sparse and positive definite. Implements the majorize-minimize algorithm described in Bien, J., and Tibshirani, R. (2011), "Sparse Estimation of a Covariance Matrix," Biometrika. 98(4). 807--820.
License: GPL-2
LazyLoad: yes
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-23 16:43:26 UTC; jacobbien
Repository: CRAN
Date/Publication: 2022-09-23 20:20:02 UTC

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New package neuronorm with initial version 1.0.2
Package: neuronorm
Title: Preprocessing of Structural MRI for Multiple Neurodegenerative Diseases
Version: 1.0.2
Maintainer: David Payares <davidpayaresg@gmail.com>
Imports: knitr, oro.nifti, fslr, stats
Suggests: rmarkdown, ANTsR, ITKR, extrantsr, MNITemplate, RAVEL, neurodata
Depends: R (>= 3.5)
Additional_repositories: https://davidpayares.github.io/drat
Description: Preprocessing pipeline for normalizing and cleaning T1-weighted, T2-weighted and FLAIR MRI images coming from different sources, diseases, patients, scanners and sites.
License: GPL-2
Encoding: UTF-8
SystemRequirements: cmake, FSL
VignetteBuilder: knitr
OS_type: unix
NeedsCompilation: no
Packaged: 2022-09-22 15:11:17 UTC; davidpayares
Author: David Payares [aut, cre], Jorge Mateu [ctb], Wiebke Schick [ctb], Nicholas J. Tustison [cph], Brian B Avants [cph], Philip A. Cook [cph], Yuanjie Zheng [cph], Alexander Egan [cph], Paul A. Yushkevich [cph], James C. Gee [cph], M. Grossman [cph], Jean [...truncated...]
Repository: CRAN
Date/Publication: 2022-09-23 20:50:02 UTC

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New package corncob with initial version 0.3.0
Package: corncob
Title: Count Regression for Correlated Observations with the Beta-Binomial
Version: 0.3.0
Description: Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.
URL: https://github.com/bryandmartin/corncob
BugReports: https://github.com/bryandmartin/corncob/issues
Depends: R (>= 3.2)
License: GPL (>= 2)
Imports: stats, utils, optimr, VGAM, numDeriv, ggplot2, trust, dplyr, magrittr, detectseparation, scales, phyloseq
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat, covr, limma, slam, R.rsp
VignetteBuilder: knitr, R.rsp
NeedsCompilation: no
Packaged: 2022-09-22 17:50:37 UTC; bmartin1
Author: Bryan D Martin [aut, cre], Daniela Witten [aut], Amy D Willis [aut]
Maintainer: Bryan D Martin <bmartin6@uw.edu>
Repository: CRAN
Date/Publication: 2022-09-23 20:20:07 UTC

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New package oews2020 with initial version 1.0.0
Package: oews2020
Title: May 2020 Occupational Employment and Wage Statistics
Version: 1.0.0
Author: Christopher Mann
Maintainer: Christopher Mann <cmann3@unl.edu>
Description: Contains data from the May 2020 Occupational Employment and Wage Statistics data release from the U.S. Bureau of Labor Statistics. The dataset covers employment and wages across occupations, industries, states, and at the national level. Metropolitan data is not included.
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Encoding: UTF-8
LazyData: true
LazyDataCompression: bzip2
NeedsCompilation: no
Packaged: 2022-09-23 11:44:00 UTC; chris
Repository: CRAN
Date/Publication: 2022-09-23 15:20:02 UTC

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New package codez with initial version 1.0.0
Package: codez
Title: Seq2Seq Encoder-Decoder Model for Time-Feature Analysis Based on Tensorflow
Version: 1.0.0
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Description: Proposes Seq2seq Time-Feature Analysis using an Encoder-Decoder to project into latent space and a Forward Network to predict the next sequence.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6)
Imports: purrr (>= 0.3.4), abind (>= 1.4-5), ggplot2 (>= 3.3.6), readr (>= 2.1.2), fANCOVA (>= 0.6-1), imputeTS (>= 3.2), modeest (>= 2.4.0), scales (>= 1.1.1), tictoc (>= 1.0.1), tensorflow (>= 2.9.0), keras (>= 2.9.0), moments (>= 0.14), narray (>= 0.4.1.1), fastDummies (>= 1.6.3), entropy (>= 1.3.1), philentropy (>= 0.5.0), greybox (>= 1.0.1), lubridate (>= 1.7.10)
URL: https://rpubs.com/giancarlo_vercellino/codez
Suggests: testthat (>= 3.0.0), reticulate (>= 1.26)
NeedsCompilation: no
Packaged: 2022-09-23 08:43:28 UTC; gvercellino
Author: Giancarlo Vercellino [aut, cre, cph]
Repository: CRAN
Date/Publication: 2022-09-23 15:10:02 UTC

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New package CMFsurrogate with initial version 1.0
Package: CMFsurrogate
Title: Calibrated Model Fusion Approach to Combine Surrogate Markers
Version: 1.0
Date: 2022-09-22
Description: Uses a calibrated model fusion approach to optimally combine multiple surrogate markers. Specifically, two initial estimates of optimal composite scores of the markers are obtained; the optimal calibrated combination of the two estimated scores is then constructed which ensures both validity of the final combined score and optimality with respect to the proportion of treatment effect explained (PTE) by the final combined score. The primary function, pte.estimate.multiple(), estimates the PTE of the identified combination of multiple surrogate markers. Details are described in Wang et al (2022) <doi:10.1111/biom.13677>.
License: GPL
Imports: splines, MASS, stats
NeedsCompilation: no
Packaged: 2022-09-23 01:33:03 UTC; parastlm
Author: Xuan Wang [aut], Layla Parast [cre]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-09-23 15:20:05 UTC

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New package cwot with initial version 0.1.0
Package: cwot
Title: Cauchy Weighted Joint Test for Pharmacogenetics Analysis
Version: 0.1.0
Description: A flexible and robust joint test of the single nucleotide polymorphism (SNP) main effect and genotype-by-treatment interaction effect for continuous and binary endpoints. Two analytic procedures, Cauchy weighted joint test (CWOT) and adaptively weighted joint test (AWOT), are proposed to accurately calculate the joint test p-value. The proposed methods are evaluated through extensive simulations under various scenarios. The results show that the proposed AWOT and CWOT control type I error well and outperform existing methods in detecting the most interesting signal patterns in pharmacogenetics (PGx) association studies. For reference, see Hong Zhang, Devan Mehrotra and Judong Shen (2022) <doi:10.13140/RG.2.2.28323.53280>.
License: GPL-2
Imports: stats, SPAtest, mvtnorm
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-22 18:54:08 UTC; consi
Author: Hong Zhang [aut, cre]
Maintainer: Hong Zhang <hzhang@wpi.edu>
Repository: CRAN
Date/Publication: 2022-09-23 14:40:02 UTC

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Thu, 22 Sep 2022

New package qlifetable with initial version 0.0.1-12
Package: qlifetable
Title: Managing and Building of Quarterly Life Tables
Version: 0.0.1-12
Description: Manages, builds and computes statistics and datasets for the construction of quarterly (sub-annual) life tables by exploiting micro-data from either a general or an insured population. References: Pavía and Lledó (2022) <doi:10.1111/rssa.12769>.
License: EPL
Encoding: UTF-8
Imports: stats, methods
Suggests: ggplot2, scales
NeedsCompilation: no
Packaged: 2022-09-22 14:44:01 UTC; Jose M Pavia
Author: Jose M. Pavia [aut, cre] , Josep Lledo [aut]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Repository: CRAN
Date/Publication: 2022-09-22 17:10:02 UTC

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New package graphPAF with initial version 1.0.0
Package: graphPAF
Title: Estimating and Displaying Population Attributable Fractions
Version: 1.0.0
Description: Estimation and display of various types of population attributable fraction and impact fractions. As well as the usual calculations of attributable fractions and impact fractions, functions are provided for continuous exposures, for pathway specific population attributable fractions, and for joint, average and sequential population attributable fractions. See O'Connell and Ferguson (2022) <doi:10.1093/ije/dyac079>, Ferguson et al. (2020) <doi:10.1186/s13690-020-00442-x>, Ferguson et al. (2019) <doi:10.1186/s12874-019-0827-4>, Ferguson et al. (2019) <doi:10.1515/em-2019-0037>, as well the accompanying package vignette, for an overview of methods implemented.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/johnfergusonNUIG/graphPAF
BugReports: https://github.com/johnfergusonNUIG/graphPAF/issues
Imports: boot, ggplot2, ggrepel, gridExtra, gtools, MASS, reshape2, survival, splines, dplyr
Depends: R (>= 3.5.0)
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2022-09-22 16:41:24 UTC; John1
Author: John Ferguson [aut, cre]
Maintainer: John Ferguson <john.ferguson@nuigalway.ie>
Repository: CRAN
Date/Publication: 2022-09-22 17:10:05 UTC

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New package glmmrBase with initial version 0.1.2
Package: glmmrBase
Title: Specification of Generalised Linear Mixed Models
Version: 0.1.2
Date: 2022-09-16
Description: Specification of generalised linear mixed models using the 'R6' object-orientated class system. The package provides classes 'Covariance', 'MeanFunction' and 'Model', which allow for flexible specification of generalised linear mixed models, as well as functionality to produce relevant matrices, values, and analyses. See <https://github.com/samuel-watson/glmmrBase/blob/master/README.md> for a detailed manual.
License: GPL (>= 2)
Imports: methods, Rcpp (>= 1.0.7), R6
LinkingTo: Rcpp (>= 0.12.0), RcppArmadillo, RcppParallel (>= 5.0.1)
NeedsCompilation: yes
Author: Sam Watson [aut, cre], Yi Pan [aut]
URL: https://github.com/samuel-watson/glmmrBase
BugReports: https://github.com/samuel-watson/glmmrBase/issues
Suggests: testthat
Biarch: true
Depends: R (>= 3.4.0), Matrix (>= 1.3-1)
SystemRequirements: GNU make
Encoding: UTF-8
Packaged: 2022-09-22 10:11:29 UTC; samue
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Repository: CRAN
Date/Publication: 2022-09-22 17:00:09 UTC

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New package rlibkriging with initial version 0.7-0
Package: rlibkriging
Title: Kriging Models using the 'libKriging' Library
Version: 0.7-0
Date: 2022-08-31
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, and 'lbfgsb_cpp' is a 'C++' wrapper by Colin Fang around 'lbfgsb' library (BSD-3 license) by Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
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
URL: https://github.com/libKriging
NeedsCompilation: yes
Packaged: 2022-09-21 09:03:30 UTC; richet
Author: Pascal Have [aut], Yann Richet [aut, cre] , Yves Deville [aut], Conrad Sanderson [ctb], Colin Fang [ctb], Ciyou Zhu [ctb], Richard Byrd [ctb], Jorge Nocedal [ctb], Jose Luis Morales [ctb]
Repository: CRAN
Date/Publication: 2022-09-22 13:50:02 UTC

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New package topdowntimeratio with initial version 0.1.0
Package: topdowntimeratio
Title: Top-Down Time Ratio Segmentation for Coordinate Trajectories
Version: 0.1.0
Description: Data collected on movement behavior is often in the form of time- stamped latitude/longitude coordinates sampled from the underlying movement behavior. These data can be compressed into a set of segments via the Top- Down Time Ratio Segmentation method described in Meratnia and de By (2004) <doi:10.1007/978-3-540-24741-8_44> which, with some loss of information, can both reduce the size of the data as well as provide corrective smoothing mechanisms to help reduce the impact of measurement error. This is an improvement on the well-known Douglas-Peucker algorithm for segmentation that operates not on the basis of perpendicular distances. Top-Down Time Ratio segmentation allows for disparate sampling time intervals by calculating the distance between locations and segments with respect to time. Provided a trajectory with timestamps, tdtr() returns a set of straight- line segments that can represent the full trajectory. McCool, Lugtig, and Schouten (2022) <doi:10.1007/s11116-022- [...truncated...]
License: GPL (>= 3)
Encoding: UTF-8
Imports: data.table (>= 1.9.8), geodist (>= 0.0.4), lubridate, magrittr, stats
Depends: R (>= 4.1)
Suggests: spelling, testthat
Language: en-US
NeedsCompilation: no
Packaged: 2022-09-21 22:39:04 UTC; Mccoo002
Author: Danielle McCool [aut, cre]
Maintainer: Danielle McCool <d.m.mccool@uu.nl>
Repository: CRAN
Date/Publication: 2022-09-22 08:50:02 UTC

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New package Rmolt with initial version 1.0.0
Package: Rmolt
Title: Graphic Visualization of the Birds' Molt
Version: 1.0.0
Date: 2022-09-16
Maintainer: Martin Bozon <bozon.etu@gmail.com>
Description: Graphical visualization of the birds' molt to facilitate the creation of molting graph for passerines having 9 (Rmolt(data,9)) or 10 primaries (Rmolt(data,10)), and also only for the 10 first primaries (Rmolt(data,"10_0")).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-21 18:00:05 UTC; Boss
Author: Martin Bozon [cre, aut]
Repository: CRAN
Date/Publication: 2022-09-22 08:40:18 UTC

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New package BiOFI with initial version 0.1.0
Package: BiOFI
Title: Feature Identification Between Metabolome and Microbiome in Disease and Health
Version: 0.1.0
Maintainer: Tianlu Chen <chentianlu@sjtu.edu.cn>
Description: A strategy that provides the identification of metabolome and microbiome (Bi-omics) feature. It is able to screen out key/driving features (metabolites, microbes, and pathway functions) by an integrated importance score (IIS),combining sub-scores derived from difference, correlation, abundance, and network analysis. It is able to identify microbe-function-metabolite chains and to rank association pairs within specific functions.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, Hmisc, ggplot2, ggrepel, htmlwidgets, igraph, magrittr, networkD3, tidyverse, visNetwork, ppcor
Depends: R (>= 3.5.0)
Author: Tianlu Chen [aut, cre]
NeedsCompilation: no
Packaged: 2022-09-21 09:26:04 UTC; sun
Repository: CRAN
Date/Publication: 2022-09-22 09:00:08 UTC

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New package adjustedCurves with initial version 0.9.0
Package: adjustedCurves
Title: Confounder-Adjusted Survival Curves and Cumulative Incidence Functions
Version: 0.9.0
Maintainer: Robin Denz <robin.denz@rub.de>
Description: Estimate and plot confounder-adjusted survival curves using either 'Direct Adjustment', 'Direct Adjustment with Pseudo-Values', various forms of 'Inverse Probability of Treatment Weighting', two forms of 'Augmented Inverse Probability of Treatment Weighting', 'Empirical Likelihood Estimation' and 'Targeted Maximum Likelihood Estimation'. Also includes a significance test for the difference between two adjusted survival curves and the calculation of adjusted restricted mean survival times. Additionally enables the user to estimate and plot cause-specific confounder-adjusted cumulative incidence functions in the competing risks setting using the same methods (with some exceptions). For details, see Denz et. al (2022) <arXiv:2203.10002v1>.
License: GPL (>= 3)
URL: https://github.com/RobinDenz1/adjustedCurves, https://robindenz1.github.io/adjustedCurves/
BugReports: https://github.com/RobinDenz1/adjustedCurves/issues
Imports: R.utils, doParallel, doRNG, dplyr (>= 1.0.0), foreach, rlang
Suggests: MASS, Matching (>= 4.9), R6, SuperLearner (>= 2.0.0), WeightIt (>= 0.11.0), cmprsk (>= 2.2), eventglm (>= 1.1.1), geepack (>= 1.3), ggplot2 (>= 3.0.0), knitr, mice (>= 3.0.0), nnet, pammtools (>= 0.5), pec (>= 2020.11.17), prodlim (>= 2019.11.13), riskRegression (>= 2020.12.08), rmarkdown, survival (>= 3.0.0), survtmle (>= 1.1), testthat (>= 3.0.0), tidyr, ggpp (>= 0.4.3), vdiffr (>= 1.0.0), covr
VignetteBuilder: knitr
Contact: <robin.denz@rub.de>
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-21 16:34:45 UTC; Robin Denz
Author: Robin Denz [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-22 08:40:13 UTC

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New package CovRegRF with initial version 1.0.1
Package: CovRegRF
Title: Covariance Regression with Random Forests
Version: 1.0.1
Description: Covariance Regression with Random Forests ('CovRegRF') is a random forest method for estimating the covariance matrix of a multivariate response given a set of covariates. Random forest trees are built with a new splitting rule which is designed to maximize the distance between the sample covariance matrix estimates of the child nodes. The method is described in Alakus et al. (2022) <arXiv:2209.08173>. 'CovRegRF' uses 'randomForestSRC' package (Ishwaran and Kogalur, 2022) <https://cran.r-project.org/package=randomForestSRC> by freezing at the version 3.1.0. The custom splitting rule feature is utilised to apply the proposed splitting rule.
Depends: R (>= 3.6.0)
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: data.table, data.tree, DiagrammeR
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-09-21 14:55:43 UTC; cansualakus
Author: Cansu Alakus [aut, cre], Denis Larocque [aut], Aurelie Labbe [aut], Hemant Ishwaran [ctb] , Udaya B. Kogalur [ctb]
Maintainer: Cansu Alakus <cansu.alakus@hec.ca>
Repository: CRAN
Date/Publication: 2022-09-22 07:40:01 UTC

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Wed, 21 Sep 2022

New package KSA with initial version 0.1.0
Package: KSA
Title: Retained Component Criterion for Principal Component Analysis
Version: 0.1.0
Date: 2022-09-20
Author: Fayed Alshammri
Maintainer: Dr. Fayed Alshammri <fayed333@hotmail.com>
Description: The Retained Component Criterion for Principal Component Analysis (RCC_PCA) is a tool to determine the optimal number of components to retain in PCA.
License: GPL-2
Depends: stats, graphics
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-21 03:08:12 UTC; User
Repository: CRAN
Date/Publication: 2022-09-21 22:20:06 UTC

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New package SCORPION with initial version 1.0.0
Package: SCORPION
Title: Single Cell Oriented Reconstruction of PANDA Individual Optimized Networks
Version: 1.0.0
Description: Constructs gene regulatory networks from single-cell gene expression data using the PANDA (Passing Attributes between Networks for Data Assimilation) algorithm.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: cli, methods, irlba, igraph, RANN, Matrix, pbapply, RhpcBLASctl
NeedsCompilation: no
Packaged: 2022-09-20 21:20:16 UTC; danie
Author: Daniel Osorio [aut, cre] , Marieke L. Kuijjer [aut]
Maintainer: Daniel Osorio <daniecos@uio.no>
Repository: CRAN
Date/Publication: 2022-09-21 16:20:11 UTC

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New package oews2021 with initial version 1.0.0
Package: oews2021
Title: May 2021 Occupational Employment and Wage Statistics
Version: 1.0.0
Author: Christopher Mann
Maintainer: Christopher Mann <cmann3@unl.edu>
Description: Contains data from the May 2021 Occupational Employment and Wage Statistics data release from the U.S. Bureau of Labor Statistics. The dataset covers employment and wages across occupations, industries, states, and at the national level. Metropolitan data is not included.
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Encoding: UTF-8
LazyData: true
LazyDataCompression: bzip2
NeedsCompilation: no
Packaged: 2022-09-21 14:20:10 UTC; chris
Repository: CRAN
Date/Publication: 2022-09-21 16:20:02 UTC

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New package binaryMM with initial version 0.1.0
Package: binaryMM
Title: Flexible Marginalized Models for Binary Correlated Outcomes
Version: 0.1.0
Description: Estimates marginalized mean and dependence model parameters for correlated binary response data. Dependence model may include transition and/or latent variable terms. Methods are described in: Heagerty (1999) <doi:10.1111/j.0006-341x.1999.00688.x>, Heagerty (2002) <doi:10.1111/j.0006-341x.2002.00342.x>, Schildcrout and Heagerty (2007) <doi:10.1111/j.1541-0420.2006.00680.x>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: fastGHQuad, MASS, Rcpp
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-09-21 13:07:24 UTC; chiaradigravio
Author: Jonathan Schildcrout [aut], Nathaniel Mercaldo [aut], Chiara Di Gravio [cre]
Maintainer: Chiara Di Gravio <chiara.di.gravio@vanderbilt.edu>
Repository: CRAN
Date/Publication: 2022-09-21 16:20:06 UTC

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New package verbaliseR with initial version 0.1
Package: verbaliseR
Title: Make your Text Mighty Fine
Version: 0.1
Description: Turn R analysis outputs into full sentences, by writing vectors into in-sentence lists, pluralising words conditionally, spelling out numbers if they are at the start of sentences, writing out dates in full following US or UK style, and managing capitalisations in tidy data.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/cararthompson/verbaliseR
BugReports: https://github.com/cararthompson/verbaliseR/issues
Maintainer: Cara Thompson <cara.r.thompson@gmail.com>
Imports: stringr
NeedsCompilation: no
Packaged: 2022-09-20 21:38:25 UTC; Cara
Author: Cara Thompson [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-21 08:50:02 UTC

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New package SDPrism2D with initial version 0.1.1
Package: SDPrism2D
Title: Visualizing the Standard Deviation as the Size of a Prism
Version: 0.1.1
Maintainer: Hieu Nguyen <hieunguyen04062003@gmail.com>
Description: We visualize the standard deviation of a data set as the size of a prism whose volume equals the total volume of several prisms made from the Empirical Cumulative Distribution Function.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-20 12:23:28 UTC; PC
Author: Hieu Nguyen [aut, cre], Tom Nguyen [aut], Mamunur Rashid [aut], Jyotirmoy Sarkar [aut]
Repository: CRAN
Date/Publication: 2022-09-21 08:20:02 UTC

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New package RPhosFate with initial version 1.0.2
Package: RPhosFate
Title: Soil and Chemical Substance Emission and Transport Model
Version: 1.0.2
Description: An enhanced version of the semi-empirical, spatially distributed emission and transport model PhosFate implemented in 'R' and 'C++'. It currently supports suspended solids (SS) and particulate phosphorus (PP). A major feature is the allocation of substance loads entering surface waters to their sources of origin, which is a basic requirement for the identification of critical source areas and in consequence a cost-effective implementation of mitigation measures. References: Hepp et al. (2022) <doi:10.1016/j.jenvman.2022.114514>; Hepp and Zessner (2019) <doi:10.3390/w11102161>; Kovacs (2013) <http://hdl.handle.net/20.500.12708/9468>.
License: AGPL (>= 3)
URL: https://gisler.github.io/RPhosFate/
BugReports: https://github.com/gisler/RPhosFate/issues
Language: en-GB
Encoding: UTF-8
ByteCompile: true
Depends: R (>= 3.5.0)
Imports: checkmate, graphics, hydroGOF, methods, raster, Rcpp, spatstat.geom, stats, utils, yaml
Suggests: knitr, rmarkdown, rgdal, tinytest, whitebox (>= 2.0.0)
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-09-20 21:42:29 UTC; ghepp
Author: Gerold Hepp [aut, cre]
Maintainer: Gerold Hepp <ghepp@iwag.tuwien.ac.at>
Repository: CRAN
Date/Publication: 2022-09-21 08:50:08 UTC

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New package rankICC with initial version 0.1.0
Package: rankICC
Title: Rank Intraclass Correlation for Clustered Data
Version: 0.1.0
Date: 2022-09-19
Description: Estimates the rank intraclass correlation coefficient (ICC) for clustered continuous, ordinal, binary, and count data <https://github.com/shengxintu/rankICC>.
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-20 16:10:05 UTC; shengxintu
Author: Shengxin Tu [aut, cre], Chun Li [aut], Donglin Zeng [aut], Bryan Shepherd [aut]
Maintainer: Shengxin Tu <shengxin.tu@vanderbilt.edu>
Repository: CRAN
Date/Publication: 2022-09-21 08:30:02 UTC

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New package mpower with initial version 0.1.0
Package: mpower
Title: Power Analysis via Monte Carlo Simulation for Correlated Data
Version: 0.1.0
Description: A flexible framework for power analysis using Monte Carlo simulation for settings in which considerations of the correlations between predictors are important. Users can set up a data generative model that preserves dependence structures among predictors given existing data (continuous, binary, or ordinal). Users can also generate power curves to assess the trade-offs between sample size, effect size, and power of a design. This package includes several statistical models common in environmental mixtures studies. For more details and tutorials, see Nguyen et al. (2022) <arXiv:2209.08036>.
License: LGPL
Encoding: UTF-8
LazyData: true
Imports: abind, boot, dplyr, doSNOW, foreach, ggplot2, MASS, magrittr, parallel, purrr, snow, sbgcop, rlang, reshape2, tibble, tidyr, tidyselect
Depends: R (>= 3.5.0)
Suggests: BMA, bkmr, bws, infinitefactor, knitr, NHANES, qgcomp, rmarkdown, rstan, testthat, openxlsx
NeedsCompilation: no
Packaged: 2022-09-20 18:32:25 UTC; phuc
Author: Phuc H. Nguyen [aut, cre]
Maintainer: Phuc H. Nguyen <phuc.nguyen.rcran@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-21 08:50:05 UTC

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New package BayesDissolution with initial version 0.1.0
Package: BayesDissolution
Title: Bayesian Models for Dissolution Testing
Version: 0.1.0
Description: Fits Bayesian models to dissolution data sets that can be used for dissolution testing. Currently the package includes the Bayesian models outlined in Pourmohamad et al. (2022) <doi:10.1111/rssc.12535>, but more models may be added over time.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: geoR, MCMCpack, mnormt, pscl
Depends: R (>= 2.10)
Suggests: ggplot2, scales
NeedsCompilation: no
Packaged: 2022-09-20 15:29:30 UTC; pourmoht
Author: Tony Pourmohamad [aut, cre]
Maintainer: Tony Pourmohamad <tpourmohamad@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-21 08:30:08 UTC

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New package REDCapTidieR with initial version 0.1.2
Package: REDCapTidieR
Title: Extract 'REDCap' Databases into Tidy 'Tibble's
Version: 0.1.2
Description: Convert 'REDCap' exports into tidy tables for easy handling of 'REDCap' repeat instruments and event arms.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: checkmate, dplyr, purrr, REDCapR (>= 1.1.0), rlang, stringi, stringr, tibble, tidyr, tidyselect
URL: https://github.com/CHOP-CGTDataOps/REDCapTidieR, https://chop-cgtdataops.github.io/REDCapTidieR/
BugReports: https://github.com/CHOP-CGTDataOps/REDCapTidieR/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2022-09-20 11:52:53 UTC; hannar1
Author: Richard Hanna [aut, cre], Stephan Kadauke [aut]
Maintainer: Richard Hanna <richardshanna91@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-21 08:00:02 UTC

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Tue, 20 Sep 2022

New package RANKS with initial version 1.1
Package: RANKS
Title: Ranking of Nodes with Kernelized Score Functions
Version: 1.1
Date: 2022-09-20
Author: Giorgio Valentini [aut, cre]
Maintainer: Giorgio Valentini <valentini@di.unimi.it>
Description: Implementation of Kernelized score functions and other semi-supervised learning algorithms for node label ranking to analyze biomolecular networks. RANKS can be easily applied to a large set of different relevant problems in computational biology, ranging from automatic protein function prediction, to gene disease prioritization and drug repositioning, and more in general to any bioinformatics problem that can be formalized as a node label ranking problem in a graph. The modular nature of the implementation allows to experiment with different score functions and kernels and to easily compare the results with baseline network-based methods such as label propagation and random walk algorithms, as well as to enlarge the algorithmic scheme by adding novel user-defined score functions and kernels.
License: GPL (>= 2)
LazyLoad: yes
Imports: methods, graph, RBGL, limma, NetPreProc, PerfMeas
Suggests: bionetdata
NeedsCompilation: yes
Packaged: 2022-09-20 15:05:16 UTC; valenti
Repository: CRAN
Date/Publication: 2022-09-20 22:40:05 UTC

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New package PRSim with initial version 1.4-2
Package: PRSim
Title: Stochastic Simulation of Streamflow Time Series using Phase Randomization
Version: 1.4-2
Date: 2022-09-16
Author: Manuela Brunner [aut, cre] , Reinhard Furrer [aut]
Maintainer: Manuela Brunner <manuela.i.brunner@gmail.com>
Description: Provides a simulation framework to simulate streamflow time series with similar main characteristics as observed data. These characteristics include the distribution of daily streamflow values and their temporal correlation as expressed by short- and long-range dependence. The approach is based on the randomization of the phases of the Fourier transform or the phases of the wavelet transform. The function prsim() is applicable to single site simulation and uses the Fourier transform. The function prsim.wave() extends the approach to multiple sites and is based on the complex wavelet transform. The function prsim.weather() extends the approach to multiple variables for weather generation. We further use the flexible four-parameter Kappa distribution, which allows for the extrapolation to yet unobserved low and high flows. Alternatively, the empirical or any other distribution can be used. A detailed description of the simulation approach for single sites and an application example can b [...truncated...]
URL: https://git.math.uzh.ch/reinhard.furrer/PRSim-devel
BugReports: https://git.math.uzh.ch/reinhard.furrer/PRSim-devel/-/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Suggests: lattice, ismev, evd, GB2, boot, MASS
Imports: stats, methods, lmomco, mev, goftest, wavScalogram, splus2R
NeedsCompilation: yes
Packaged: 2022-09-20 12:28:41 UTC; Brunner
Repository: CRAN
Date/Publication: 2022-09-20 22:50:02 UTC

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New package CytobankAPI with initial version 2.1.0
Package: CytobankAPI
Title: Cytobank API Wrapper for R
Version: 2.1.0
Description: Tools to interface with Cytobank's API via R, organized by endpoints that represent various areas of Cytobank functionality. Learn more about Cytobank at <https://www.beckman.com/flow-cytometry/software>.
License: GPL-3
Depends: R (>= 3.5.0), curl (>= 2.7), httr (>= 1.2.1)
Imports: jsonlite, methods, stats, aws.s3, uuid, jose
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
Copyright: 2020 Beckman Coulter, Inc.
NeedsCompilation: no
Packaged: 2022-09-19 03:50:15 UTC; sgao
Author: Angel Figueroa [aut, cre], Qihao Qi [aut], Stefanie Trop [aut], Louis Liu [aut], Preston Ng [aut], Chris Ciccolella [aut], Katherine Drake [aut]
Maintainer: Angel Figueroa <afigueroa03@beckman.com>
Repository: CRAN
Date/Publication: 2022-09-20 22:30:18 UTC

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New package Correlplot with initial version 1.0.3
Package: Correlplot
Title: A Collection of Functions for Graphing Correlation Matrices
Version: 1.0.3
Date: 2022-09-15
Author: Jan Graffelman
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Depends: R (>= 1.8.0), calibrate
Imports: corrplot, xtable, MASS
Description: Routines for the graphical representation of correlation matrices by means of correlograms, biplots and MDS maps.
License: GPL (>= 2)
URL: https://www.r-project.org, http://www-eio.upc.es/~jan/
NeedsCompilation: no
Packaged: 2022-09-20 10:12:41 UTC; jangr
Repository: CRAN
Date/Publication: 2022-09-20 22:40:09 UTC

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New package RestoreNet with initial version 1.0
Package: RestoreNet
Title: Random-Effects Stochastic Reaction Networks
Version: 1.0
Description: A random-effects stochastic model that allows quick detection of clonal dominance events from clonal tracking data collected in gene therapy studies. Starting from the Ito-type equation describing the dynamics of cells duplication, death and differentiation at clonal level, we first considered its local linear approximation as the base model. The parameters of the base model, which are inferred using a maximum likelihood approach, are assumed to be shared across the clones. Although this assumption makes inference easier, in some cases it can be too restrictive and does not take into account possible scenarios of clonal dominance. Therefore we extended the base model by introducing random effects for the clones. In this extended formulation the dynamic parameters are estimated using a tailor-made expectation maximization algorithm. Further details on the methods can be found in L. Del Core et al., (2022) <doi:10.1101/2022.05.31.494100>.
License: GPL-3
Encoding: UTF-8
Imports: Matrix, xtable, scales, stringr, ggplot2, scatterpie, RColorBrewer
Depends: R (>= 2.10)
LazyData: true
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2022-09-20 08:13:12 UTC; delcore.luca
Author: Luca Del Core [aut, cre, cph] , Marco Grzegorczyk [aut, ths] , Ernst Wit [aut, ths]
Maintainer: Luca Del Core <l.del.core@rug.nl>
Repository: CRAN
Date/Publication: 2022-09-20 10:46:14 UTC

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New package OptiSembleForecasting with initial version 0.1.0
Package: OptiSembleForecasting
Title: Optimization Based Ensemble Forecasting Using MCS Algorithm
Version: 0.1.0
Author: Dr. Md Yeasin [aut, cre], Dr. Ranjit Kumar Paul [aut]
Maintainer: Dr. Md Yeasin <yeasin.iasri@gmail.com>
Description: The real-life data is complex in nature. No single model can capture all aspect of complex time series data. In this package, 14 models, namely Recurrent Neural Network (RNN), Gated Recurrent Unit (GRU), Long Short-Term Memory (LSTM), Bidirectional LSTM, Deep LSTM, Artificial Neural Network (ANN), Support Vector Regression (SVR), Random Forest (RF), k-Nearest Neighbour (KNN), XGBoost (XGB), Autoregressive Integrated Moving Average (ARIMA), Error-Trend-Seasonality (ETS) and TBATS models, have been implemented and their accuracy have been checked. An PCA based error index has been proposed to select a group of best models using MCS algorithms. After selecting the models, the forecasts from these models have been ensembled using optimization techniques. This package allows to implement 20 optimization techniques, namely, Artificial Bee Colony (ABC), Ant Lion Optimizer (ALO), Bat Algorithm (BA), Black Hole Optimization Algorithm (BHO), Clonal Selection Algorithm (CLONALG), Cuckoo Search (C [...truncated...]
License: GPL-3
Encoding: UTF-8
Imports: stats, keras, tsutils, readxl, tibble, tensorflow, Metrics, forecast, dplyr, neuralnet, MCS, caretForecast, kknn, metaheuristicOpt, FactoMineR, factoextra, utils
NeedsCompilation: no
Packaged: 2022-09-20 05:57:54 UTC; YEASIN
Repository: CRAN
Date/Publication: 2022-09-20 10:36:10 UTC

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New package neuRosim with initial version 0.2-13
Package: neuRosim
Title: Simulate fMRI Data
Version: 0.2-13
Date: 2022-09-02
Depends: R (>= 3.1.1), deSolve
Description: Generates functional Magnetic Resonance Imaging (fMRI) time series or 4D data. Some high-level functions are created for fast data generation with only a few arguments and a diversity of functions to define activation and noise. For more advanced users it is possible to use the low-level functions and manipulate the arguments. See Welvaert et al. (2011) <doi:10.18637/jss.v044.i10>.
License: GPL (>= 2)
LazyLoad: yes
Repository: CRAN
Date/Publication: 2022-09-20 10:46:11 UTC
Packaged: 2022-09-20 09:27:38 UTC; tabelow
NeedsCompilation: yes
Author: Marijke Welvaert [aut], Joke Durnez [ctb], Beatrijs Moerkerke [ctb], Yves Rosseel [ctb], Karsten Tabelow [ctb, cre], Geert Verdoolaege [ctb]
Maintainer: Karsten Tabelow <karsten.tabelow@wias-berlin.de>

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New package DynForest with initial version 1.0.0
Package: DynForest
Title: Random Forest with Multivariate Longitudinal Predictors
Version: 1.0.0
Description: Based on random forest principle, 'DynForest' is able to include multiple longitudinal predictors to provide individual predictions. Longitudinal predictors are modeled through the random forest. The methodology is fully described for a survival outcome in: Devaux, Helmer, Dufouil, Genuer & Proust-Lima (2022) <doi: 10.48550/arXiv.2208.05801>.
Imports: DescTools, cmprsk, doParallel, foreach, ggplot2, lcmm, methods, pbapply, pec, prodlim, stringr, survival, zoo
Depends: R (>= 3.5.0)
License: LGPL (>= 3)
Encoding: UTF-8
URL: https://github.com/anthonydevaux/DynForest
BugReports: https://github.com/anthonydevaux/DynForest/issues
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-20 08:34:19 UTC; antho
Author: Anthony Devaux [aut, cre]
Maintainer: Anthony Devaux <anthony.devaux@u-bordeaux.fr>
Repository: CRAN
Date/Publication: 2022-09-20 10:46:17 UTC

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New package SiPhyNetwork with initial version 1.0.0
Package: SiPhyNetwork
Title: A Phylogenetic Simulator for Reticulate Evolution
Version: 1.0.0
Description: A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.
License: GPL-3
Encoding: UTF-8
Suggests: testthat, knitr, rmarkdown, markdown
Imports: stats, ape, Rcpp, rstackdeque
VignetteBuilder: knitr
LinkingTo: Rcpp,
NeedsCompilation: yes
Packaged: 2022-09-19 17:55:08 UTC; justison
Author: Joshua Justison [aut, cre, cph], Claudia Solis-Lemus [aut, cph], Tracy A. Heath [aut, cph], Klaus Schliep [cph] , Emmanuel Paradis [cph] , Daniel Lawson [cph]
Maintainer: Joshua Justison <justisnojo@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-20 09:16:19 UTC

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New package saccadr with initial version 0.1.1
Package: saccadr
Title: Extract Saccades via an Ensemble of Methods Approach
Version: 0.1.1
Date: 2022-09-18
Description: A modular and extendable approach to extract (micro)saccades from gaze samples via an ensemble of methods. Although there is an agreement about a general definition of a saccade, the more specific details are harder to agree upon. Therefore, there are numerous algorithms that extract saccades based on various heuristics, which differ in the assumptions about velocity, acceleration, etc. The package uses three methods (Engbert and Kliegl (2003) <doi:10.1016/S0042-6989(03)00084-1>, Otero-Millan et al. (2014)<doi:10.1167/14.2.18>, and Nyström and Holmqvist (2010) <doi:10.3758/BRM.42.1.188>) to label individual samples and then applies a majority vote approach to identify saccades. The package includes three methods but can be extended via custom functions. It also uses a modular approach to compute velocity and acceleration from noisy samples. Finally, you can obtain methods votes per gaze sample instead of saccades.
License: GPL (>= 3)
URL: https://github.com/alexander-pastukhov/saccadr/, https://alexander-pastukhov.github.io/saccadr/
BugReports: https://github.com/alexander-pastukhov/saccadr/issues/
Imports: magrittr, Rcpp (>= 1.0.8)
LinkingTo: Rcpp
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Depends: R (>= 4.1.0), dplyr, rlang, cluster, signal, tidyr
Suggests: rmarkdown, knitr, ggplot2, spelling, testthat (>= 3.0.0)
Language: en-US
NeedsCompilation: yes
Packaged: 2022-09-19 19:23:05 UTC; pastu
Author: Alexander Pastukhov [aut, cre]
Maintainer: Alexander Pastukhov <pastukhov.alexander@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-20 09:16:09 UTC

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New package LMD with initial version 1.0.0
Package: LMD
Date: 2022-09-10
Title: A Self-Adaptive Approach for Demodulating Multi-Component Signal
Version: 1.0.0
Maintainer: Shubhra Prakash <shubhraprakash279@gmail.com>
Description: Local Mean Decomposition is an iterative and self-adaptive approach for demodulating, processing, and analyzing multi-component amplitude modulated and frequency modulated signals. This R package is based on the approach suggested by Smith (2005) <doi:10.1098/rsif.2005.0058> and the 'Python' library 'PyLMD'.
License: Apache License (>= 2)
Depends: R (>= 3.6.0)
BugReports: https://github.com/shubhra-opensource/LMD/issues
URL: https://github.com/shubhra-opensource/LMD
Encoding: UTF-8
Suggests: knitr, rmarkdown, ggformula, testthat (>= 3.0.0)
VignetteBuilder: knitr
Imports: EMD, ggplot2, patchwork
NeedsCompilation: no
Packaged: 2022-09-20 02:27:01 UTC; shubh
Author: Shubhra Prakash [trl, aut, cre]
Repository: CRAN
Date/Publication: 2022-09-20 09:56:07 UTC

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New package gasmodel with initial version 0.1.0
Package: gasmodel
Title: Generalized Autoregressive Score Models
Version: 0.1.0
Author: Vladimir Holý
Maintainer: Vladimir Holý <vladimir.holy@vse.cz>
Description: Estimation, forecasting, and simulation of generalized autoregressive score (GAS) models of Creal, Koopman, and Lucas (2013) <doi:10.1002/jae.1279> and Harvey (2013) <doi:10.1017/cbo9781139540933>. Model specification allows for various conditional distributions, different parametrizations, exogenous variables, higher score and autoregressive orders, custom and unconditional initial values of time-varying parameters, fixed and bounded values of coefficients, and missing values. Model estimation is performed by the maximum likelihood method and the Hessian matrix.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: abind, arrangements, Matrix, mvnfast, nloptr, numDeriv, pracma
Suggests: knitr, rmarkdown, testthat, tidyverse
Depends: R (>= 2.10)
VignetteBuilder: knitr
URL: https://github.com/vladimirholy/gasmodel
BugReports: https://github.com/vladimirholy/gasmodel/issues
NeedsCompilation: no
Packaged: 2022-09-19 17:03:53 UTC; mira
Repository: CRAN
Date/Publication: 2022-09-20 09:16:12 UTC

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New package FieldSimR with initial version 1.0.0
Package: FieldSimR
Title: Simulation of Plot-Level Data in Plant Breeding Field Trials
Version: 1.0.0
Date: 2022-09-19
Maintainer: Christian Werner <werner.christian@proton.me>
Description: Simulates plot-level data in plant breeding field trials for multiple traits in multiple environments. Its core function simulates spatially correlated plot-level errors across correlated traits using bivariate interpolation or a two-dimensional autoregressive process of order one (AR1:AR1). 'FieldSimR' then combines this spatial error with random measurement error at a user-defined ratio. The simulated plot-level errors can be combined with genetic values (e.g. true, simulated or predicted) to generate plot-level phenotypes. 'FieldSimR' provides wrapper functions to simulate the genetic values for multiple traits in multiple environments using the 'R' package 'AlphaSimR'.
License: GPL (>= 3)
URL: https://github.com/crWerner/fieldsimr
Encoding: UTF-8
Imports: fields, interp, matrixcalc, mbend
Suggests: AlphaSimR
NeedsCompilation: no
Packaged: 2022-09-19 21:31:04 UTC; CWERNER
Author: Christian Werner [aut, cre] , Daniel Tolhurst [aut] , Chris Gaynor [ctb] , Giovanny Covarrubias-Pazaran [ctb] , Lorena Batista [ctb]
Repository: CRAN
Date/Publication: 2022-09-20 09:46:06 UTC

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New package CommKern with initial version 1.0.0
Package: CommKern
Version: 1.0.0
Title: Network-Based Communities and Kernel Machine Methods
Description: Analysis of network community objects with applications to neuroimaging data. There are two main components to this package. The first is the hierarchical multimodal spinglass (HMS) algorithm, which is a novel community detection algorithm specifically tailored to the unique issues within brain connectivity. The other is a suite of semiparametric kernel machine methods that allow for statistical inference to be performed to test for potential associations between these community structures and an outcome of interest (binary or continuous).
Depends: R (>= 4.0.0)
License: GPL (>= 2)
Encoding: UTF-8
URL: https://github.com/aljensen89/CommKern
Language: en-us
LazyData: true
Imports: ggnewscale, ggplot2, gridExtra, Matrix, RColorBrewer, reshape2
Suggests: knitr, matrixcalc, pheatmap, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-19 23:08:56 UTC; jenseale
Author: Alexandria Jensen [aut, cre] , Peter DeWitt [ctb] , Debashis Ghosh [ths]
Maintainer: Alexandria Jensen <alexandria.jensen@cuanschutz.edu>
Repository: CRAN
Date/Publication: 2022-09-20 09:46:09 UTC

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New package betaSandwich with initial version 1.0.1
Package: betaSandwich
Title: Robust Confidence Intervals for Standardized Regression Coefficients
Version: 1.0.1
Description: Generates robust confidence intervals for standardized regression coefficients using heteroskedasticity-consistent standard errors for models fitted by lm() as described in Dudgeon (2017) <doi:10.1007/s11336-017-9563-z>.
URL: https://github.com/jeksterslab/betaSandwich, https://jeksterslab.github.io/betaSandwich/
BugReports: https://github.com/jeksterslab/betaSandwich/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), methods
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2022-09-19 17:49:41 UTC; r1125663
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-20 09:16:16 UTC

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New package usincometaxes with initial version 0.5.2
Package: usincometaxes
Title: Calculate Federal and State Income Taxes in the United States
Version: 0.5.2
Description: Calculates federal and state income taxes in the United States. It acts as a wrapper to the NBER's TAXSIM 35 (<http://taxsim.nber.org/taxsim35/>) tax simulator. TAXSIM 35 conducts the calculations, while 'usincometaxes' prepares the data for TAXSIM 35, sends the data to TAXSIM 35's server or communicates with the Web Assembly file, retrieves the data, and places it into a data frame. All without the user worrying about this process.
License: MIT + file LICENSE
URL: https://github.com/shanejorr/usincometaxes, https://shaneorr.io/r/usincometaxes
BugReports: https://github.com/shanejorr/usincometaxes/issues
Depends: R (>= 3.1)
Imports: datasets, vroom, httr, tibble, utils, V8
Suggests: dplyr, ggplot2, knitr, rmarkdown, scales, testthat (>= 3.0.0), tidyr, tools
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-20 01:40:56 UTC; shane
Author: Shane Orr [aut, cre, cph], Thomas Wells [ctb]
Maintainer: Shane Orr <shane.j.orr@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-20 08:10:02 UTC

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New package rocbc with initial version 0.1.0
Package: rocbc
Title: Statistical Inference for Box-Cox Based Receiver Operating Characteristic Curves
Version: 0.1.0
Maintainer: Benjamin Brewer <tennisbenj@gmail.com>
Description: Generation of Box-Cox based ROC curves and several aspects of inferences and hypothesis testing. Can be used when inferences for one biomarker (Bantis LE, Nakas CT, Reiser B. (2018) <doi:10.1002/bimj.201700107>) are of interest or when comparisons of two correlated biomarkers (Bantis LE, Nakas CT, Reiser B. (2021) <doi:10.1002/bimj.202000128>) are of interest. Provides inferences and comparisons around the AUC, the Youden index, the sensitivity at a given specificity level (and vice versa), the optimal operating point of the ROC curve (in the Youden sense), and the Youden based cutoff.
License: GPL-3
Encoding: UTF-8
Imports: pracma, clinfun, splancs, mvtnorm
Suggests: knitr, markdown
VignetteBuilder: knitr
Author: Leonidas Bantis [aut], Benjamin Brewer [cre, ctb]
NeedsCompilation: no
Packaged: 2022-09-19 12:51:21 UTC; benbrewer
Repository: CRAN
Date/Publication: 2022-09-20 08:56:09 UTC

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New package RoBTT with initial version 1.0.0
Package: RoBTT
Title: Robust Bayesian T-Test
Version: 1.0.0
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Description: An implementation of Bayesian model-averaged t-test that allows users to draw inference about the presence vs absence of the effect, heterogeneity of variances, and outliers. The 'RoBTT' packages estimates model ensembles of models created as a combination of the competing hypotheses and uses Bayesian model-averaging to combine the models using posterior model probabilities. Users can obtain the model-averaged posterior distributions and inclusion Bayes factors which account for the uncertainty in the data generating process (Maier et al., 2022, <doi:10.31234/osf.io/d5zwc>). Users can define a wide range of informative priors for all parameters of interest. The package provides convenient functions for summary, visualizations, and fit diagnostics.
URL: https://fbartos.github.io/RoBTT/
BugReports: https://github.com/FBartos/RoBTT/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
SystemRequirements: GNU make
NeedsCompilation: yes
ByteCompile: true
LinkingTo: StanHeaders (>= 2.18.1), rstan (>= 2.21.2), BH (>= 1.69.0), Rcpp (>= 0.12.15), RcppEigen (>= 0.3.3.4.0), RcppParallel (>= 5.0.1)
Depends: R (>= 4.0.0), Rcpp (>= 0.12.19)
Imports: rstan(>= 2.21.2), rstantools(>= 1.5.0), RcppParallel (>= 5.0.1), BayesTools (>= 0.2.12), bridgesampling, methods, Rdpack
Suggests: parallel, testthat, vdiffr, knitr, rmarkdown, covr
VignetteBuilder: knitr
Packaged: 2022-09-19 14:38:37 UTC; fbart
Author: Frantisek Bartos [aut, cre] , Maximilian Maier [aut]
Repository: CRAN
Date/Publication: 2022-09-20 08:06:09 UTC

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New package kernstadapt with initial version 0.0.1
Package: kernstadapt
Title: Spatio-Temporal Adaptive Kernel Estimators for Intensities
Version: 0.0.1
Maintainer: Jonatan A Gonzalez <jonathan.gonzalez@kaust.edu.sa>
Description: Adaptive estimation of the first-order intensity function of a spatio-temporal point process using kernels and variable bandwidths. The methodology used for estimation is presented in González and Moraga (2022). <arXiv:2208.12026>.
License: MIT + file LICENSE
Language: en-GB
Encoding: UTF-8
Imports: misc3d, sparr, spatstat.core, spatstat.geom, spatstat.random, spatstat.utils
Suggests: knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
Depends: R (>= 3.5)
NeedsCompilation: no
Packaged: 2022-09-19 11:16:45 UTC; gonzalja
Author: Jonatan A Gonzalez [aut, cre] , Paula Moraga [aut]
Repository: CRAN
Date/Publication: 2022-09-20 08:56:12 UTC

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New package gsbm with initial version 0.2.2
Package: gsbm
Title: Estimate Parameters in the Generalized SBM
Version: 0.2.2
Maintainer: Solenne Gaucher <solenne.gaucher@math.u-psud.fr>
Description: Given an adjacency matrix drawn from a Generalized Stochastic Block Model with missing observations, this package robustly estimates the probabilities of connection between nodes and detects outliers nodes, as describes in Gaucher, Klopp and Robin (2019) <arXiv:1911.13122>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: softImpute, RSpectra, doParallel, Matrix, foreach
Suggests: knitr, rmarkdown, igraph, missSBM, RColorBrewer, combinat, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-02 02:43:32 UTC; solenne
Author: Genevieve Robin [aut], Solenne Gaucher [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-20 08:16:14 UTC

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New package defineR with initial version 0.0.4
Package: defineR
Title: Creates Define XML Documents
Version: 0.0.4
Maintainer: David Bosak <dbosak01@gmail.com>
Description: Creates 'define.xml' documents used for regulatory submissions based on spreadsheet metadata. Can also help create metadata and generate HTML data explorer.
License: CC0
Encoding: UTF-8
Depends: R (>= 3.6.0), common, glue
Suggests: knitr, rmarkdown, magrittr, testthat (>= 3.0.0),
Imports: readxl, xml2, xslt, reporter, libr, openxlsx, stats
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-19 16:03:00 UTC; dbosa
Author: David Bosak [aut, cre], Aheer Alvi [aut], Jonathan Stallings [ctb]
Repository: CRAN
Date/Publication: 2022-09-20 08:26:07 UTC

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New package compareMCMCs with initial version 0.5.0
Package: compareMCMCs
Title: Compare MCMC Efficiency from 'nimble' and/or Other MCMC Engines
Version: 0.5.0
Maintainer: Perry de Valpine <pdevalpine@berkeley.edu>
Description: Manages comparison of MCMC performance metrics from multiple MCMC algorithms. These may come from different MCMC configurations using the 'nimble' package or from other packages. Plug-ins for JAGS via 'rjags' and Stan via 'rstan' are provided. It is possible to write plug-ins for other packages. Performance metrics are held in an MCMCresult class along with samples and timing data. It is easy to apply new performance metrics. Reports are generated as html pages with figures comparing sets of runs. It is possible to configure the html pages, including providing new figure components.
License: BSD_3_clause + file LICENSE | GPL (>= 2)
Encoding: UTF-8
Depends: nimble
Imports: R6, ggplot2, grid, reshape2, xtable, coda
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, rjags, rstan
URL: https://github.com/nimble-dev/compareMCMCs
BugReports: https://github.com/nimble-dev/compareMCMCs/issues
NeedsCompilation: no
Packaged: 2022-08-25 19:01:15 UTC; perry
Author: Perry de Valpine [aut, cre], Sally Paganin [aut], Daniel Turek [aut], Christopher Paciorek [aut]
Repository: CRAN
Date/Publication: 2022-09-20 08:26:10 UTC

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New package grandR with initial version 0.2.0
Package: grandR
Version: 0.2.0
Title: Comprehensive Analysis of Nucleotide Conversion Sequencing Data
Description: Nucleotide conversion sequencing experiments have been developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such experiments require specialized tools for primary processing such as GRAND-SLAM, (see 'Jürges et al' <doi:10.1093/bioinformatics/bty256>) and specialized tools for downstream analyses. 'grandR' provides a comprehensive toolbox for quality control, kinetic modeling, differential gene expression analysis and visualization of such data.
Author: Florian Erhard [aut, cre] , Teresa Rummel [ctb], Lygeri Sakellaridi [ctb]
Maintainer: Florian Erhard <Florian.Erhard@uni-wuerzburg.de>
License: Apache License (>= 2)
Encoding: UTF-8
URL: https://github.com/erhard-lab/grandR
BugReports: https://github.com/erhard-lab/grandR/issues
Imports: stats, Matrix, ggplot2, grDevices, patchwork, plyr, parallel, reshape2, MASS, cowplot, minpack.lm, lfc, methods, utils, numDeriv
Suggests: knitr, rmarkdown, circlize, Seurat, ComplexHeatmap, ggrepel, RCurl, DESeq2, clusterProfiler, msigdbr, fgsea, rclipboard, cubature, lamW, DT, RColorBrewer, eulerr, gsl, htmltools, labeling, matrixStats, monocle, VGAM, quantreg, rlang, graphics, scales, shiny
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-19 11:24:31 UTC; erhard
Repository: CRAN
Date/Publication: 2022-09-20 07:56:10 UTC

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New package fdaconcur with initial version 0.1.0
Package: fdaconcur
Title: Concurrent Regression and History Index Models for Functional Data
URL: https://github.com/functionaldata/tFDAconcur
BugReports: https://github.com/functionaldata/tFDAconcur/issues
Version: 0.1.0
Encoding: UTF-8
Date: 2022-08-25
Maintainer: Satarupa Bhattacharjee <sbhattacharjee@ucdavis.edu>
Description: Provides implementation of concurrent or varying coefficient regression methods for functional data. The implementations are done for both dense and sparsely observed functional data. Pointwise confidence bands can be constructed for each case. Further, the influence of past predictor values is modeled by a smooth history index function, while the effects on the response are described by smooth varying coefficient functions, which are very useful in analyzing real data such as COVID data. References: Yao, F., Müller, H.G., Wang, J.L. (2005) <doi: 10.1214/009053605000000660>. Sentürk, D., Müller, H.G. (2010) <doi: 10.1198/jasa.2010.tm09228>.
License: BSD_3_clause + file LICENSE
Imports: fdapace, stats
Suggests: MASS, Rcpp (>= 0.11.5), Matrix, pracma, numDeriv, testthat
NeedsCompilation: no
Packaged: 2022-09-15 03:39:28 UTC; satar
Author: Satarupa Bhattacharjee [aut, cre], Yaqing Chen [aut], Changbo Zhu [aut], Han Chen [aut], Yidong Zhou [aut], Álvaro Gajardo [aut], Hans-Georg Mueller [cph, ths, aut]
Repository: CRAN
Date/Publication: 2022-09-20 07:56:15 UTC

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Mon, 19 Sep 2022

New package alqrfe with initial version 1.0
Package: alqrfe
Title: Adaptive Lasso Quantile Regression with Fixed Effects
Version: 1.0
Date: 2022-09-19
Description: Quantile regression with fixed effects solves longitudinal data, considering the individual intercepts as fixed effects. The parametric set of this type of problem used to be huge. Thus penalized methods such as Lasso are currently applied. Adaptive Lasso presents oracle proprieties, which include Gaussianity and correct model selection. Bayesian information criteria (BIC) estimates the optimal tuning parameter lambda. Plot tools are also available.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.5), MASS (>= 7.3-49)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2022-09-19 13:38:07 UTC; ian
Author: Ian Meneghel Danilevicz [aut, cre]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-19 23:36:13 UTC

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New package rGV with initial version 0.0.2
Package: rGV
Version: 0.0.2
Date: 2022-09-17
Title: Analysis of Continuous Glucose Monitor Data
Author: Evan Olawsky [aut, cre], Yuan Zhang [ctb], Lynn Eberly [ctb]
Maintainer: Evan Olawsky <evanolawsky@gmail.com>
Depends: R (>= 3.2.0), chron
Description: Reads in continuous glucose monitor data of many different formats, calculates a host of glycemic variability metrics, and plots glucose over time.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-09-17 15:32:23 UTC; overlord
Repository: CRAN
Date/Publication: 2022-09-19 22:56:12 UTC

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New package snappier with initial version 0.2.0
Package: snappier
Title: Compress and Decompress 'Snappy' Encoded Data
Version: 0.2.0
Description: Provides compression and decompression of 'Snappy' encoded data. Includes and provides bindings to the 'Snappy' compression library, with a safe R interface.
Depends: R (>= 3.3.0)
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
Suggests: testthat, hedgehog
NeedsCompilation: yes
Packaged: 2022-09-19 11:50:10 UTC; hcampbell
Author: Huw Campbell [aut, cre], Jeff Dean [ctb], Sanjay Ghemawat [ctb], Steinar Gunderson [ctb], Martin Gieseking [ctb], Google Inc. [cph]
Maintainer: Huw Campbell <huw.campbell@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-19 14:16:13 UTC

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New package recurrentpseudo with initial version 1.0.0
Package: recurrentpseudo
Title: Creates Pseudo-Observations and Analysis for Recurrent Event Data
Version: 1.0.0
Description: Computation of one-, two- and three-dimensional pseudo-observations based on recurrent events and terminal events. Generalised linear models are fitted using generalised estimating equations. Technical details on the bivariate procedure can be found in "Bivariate pseudo-observations for recurrent event analysis with terminal events" (Furberg et al., 2021) <doi:10.1007/s10985-021-09533-5>.
License: GPL (>= 2)
URL: https://github.com/JulieKFurberg/recurrentpseudo
Encoding: UTF-8
Imports: survival, geepack, stringr, prodlim
Depends: magrittr, dplyr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-19 12:23:25 UTC; JUKF
Author: Julie Kjaerulff Furberg [aut, cre]
Maintainer: Julie Kjaerulff Furberg <julie_furberg@hotmail.com>
Repository: CRAN
Date/Publication: 2022-09-19 14:16:16 UTC

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New package TSCI with initial version 1.0.0
Package: TSCI
Title: Tools for Causal Inference with Possibly Invalid Instrumental Variables
Version: 1.0.0
Description: Two stage curvature identification with machine learning for causal inference in settings when instrumental variable regression is not suitable because of potentially invalid instrumental variables. Based on Guo and Buehlmann (2022) "Two Stage Curvature Identification with Machine Learning: Causal Inference with Possibly Invalid Instrumental Variables" <arXiv:2203.12808> .
URL: https://github.com/dlcarl/TSML
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.0.0)
Suggests: fda, MASS, testthat (>= 3.0.0), withr
Imports: xgboost, Rfast, stats, ranger, parallel
NeedsCompilation: no
Packaged: 2022-09-18 12:26:38 UTC; david
Author: David Carl [aut, cre] , Corinne Emmenegger [aut] , Wei Yuan [aut], Zijian Guo [aut]
Maintainer: David Carl <dcarl@ethz.ch>
Repository: CRAN
Date/Publication: 2022-09-19 13:16:10 UTC

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New package unitquantreg with initial version 0.0.3
Package: unitquantreg
Title: Parametric Quantile Regression Models for Bounded Data
Version: 0.0.3
Maintainer: Andre F. B. Menezes <andrefelipemaringa@gmail.com>
Description: A collection of parametric quantile regression models for bounded data. At present, the package provides 13 parametric quantile regression models. It can specify regression structure for any quantile and shape parameters. It also provides several S3 methods to extract information from fitted model, such as residual analysis, prediction, plotting, and model comparison. For more computation efficient the [dpqr]'s, likelihood, score and hessian functions are written in C++. For further details see Mazucheli et. al (2022) <doi:10.1016/j.cmpb.2022.106816>.
License: Apache License (>= 2)
Encoding: UTF-8
ByteCompile: yes
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp, optimx, stats, quantreg, Formula, MASS, numDeriv
Suggests: testthat (>= 3.0.0), rmarkdown, knitr, lmtest, ggplot2, covr
Depends: R (>= 3.5.0)
NeedsCompilation: yes
URL: https://andrmenezes.github.io/unitquantreg/
BugReports: https://github.com/AndrMenezes/unitquantreg/issues
VignetteBuilder: knitr
Packaged: 2022-09-16 15:31:50 UTC; amenezes
Author: Andre F. B. Menezes [aut, cre] , Josmar Mazucheli [aut]
Repository: CRAN
Date/Publication: 2022-09-19 12:30:02 UTC

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New package SparseChol with initial version 0.1.1
Package: SparseChol
Title: Sparse Cholesky LDL Decomposition of Symmetric Matrices
Version: 0.1.1
Date: 2022-08-16
Description: 'C++' implementation of sparse LDL decomposition of symmetric matrices and solvers described by Timothy A. Davis (2016) <https://fossies.org/linux/SuiteSparse/LDL/Doc/ldl_userguide.pdf>. Provides the header file 'SparseChol.h' that specifies the 'SparseChol' class to implement sparse LDL decomposition in 'Rcpp' functions. A limited set of 'R' functions that implement the method are also included.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.7)
LinkingTo: Rcpp (>= 1.0.7)
NeedsCompilation: yes
Author: Sam Watson [aut, cre], Timothy A. Davis [aut, ctb]
URL: https://github.com/samuel-watson/SparseChol
BugReports: https://github.com/samuel-watson/SparseChol/issues
Suggests: testthat
Biarch: true
Depends: R (>= 3.4.0), Matrix (>= 1.3-4)
SystemRequirements: GNU make
Encoding: UTF-8
Packaged: 2022-09-16 16:42:54 UTC; samue
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Repository: CRAN
Date/Publication: 2022-09-19 12:36:14 UTC

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New package fwb with initial version 0.1.0
Package: fwb
Title: Fractional Weighted Bootstrap
Version: 0.1.0
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020) <doi:10.1080/00031305.2020.1731599> for details.
Depends: R (>= 3.0.0)
Imports: chk, pbapply
Suggests: survival, boot, sandwich (>= 2.4-0), lmtest, parallel
License: GPL (>= 2)
Encoding: UTF-8
URL: https://github.com/ngreifer/fwb, https://ngreifer.github.io/fwb/
BugReports: https://github.com/ngreifer/fwb/issues
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-16 21:21:31 UTC; NoahGreifer
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-19 12:56:16 UTC

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New package attachment with initial version 0.3.0
Package: attachment
Title: Deal with Dependencies
Version: 0.3.0
Description: Manage dependencies during package development. This can retrieve all dependencies that are used in ".R" files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2' documentation of functions. There is a function to update the "DESCRIPTION" file of your package with 'CRAN' packages or any other remote package. All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can be used independently of a package development.
License: GPL-3
URL: https://thinkr-open.github.io/attachment/, https://github.com/ThinkR-open/attachment
BugReports: https://github.com/ThinkR-open/attachment/issues
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 3.4)
Imports: cli, desc (>= 1.2.0), glue (>= 1.3.0), knitr (>= 1.20), magrittr (>= 1.5), rmarkdown (>= 1.10), roxygen2, stats, stringr (>= 1.3.1), utils, withr
Suggests: lifecycle, renv (>= 0.8.4), rstudioapi, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-09-15 16:00:47 UTC; srochett
Author: Sebastien Rochette [cre, aut] , Vincent Guyader [aut] , ThinkR [cph, fnd]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Repository: CRAN
Date/Publication: 2022-09-19 12:26:10 UTC

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New package NetPreProc with initial version 1.2
Package: NetPreProc
Title: Network Pre-Processing and Normalization
Version: 1.2
Date: 2022-09-14
Author: Giorgio Valentini [aut, cre]
Maintainer: Giorgio Valentini <valentini@di.unimi.it>
Description: Network Pre-Processing and normalization. Methods for normalizing graphs, including Chua normalization, Laplacian normalization, Binary magnification, min-max normalization and others. Methods to sparsify adjacency matrices. Methods for graph pre-processing and for filtering edges of the graph.
License: GPL (>= 2)
LazyLoad: yes
Depends: methods
Imports: graph
Suggests: bionetdata
NeedsCompilation: yes
Packaged: 2022-09-16 16:36:46 UTC; valenti
Repository: CRAN
Date/Publication: 2022-09-19 11:06:10 UTC

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New package refdb with initial version 0.1.0
Package: refdb
Title: A DNA Reference Library Manager
Version: 0.1.0
Maintainer: Francois Keck <francois.keck@gmail.com>
Description: Reference database manager offering a set of functions to import, organize, clean, filter, audit and export reference genetic data. Provide functions to download sequence data from Bold Systems (<https://www.boldsystems.org/>) and NCBI GenBank <https://www.ncbi.nlm.nih.gov/genbank/>. Designed as an environment for semi-automatic and assisted construction of reference databases and to improve standardization and repeatability in barcoding and metabarcoding studies.
License: GPL-3
URL: https://fkeck.github.io/refdb/
BugReports: https://github.com/fkeck/refdb/issues
Encoding: UTF-8
Depends: R (>= 3.1.0)
Imports: tibble, readr, dplyr, stringr, tidyr, rentrez, bold, taxize, xml2, bioseq, ape, igraph, ggplot2, ggraph, yaml, rlang, rmarkdown, leaflet
Suggests: testthat (>= 3.0.0), covr, DT, knitr, forcats
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-15 11:16:33 UTC; ecoadmin
Author: Francois Keck [aut, cre, cph]
Repository: CRAN
Date/Publication: 2022-09-19 08:26:12 UTC

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New package RcmdrPlugin.cpd with initial version 0.2.0
Package: RcmdrPlugin.cpd
Title: R Commander Plug-in for Complex Pearson Distributions
Version: 0.2.0
Date: 2022-09-10
Maintainer: Silverio Vilchez-Lopez <svilchez@ujaen.es>
Depends: R (>= 4.2.0), cpd (>= 0.3.0), RcmdrMisc (>= 2.7-2)
Imports: Rcmdr (>= 2.7-0)
Description: Provides an 'Rcmdr' plug-in based on the 'cpd' package.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-09-15 20:55:40 UTC; svilc_000
Author: Silverio Vilchez-Lopez [aut, cre], Maria Jose Olmo-Jimenez [aut]
Repository: CRAN
Encoding: UTF-8
Date/Publication: 2022-09-19 08:46:09 UTC

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New package Qindex with initial version 0.1.0
Package: Qindex
Title: Quantile-Based Predictors for Survival Outcome
Version: 0.1.0
Date: 2022-09-14
Author: Misung Yi [aut, cph], Tingting Zhan [aut, cre, cph] , Inna Chervoneva [aut, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Description: Select optimal quantile-based predictors for survival outcome, to include the means to handle dichotomizing the quantiles, mean-signal-intensity or other continuous markers, and to obtain estimates for dichotomized predictors by Bootstrap-based bias correction.
LazyData: true
LazyDataCompression: xz
Encoding: UTF-8
License: GPL-2
Depends: R (>= 4.2),
Language: en-US
Imports: stats, boot, rpart, survival, matrixStats
Suggests: knitr
NeedsCompilation: no
Packaged: 2022-09-15 15:07:35 UTC; tingtingzhan
Repository: CRAN
Date/Publication: 2022-09-19 08:36:11 UTC

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New package Ease with initial version 0.1.0
Package: Ease
Title: Simulating Explicit Population Genetics Models
Version: 0.1.0
Author: Ehouarn Le Faou <ehouarnlefaou@orange.fr> [aut, cre]
Maintainer: Ehouarn Le Faou <ehouarnlefaou@orange.fr>
Description: Implementation in a simple and efficient way of fully customisable population genetics simulations, considering multiple loci that have epistatic interactions. Specifically suited to the modelling of multilocus nucleocytoplasmic systems (with both diploid and haploid loci), it is nevertheless possible to simulate purely diploid (or purely haploid) genetic models. Examples of models that can be simulated with Ease are numerous, for example models of genetic incompatibilities as presented by Marie-Orleach et al. (2022) <doi:10.1101/2022.07.25.501356>. Many others are conceivable, although few are actually explored, Ease having been developed in particular to provide a solution so that these kinds of models can be simulated simply.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: methods, Rcpp (>= 1.0.7), ggplot2, ggpubr, RcppProgress (>= 0.1), tidyr
LinkingTo: Rcpp, RcppProgress
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-09-15 10:25:26 UTC; ehoua
Repository: CRAN
Date/Publication: 2022-09-19 08:26:19 UTC

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Sun, 18 Sep 2022

New package hockeystick with initial version 0.6.3
Package: hockeystick
Title: Download and Visualize Essential Climate Change Data
Version: 0.6.3
Description: Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, emissions, instrumental and proxy temperature records, sea levels, Arctic/Antarctic sea-ice, Hurricanes, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.html>, Vostok Paleo carbon dioxide and [...truncated...]
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://cortinah.github.io/hockeystick/, https://github.com/cortinah/hockeystick
BugReports: https://github.com/cortinah/hockeystick/issues
Imports: ggplot2, lubridate, tools, readr, dplyr, tidyr, patchwork, scales, rvest, tibble
Depends: R (>= 4.0.0)
Suggests: rmarkdown, knitr, spelling, viridisLite
Language: en-US
NeedsCompilation: no
Packaged: 2022-09-16 13:23:21 UTC; hch
Author: Hernando Cortina [aut, cre]
Maintainer: Hernando Cortina <hch@alum.mit.edu>
Repository: CRAN
Date/Publication: 2022-09-18 21:36:05 UTC

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Fri, 16 Sep 2022

New package crosstalkr with initial version 0.8.0
Package: crosstalkr
Title: Analysis of Graph-Structured Data with a Focus on Protein-Protein Interaction Networks
Version: 0.8.0
Description: Provides a general framework for the identification of nodes that are functionally related to a set of seeds in graph structured data. In addition to being optimized for use with generic graphs, we also provides support to analyze protein-protein interactions networks from online repositories. For more details on core method, refer to Nibbe et al. (2010) <doi:10.1371/journal.pcbi.1000639>.
License: GPL (>= 3)
Imports: rlang, stats, magrittr, withr, readr, dplyr, stringr, tidyr, tibble, igraph (>= 1.2.0), Matrix, ensembldb, foreach, doParallel, ggplot2, EnsDb.Hsapiens.v79, STRINGdb
Encoding: UTF-8
Suggests: tidygraph, ggraph, testthat (>= 2.0.0), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-16 13:25:27 UTC; dtw43
Author: Davis Weaver [aut, cre]
Maintainer: Davis Weaver <davis.weaver@case.edu>
Repository: CRAN
Date/Publication: 2022-09-16 22:36:10 UTC

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New package blscrapeR with initial version 3.2.2
Package: blscrapeR
Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Version: 3.2.2
Description: Scrapes various data from <https://www.bls.gov/>. The U.S. Bureau of Labor Statistics is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Depends: R (>= 3.5.0)
Imports: httr, jsonlite, ggplot2, magrittr, utils, stats, grDevices, dplyr, purrr, tibble, stringr
Suggests: testthat, knitr, rmarkdown
License: MIT + file LICENSE
URL: https://github.com/keberwein/blscrapeR
BugReports: https://github.com/keberwein/blscrapeR/issues
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-15 17:29:13 UTC; anon
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <kris.eberwein@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-16 22:36:13 UTC

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Thu, 15 Sep 2022

New package N2H4 with initial version 0.8.2
Package: N2H4
Title: Handling Methods for Naver News Text Crawling
Version: 0.8.2
Description: Provides some functions to get Korean text sample from news articles in Naver which is popular news portal service <https://news.naver.com/> in Korea.
License: MIT + file LICENSE
URL: https://github.com/forkonlp/N2H4
BugReports: https://github.com/forkonlp/N2H4/issues
Depends: R (>= 3.5.0)
Encoding: UTF-8
Suggests: testthat, devtools, usethis
Imports: rvest, jsonlite, tibble, purrr, httr2, magrittr
NeedsCompilation: no
Packaged: 2022-09-13 20:24:58 UTC; mrchypark
Author: Chanyub Park [aut, cre]
Maintainer: Chanyub Park <mrchypark@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-15 09:20:02 UTC

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New package C19dNUTS with initial version 1.0.0
Package: C19dNUTS
Title: Dataset of Regional COVID-19 Deaths per 100,000 Pop (NUTS)
Version: 1.0.0
Date: 2022-09-14
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.kit@googlemail.com>
Description: Dataset containing COVID-19 deaths (absolute and per 100,000 pop) at the regional level (mostly NUTS 3) for 31 EU/EFTA countries.
Depends: R (>= 3.5.0)
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-09-14 13:48:10 UTC; Thomas Wieland
Repository: CRAN
Date/Publication: 2022-09-15 09:50:02 UTC

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New package alkahest with initial version 1.0.0
Package: alkahest
Title: Pre-Processing XY Data from Experimental Methods
Version: 1.0.0
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Description: A lightweight, dependency-free toolbox for pre-processing XY data from experimental methods (i.e. any signal that can be measured along a continuous variable). This package provides methods for baseline estimation and correction, smoothing, normalization, integration and peaks detection. Baseline correction methods includes polynomial fitting as described in Lieber and Mahadevan-Jansen (2003) <doi:10.1366/000370203322554518>, Rolling Ball algorithm after Kneen and Annegarn (1996) <doi:10.1016/0168-583X(95)00908-6>, SNIP algorithm after Ryan et al. (1988) <doi:10.1016/0168-583X(88)90063-8>, 4S Peak Filling after Liland (2015) <doi:10.1016/j.mex.2015.02.009> and more.
License: GPL (>= 3)
URL: https://packages.tesselle.org/alkahest/, https://github.com/tesselle/alkahest
BugReports: https://github.com/tesselle/alkahest/issues
Depends: R (>= 3.3)
Encoding: UTF-8
Imports: grDevices, methods, stats, utils
Suggests: knitr, Matrix, rmarkdown, testthat (>= 3.0.0)
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-15 09:25:48 UTC; nicolas
Author: Nicolas Frerebeau [aut, cre] , Brice Lebrun [ctb]
Repository: CRAN
Date/Publication: 2022-09-15 10:00:02 UTC

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New package TPCselect with initial version 0.8.1
Package: TPCselect
Title: Variable Selection via Threshold Partial Correlation
Version: 0.8.1
Description: A threshold partial correlation approach to selecting important variables in linear models of L. and others (2017) at <doi:10.5705/ss.202015.0473>, and in partial linear models of L. and others (2018) at <doi:10.1016/j.jmva.2018.06.005>. This package also extends the PC-simple algorithm of B. and others (2010) at <doi:10.1093/biomet/asq008> to partial linear models.
License: GPL-3
Encoding: UTF-8
Imports: stats,corpcor,psych,MASS,KernSmooth
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-09-15 02:19:16 UTC; cynyu
Author: Cynthia Shao [aut, trl, cre], Runze Li [aut]
Maintainer: Cynthia Shao <cynyu.shao@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-15 08:00:12 UTC

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New package tidyrgee with initial version 0.1.0
Package: tidyrgee
Title: 'tidyverse' Methods for 'Earth Engine'
Version: 0.1.0
Description: Provides 'tidyverse' methods for wrangling and analyzing 'Earth Engine' <https://earthengine.google.com/> data. These methods help the user with filtering, joining and summarising 'Earth Engine' image collections.
License: MIT + file LICENSE
URL: https://github.com/r-tidy-remote-sensing/tidyrgee
BugReports: https://github.com/r-tidy-remote-sensing/tidyrgee/issues/
Depends: R (>= 4.1)
Imports: assertthat, crayon, dplyr, glue, lubridate, purrr, readr, reticulate (>= 1.24), rgee, rlang, sf, stringr, tidyr
Suggests: knitr, rmarkdown, tibble, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-15 05:31:35 UTC; zack.arno
Author: Zack Arno [aut, cre, cph], Josh Erickson [aut, cph]
Maintainer: Zack Arno <zackarno@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-15 08:00:02 UTC

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New package Karen with initial version 1.0
Package: Karen
Title: Kalman Reaction Networks
Version: 1.0
Description: This is a stochastic framework that combines biochemical reaction networks with extended Kalman filter and Rauch-Tung-Striebel smoothing. This framework allows to investigate the dynamics of cell differentiation from high-dimensional clonal tracking data subject to measurement noise, false negative errors, and systematically unobserved cell types. Our tool can provide statistical support to biologists in gene therapy clonal tracking studies for a deeper understanding of clonal reconstitution dynamics. Further details on the methods can be found in L. Del Core et al., (2022) <doi:10.1101/2022.07.08.499353>.
License: GPL-3
Encoding: UTF-8
Imports: Matrix, parallel, gaussquad, splines, scales, mvtnorm, tmvtnorm, MASS, igraph, xtable, stringr, abind, expm, methods
Depends: R (>= 2.10)
LazyData: true
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2022-09-14 16:28:19 UTC; delcore.luca
Author: Luca Del Core [aut, cre, cph] , Danilo Pellin [aut] , Marco Grzegorczyk [aut, ths] , Ernst Wit [aut, ths]
Maintainer: Luca Del Core <l.del.core@rug.nl>
Repository: CRAN
Date/Publication: 2022-09-15 07:40:02 UTC

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New package VedicDateTime with initial version 0.1.1
Package: VedicDateTime
Title: Vedic Calendar System
Version: 0.1.1
Description: Provides platform for Vedic calendar system having several functionalities to facilitate conversion between Gregorian and Vedic calendar systems, and helpful in examining its impact in the time series analysis domain. The background is described in Neeraj Dhanraj Bokde et al. (2021) <doi:10.48550/arXiv.2111.03441>, Karanam L. Ramakumar et al. (2011) <https:archive.org/details/PanchangamCalculations>, K. S. Charak et al. (2012, ISBN:8190100807), Satish BD et al. (2013) <https:github.com/webresh/drik-panchanga>.
URL: https://www.neerajbokde.in/viggnette/2022-09-05-VedicDateTime
BugReports: https://github.com/prajwalkpatil/VedicDateTime/issues
License: GPL (>= 2)
Encoding: UTF-8
Depends: R (>= 3.1.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), qpdf, formatR, spelling, tinytex
VignetteBuilder: knitr
Imports: swephR
Language: en-US
NeedsCompilation: no
Packaged: 2022-09-14 09:26:56 UTC; saradindu
Author: Neeraj Dhanraj Bokde [aut, cre, cph], Prajwal Kailasnath Patil [aut], Saradindu Sengupta [aut], Andres Elias Feijoo Lorenzo [aut]
Maintainer: Neeraj Dhanraj Bokde <neerajdhanraj@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-15 06:30:05 UTC

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New package numbat with initial version 1.0.2
Package: numbat
Title: Haplotype-Aware CNV Analysis from scRNA-Seq
URL: https://github.com/kharchenkolab/numbat
Version: 1.0.2
Description: A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. (2022) <doi:10.1101/2022.02.07.479314>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0), Matrix
Imports: ape, argparse, caTools, data.table, dendextend, dplyr, GenomicRanges, ggplot2, ggraph, ggtree, glue, igraph, IRanges, logger, magrittr, methods, parallel, parallelDist, patchwork, pryr, purrr, Rcpp, RcppParallel, RhpcBLASctl, R.utils, reshape2, scales, stats4, stringr, tibble, tidygraph, tidyr, tidyverse, vcfR, zoo
Suggests: ggrastr, ggrepel, knitr, matrixStats, testthat (>= 3.0.0),
LinkingTo: Rcpp, RcppArmadillo, RcppParallel, roptim
NeedsCompilation: yes
SystemRequirements: C++11, GNU make
Author: Teng Gao [cre, aut], Hirak Sarkar [aut], Evan Biederstedt [aut], Peter Kharchenko [aut]
Maintainer: Teng Gao <tgao@g.harvard.edu>
Packaged: 2022-09-13 15:41:29 UTC; tenggao
Repository: CRAN
Date/Publication: 2022-09-15 06:10:02 UTC

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New package litterfitter with initial version 0.1.2
Package: litterfitter
Title: Fit a Collection of Curves to Single Cohort Decomposition Data
Version: 0.1.2
Date: 2022-09-05
Description: There is a long tradition of studying the flux of carbon from the biosphere to the atmosphere by following a particular cohort of litter (wood, leaves, roots, or other organic material) through time. The resulting data are mass remaining and time. A variety of functional forms may be used to fit the resulting data. Some work better empirically. Some are better connected to a process-based understanding. Some have a small number of free parameters; others have more. This package matches decomposition data to a family of these curves using likelihood--based fitting. This package is based on published research by Cornwell & Weedon (2013) <doi:10.1111/2041-210X.12138>.
Depends: R (>= 3.1.0)
LazyData: true
Encoding: UTF-8
Imports: plyr, stats, graphics, grDevices, methods
Suggests: testthat, knitr, roxygen2, devtools, rmarkdown
License: MIT + file LICENSE
URL: https://github.com/cornwell-lab-unsw/litterfitter, http://cornwell-lab-unsw.github.io/litterfitter/
VignetteBuilder: knitr
BugReports: https://github.com/cornwell-lab-unsw/litterfitter/issues
NeedsCompilation: no
Packaged: 2022-09-14 09:54:26 UTC; z3484779
Author: Will Cornwell [aut, cre] , James Weedon [aut], Guofang Liu [ctb]
Maintainer: Will Cornwell <wcornwell@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-15 06:30:02 UTC

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New package bundle with initial version 0.1.0
Package: bundle
Title: Serialize Model Objects with a Consistent Interface
Version: 0.1.0
Description: Typically, models in 'R' exist in memory and can be saved via regular 'R' serialization. However, some models store information in locations that cannot be saved using 'R' serialization alone. The goal of 'bundle' is to provide a common interface to capture this information, situate it within a portable object, and restore it for use in new settings.
License: MIT + file LICENSE
URL: https://github.com/rstudio/bundle, https://rstudio.github.io/bundle/
BugReports: https://github.com/rstudio/bundle/issues
Imports: glue, purrr, rlang, utils, withr
Suggests: bonsai, butcher, callr, caret, covr, embed, h2o, keras, kernlab, knitr, luz, MASS, modeldata, parsnip, recipes, renv, rmarkdown, stacks, testthat (>= 3.0.0), tensorflow, torch, torchvision, uwot, vetiver, workflows, xgboost
VignetteBuilder: knitr
Config/Needs/website: tidyverse/tidytemplate
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-14 16:12:59 UTC; juliasilge
Author: Julia Silge [aut, cre] , Simon Couch [aut], Qiushi Yan [aut], Max Kuhn [aut], RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>
Repository: CRAN
Date/Publication: 2022-09-15 06:40:02 UTC

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Wed, 14 Sep 2022

New package sleeperapi with initial version 1.0.4
Package: sleeperapi
Title: Wrapper Functions Around 'Sleeper' (Fantasy Sports) API
Version: 1.0.4
Description: For those wishing to interact with the 'Sleeper' (Fantasy Sports) API (<https://api.sleeper.app/>) without looking too much into its documentation (found at <https://docs.sleeper.app/>), this package offers wrapper functions around the available API calls to make it easier.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: httr, jsonlite, plyr
Suggests: testthat (>= 2.0.0)
NeedsCompilation: no
Packaged: 2022-09-14 02:30:11 UTC; nickbultman
Author: Nick Bultman [aut, cre, cph]
Maintainer: Nick Bultman <njbultman74@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-14 06:50:02 UTC

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New package rrnni with initial version 0.1.0
Package: rrnni
Title: Manipulate with RNNI Tree Space
Version: 0.1.0
Date: 2022-08-31
Description: Calculate RNNI distance between and manipulate with ranked trees. RNNI stands for Ranked Nearest Neighbour Interchange and is an extension of the classical NNI space (space of trees created by the NNI moves) to ranked trees, where internal nodes are ordered according to their heights (usually assumed to be times). The RNNI distance takes the tree topology into account, as standard NNI does, but also penalizes changes in the order of internal nodes, i.e. changes in the order of times of evolutionary events. For more information about the RNNI space see: Gavryushkin et al. (2018) <doi:10.1007/s00285-017-1167-9>, Collienne & Gavryushkin (2021) <doi:10.1007/s00285-021-01567-5>, Collienne et al. (2021) <doi:10.1007/s00285-021-01685-0>, and Collienne (2021) <http://hdl.handle.net/10523/12606>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: methods, ape
Suggests: testthat (>= 3.0.0)
URL: https://biods.github.io/rrnni/, https://github.com/biods/rrnni
BugReports: https://github.com/biods/rrnni/issues
NeedsCompilation: yes
Packaged: 2022-09-13 22:25:37 UTC; jmoravec
Author: Jiri C. Moravec [aut, cre], Lena Collienne [aut]
Maintainer: Jiri C. Moravec <jiri.c.moravec@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-14 06:50:05 UTC

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New package receptiviti with initial version 0.1.0
Package: receptiviti
Title: Text Analysis Through the 'Receptiviti' API
Version: 0.1.0
Date: 2022-09-08
Description: Send text to the <https://www.receptiviti.com> API to be scored by all available frameworks.
License: MIT + file LICENSE
Imports: curl, jsonlite, digest, arrow, dplyr, future.apply, progressr
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
URL: https://receptiviti.github.io/receptiviti-r/, https://github.com/Receptiviti/receptiviti-r
BugReports: https://github.com/Receptiviti/receptiviti-r/issues
NeedsCompilation: no
Packaged: 2022-09-14 00:06:58 UTC; Admin
Author: Receptiviti Inc. [fnd, cph], Kent English [cre], Micah Iserman [aut, ctr]
Maintainer: Kent English <kenglish@receptiviti.com>
Repository: CRAN
Date/Publication: 2022-09-14 06:50:08 UTC

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New package PerfMeas with initial version 1.2.5
Package: PerfMeas
Title: Performance Measures for Ranking and Classification Tasks
Version: 1.2.5
Date: 2022-09-09
Author: Giorgio Valentini [aut, cre]
Maintainer: Giorgio Valentini <valentini@di.unimi.it>
Description: Implementation of different performance measures for classification and ranking tasks including Area Under the Receiving Characteristic Curve (AUROC) and Area Under the Precision Recall Curve (AUPRC), precision at a given recall, F-score for single and multiple classes.
License: GPL (>= 2)
LazyLoad: yes
Depends: limma, graph, RBGL
NeedsCompilation: yes
Packaged: 2022-09-13 17:41:31 UTC; valenti
Repository: CRAN
Date/Publication: 2022-09-14 06:10:02 UTC

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New package ingres with initial version 1.0.0
Package: ingres
Title: Infer Gene Probabilistic Boolean Networks from Single-Cell Data
Version: 1.0.0
Description: Given a gene regulatory boolean network and a RNA-seq dataset, this package computes protein activity normalised enrichment scores using 'VIPER', and then produces a probabilistic network using the scores as probabilities for fixed node activation or deactivation, in addition to the original Boolean functions. For more information, refer to the preprint: Victori and Buffa (2022) <doi:10.1101/2022.09.04.506528>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Imports: methods, viper, tidygraph, AnnotationDbi, org.Hs.eg.db, dplyr, tidyr, tidyselect, scales, ggplot2, ggraph, stringr, ggpubr, tibble, magrittr, igraph, purrr, readr, usethis, rlang, Seurat
Suggests: testthat (>= 3.0.0), shiny, plotly (>= 4.10.0), aracne.networks, BoolNet, covr, withr, knitr, rmarkdown
URL: https://github.com/CBigOxf/ingres, https://cbigoxf.github.io/ingres/
BugReports: https://github.com/CBigOxf/ingres/issues
VignetteBuilder: knitr
Language: en-GB
NeedsCompilation: no
Packaged: 2022-09-13 19:46:16 UTC; pedro
Author: Pedro Victori [aut, cre] , Francesca M. Buffa [aut]
Maintainer: Pedro Victori <pedroluisvictori@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-14 06:30:02 UTC

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New package vglmer with initial version 1.0.0
Package: vglmer
Title: Variational Inference for Hierarchical Generalized Linear Models
Version: 1.0.0
Encoding: UTF-8
License: GPL (>= 2)
Description: Estimates hierarchical models using mean-field variational Bayes. At present, it can estimate logistic, linear, and negative binomial models. It can accommodate models with an arbitrary number of random effects and requires no integration to estimate. It also provides the ability to improve the quality of the approximation using marginal augmentation. Goplerud (2022) <doi:10.1214/21-BA1266> provides details on the variational algorithms.
Imports: Rcpp (>= 1.0.1), lme4, CholWishart, mvtnorm, Matrix, stats, graphics, methods, lmtest, splines, mgcv
Depends: R (>= 3.0.2)
Suggests: SuperLearner, MASS, tictoc, testthat
LinkingTo: Rcpp, RcppEigen (>= 0.3.3.4.0)
NeedsCompilation: yes
Packaged: 2022-09-13 13:42:24 UTC; MHG23
Author: Max Goplerud [aut, cre]
Maintainer: Max Goplerud <mgoplerud@pitt.edu>
Repository: CRAN
Date/Publication: 2022-09-14 06:00:02 UTC

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New package Rduinoiot with initial version 0.1.0
Package: Rduinoiot
Title: 'Arduino Iot Cloud API' R Client
Version: 0.1.0
Maintainer: Flavio Leccese <flavioleccese92@gmail.com>
Description: Easily interact with the 'Arduino Iot Cloud API' <https://www.arduino.cc/reference/en/iot/api/>, managing devices, things, properties and data.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://flavioleccese92.github.io/Rduinoiot/
BugReports: https://github.com/FlavioLeccese92/Rduinoiot/issues/
Language: en-US
Imports: httr, jsonlite, tibble, cli, purrr, methods
Suggests: knitr, rmarkdown, dplyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-13 14:38:14 UTC; fleccese
Author: Flavio Leccese [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-14 06:00:11 UTC

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New package lmap with initial version 0.1.1
Package: lmap
Title: Logistic Mapping
Version: 0.1.1
Date: 2022-09-09
Maintainer: Mark de Rooij <rooijm@fsw.leidenuniv.nl>
Description: Set of tools for mapping of categorical response variables based on principal component analysis (pca) and multidimensional unfolding (mdu).
Depends: R (>= 3.5.0), ggplot2, ggrepel, ggforce, tidyverse, dplyr
Imports: nnet, stats
License: GPL-3
Encoding: UTF-8
LazyData: TRUE
Author: Mark de Rooij [aut, cre, cph], Frank Busing [aut], Juan Claramunt Gonzalez [ctb]
NeedsCompilation: yes
Packaged: 2022-09-09 11:55:36 UTC; prueba
Repository: CRAN
Date/Publication: 2022-09-14 05:30:02 UTC

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New package kimfilter with initial version 1.0.0
Package: kimfilter
Title: Kim Filter
Version: 1.0.0
Date: 2022-09-01
Description: 'Rcpp' implementation of the multivariate Kim filter, which combines the Kalman and Hamilton filters for state probability inference. The filter is designed for state space models and can handle missing values and exogenous data in the observation and state equations. Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.9)
LinkingTo: Rcpp, RcppArmadillo
Suggests: data.table (>= 1.14.2), maxLik (>= 1.5-2), ggplot2 (>= 3.3.6), gridExtra (>= 2.3), knitr, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-09-13 16:15:54 UTC; alex.hubbard
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-09-14 06:00:05 UTC

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New package epimdr2 with initial version 1.0-7
Package: epimdr2
Title: Functions and Data for "Epidemics: Models and Data in R (2nd Edition)"
Version: 1.0-7
Date: 2022-09-10
Author: Ottar N. Bjornstad [aut, cre]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>
Description: Functions, data sets and shiny apps for "Epidemics: Models and Data in R (2nd edition)" by Ottar N. Bjornstad (2022, ISBN: 978-3-031-12055-8) <https://link.springer.com/book/10.1007/978-3-319-97487-3>. The package contains functions to study the Susceptible-Exposed-Infected-Removed SEIR model, spatial and age-structured Susceptible-Infected-Removed SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the 'Coursera' Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Depends: R (>= 4.0.0), shiny, deSolve, plotly
Imports: polspline, phaseR, ggplot2
Suggests: ade4, bbmle, fields, forecast, imputeTS, lme4, ncf, nleqslv, nlme, nlts, plotrix, pomp, rootSolve, Rwave, rworldmap, statnet, scatterplot3d
License: GPL-3
URL: <https://github.com/objornstad/epimdr2>, <https://link.springer.com/book/10.1007/978-3-319-97487-3>, <https://ento.psu.edu/directory/onb1>
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-13 13:04:27 UTC; onb1
Repository: CRAN
Date/Publication: 2022-09-14 06:00:08 UTC

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New package elections.dtree with initial version 1.0.0
Package: elections.dtree
Title: Ranked Voting Election Audits with Dirichlet-Trees
Description: Perform ballot-polling Bayesian audits for ranked voting elections using Dirichlet-tree prior distributions. Everest et al. (2022) <arXiv:2206.14605>, <arXiv:2209.03881>.
Version: 1.0.0
Depends: R (>= 4.0.0)
SystemRequirements: C++17
License: GPL-3
LinkingTo: Rcpp, RcppThread, testthat
Imports: Rcpp, methods, Rdpack, R6, parallel
Suggests: covr, testthat (>= 3.0.0), xml2
Encoding: UTF-8
URL: https://fleverest.github.io/elections.dtree/, https://github.com/fleverest/elections.dtree/
BugReports: https://github.com/fleverest/elections.dtree/issues/
NeedsCompilation: yes
Packaged: 2022-09-13 12:00:01 UTC; floyd
Author: Floyd Everest [aut, cre, cph] , Damjan Vukcevic [aut]
Maintainer: Floyd Everest <me@floydeverest.com>
Repository: CRAN
Date/Publication: 2022-09-14 05:30:05 UTC

More information about elections.dtree at CRAN
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New package cropcircles with initial version 0.1.0
Package: cropcircles
Title: Crops an Image to a Circle
Version: 0.1.0
URL: https://github.com/doehm/cropcircles
BugReports: https://github.com/doehm/cropcircles/issues
Description: Images are cropped to a circle with a transparent background. The function takes a vector of images, either local or from a link, and circle crops the image. Paths to the cropped image are returned for plotting with 'ggplot2'.
Depends: R (>= 3.5.0)
Imports: glue, magick, purrr
License: CC0
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-13 12:48:22 UTC; Dan
Author: Daniel Oehm [aut, cre]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-14 05:30:10 UTC

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Tue, 13 Sep 2022

New package SpectralClMixed with initial version 1.0
Package: SpectralClMixed
Title: Spectral Clustering for Mixed Type Data
Version: 1.0
Maintainer: Cristina Tortora <grikris1@gmail.com>
Description: Performs cluster analysis of mixed-type data using Spectral Clustering, see F. Mbuga and, C. Tortora (2022) <doi:10.3390/stats5010001>.
License: GPL (>= 2)
Depends: R (>= 3.5)
Imports: RSpectra, cluster, ggplot2, GGally
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-13 10:30:03 UTC; cristina
Author: Cristina Tortora [aut, cre, cph] , Felix Mbuga [aut], Zander Bonnet [aut]
Repository: CRAN
Date/Publication: 2022-09-13 12:10:02 UTC

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New package GRIDCOPULA with initial version 1.0.0
Package: GRIDCOPULA
Title: Bivariate Copula Functions Based on Regular Grid
Description: Estimates grid type bivariate copula functions, calculates some association measures and provides several copula graphics.
Version: 1.0.0
License: GPL-3
Encoding: UTF-8
Packaged: 2022-09-12 20:27:58 UTC; Abraham
Imports: Rsolnp, fields, limSolve, ggplot2, pracma, reshape2
NeedsCompilation: no
Author: Rogelio Salinas Gutierrez Developer [aut, cre, cph], Angelica Hernandez Quintero Dev [aut], Pedro Abraham Montoya Calzada Dev [cph]
Maintainer: Rogelio Salinas Gutierrez Developer <rsalinas@correo.uaa.mx>
Repository: CRAN
Date/Publication: 2022-09-13 11:40:02 UTC

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New package CpmERCCutoff with initial version 1.0.0
Package: CpmERCCutoff
Title: Calculation of Log2 Counts per Million Cutoff from ERCC Controls
Version: 1.0.0
Description: Implementation of the empirical method to derive log2 counts per million (CPM) cutoff to filter out lowly expressed genes using ERCC spike-ins as described in Goll and Bosinger et.al (2022)<doi:10.1101/2022.06.23.497396>. This package utilizes the synthetic mRNA control pairs developed by the External RNA Controls Consortium (ERCC) (ERCC 1 / ERCC 2) that are spiked into sample pairs at known ratios at various absolute abundances. The relationship between the observed and expected fold changes is then used to empirically determine an optimal log2 CPM cutoff for filtering out lowly expressed genes.
Depends: R (>= 3.6)
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: stats, graphics
Suggests: spelling, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-09-12 18:36:42 UTC; ksteenbergen
Language: en-US
Author: Tyler Grimes [aut] , Travis L. Jensen [aut] , Kristen Steenbergen [ctb, cre], The Emmes Company LLC [cph] 2022)), Johannes B. Goll [aut]
Maintainer: Kristen Steenbergen <ksteenbergen@emmes.com>
Repository: CRAN
Date/Publication: 2022-09-13 11:20:07 UTC

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New package argosfilter with initial version 0.70
Package: argosfilter
Version: 0.70
Date: 2022-09-12
Title: Argos Locations Filter
Author: Carla Freitas [aut, cre]
Maintainer: Carla Freitas <carla.freitas.brandt@hi.no>
Description: Filters animal satellite tracking data obtained from the Argos system(<https://www.argos-system.org/>), following the algorithm described in Freitas et al (2008) <doi:10.1111/j.1748-7692.2007.00180.x>. It is especially indicated for telemetry studies of marine animals, where Argos locations are predominantly of low-quality.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-09-12 14:26:08 UTC; a22070
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-09-13 11:10:05 UTC

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New package AGread with initial version 1.3.2
Package: AGread
Title: Read Data Files from ActiGraph Monitors
Version: 1.3.2
Description: Standardize the process of bringing various modes of output files into 'R'. Additionally, processes are provided to read and minimally pre- process raw data from primary accelerometer and inertial measurement unit files, as well as binary .gt3x files. ActiGraph monitors are used to estimate physical activity outcomes via body-worn sensors that measure (e.g.) acceleration or rotational velocity.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Imports: anytime (>= 0.3.0), data.table (>= 1.10.4), DescTools (>= 0.99.20), dplyr (>= 0.5.0), lubridate (>= 1.7.4), magrittr (>= 2.0.2), PAutilities (>= 1.1.0), Rcpp (>= 1.0.1), reshape2 (>= 1.4.3), rlang (>= 0.2.0), R.utils, read.gt3x, stats, stringr (>= 1.3.0), tools, utils, readr, RSQLite, DBI
Encoding: UTF-8
LazyData: true
URL: https://github.com/paulhibbing/AGread
BugReports: https://github.com/paulhibbing/AGread/issues
Suggests: GGIR (>= 1.5.0), seewave (>= 2.0.5), testthat (>= 3.0.0)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2022-09-13 03:15:57 UTC; prhibbing
Author: Paul R. Hibbing [aut, cre], Vincent T. van Hees [ctb], Samuel R. LaMunion [ctb], John Muschelli [ctb], Daniel Judge [ctb], Judge Maygarden [ctb], ActiGraph LLC [cph]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-13 11:50:02 UTC

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New package yahoofinancer with initial version 0.1.0
Package: yahoofinancer
Title: Fetch Data from Yahoo Finance API
Version: 0.1.0
Description: Obtain historical and near real time data related to stocks, index and currencies from the Yahoo Finance API. This package is community maintained and is not officially supported by 'Yahoo'. The accuracy of data is only as correct as provided on <https://finance.yahoo.com/>.
Depends: R(>= 3.4)
Imports: httr, jsonlite, lubridate, magrittr, purrr, R6, stringr
Suggests: covr, dplyr, httptest, testthat (>= 3.0.0)
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://yahoofinancer.rsquaredacademy.com/, https://github.com/rsquaredacademy/yahoofinancer
BugReports: https://github.com/rsquaredacademy/yahoofinancer/issues
NeedsCompilation: no
Packaged: 2022-09-12 06:43:57 UTC; HP
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-13 10:10:02 UTC

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New package stockAnalyst with initial version 1.0.1
Package: stockAnalyst
Title: Equity Valuation using Methods of Fundamental Analysis
Version: 1.0.1
Author: MaheshP Kumar [aut, cre]
Maintainer: MaheshP Kumar <maheshparamjitkumar@gmail.com>
Imports: stats
Description: Methods of Fundamental Analysis for Valuation of Equity included here serve as a quick reference for undergraduate courses on Stock Valuation and Chartered Financial Analyst Levels 1 and 2 Readings on Equity Valuation. Jerald E. Pinto (“Equity Asset Valuation (4th Edition)”, 2020, ISBN: 9781119628194). Chartered Financial Analyst Institute ("Chartered Financial Analyst Program Curriculum 2020 Level I Volumes 1-6. (Vol. 4, pp. 445-491)", 2019, ISBN: 9781119593577). Chartered Financial Analyst Institute ("Chartered Financial Analyst Program Curriculum 2020 Level II Volumes 1-6. (Vol. 4, pp. 197-447)", 2019, ISBN: 9781119593614).
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-12 22:29:46 UTC; mahes
Repository: CRAN
Date/Publication: 2022-09-13 10:20:02 UTC

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New package semmcci with initial version 1.0.1
Package: semmcci
Title: Monte Carlo Confidence Intervals in Structural Equation Modeling
Version: 1.0.1
Description: Monte Carlo confidence intervals for free and defined parameters in models fitted in the structural equation modeling package 'lavaan' can be generated using the 'semmcci' package. 'semmcci' has two main functions, namely, MC() and MCStd(). The output of 'lavaan' is passed as the first argument to the MC() function to generate Monte Carlo confidence intervals. Monte Carlo confidence intervals for the standardized estimates can also be generated by passing the output of the MC() function to the MCStd() function. Preacher and Selig (2012) <doi:10.1080/19312458.2012.679848>.
URL: https://github.com/jeksterslab/semmcci
BugReports: https://github.com/jeksterslab/semmcci/issues
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.0.0), stats, MASS, lavaan, methods
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2022-09-12 14:01:58 UTC; r1091537
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph] , Shu Fai Cheung [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-13 10:30:02 UTC

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New package openairmaps with initial version 0.4.3
Package: openairmaps
Title: Create Interactive Web Maps of Air Pollution Data
Version: 0.4.3
Description: Combine the air quality data analysis methods of 'openair' with the JavaScript 'Leaflet' (<https://leafletjs.com/>) library. Functionality includes plotting site maps, "directional analysis" figures such as polar plots, and air mass trajectories.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.2.0)
Imports: openair, dplyr, leaflet, purrr, magrittr, rlang, lubridate, tibble, stringr, forcats
Suggests: worldmet
Language: en-GB
NeedsCompilation: no
Packaged: 2022-09-12 10:08:19 UTC; Jack
Author: Jack Davison [cre, aut], David Carslaw [aut]
Maintainer: Jack Davison <davison.jack.jd@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-13 10:10:05 UTC

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New package kgp with initial version 1.0.0
Package: kgp
Title: 1000 Genomes Project Metadata
Version: 1.0.0
Description: Metadata about populations and data about samples from the 1000 Genomes Project, including the 2,504 samples sequenced for the Phase 3 release and the expanded collection of 3,202 samples with 602 additional trios. The data is described in Auton et al. (2015) <doi:10.1038/nature15393> and Byrska-Bishop et al. (2022) <doi:10.1016/j.cell.2022.08.004>, and raw data is available at <http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/>.
URL: https://github.com/stephenturner/kgp, https://stephenturner.github.io/kgp/
License: Apache License (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Suggests: tibble
NeedsCompilation: no
Packaged: 2022-09-12 10:38:53 UTC; turner
Author: Stephen Turner [aut, cre]
Maintainer: Stephen Turner <vustephen@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-13 10:10:08 UTC

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New package implicitExpansion with initial version 0.0.1
Package: implicitExpansion
Version: 0.0.1
Title: Array Operations for Arrays of Mismatching Sizes
Description: Support for implicit expansion of arrays in operations involving arrays of mismatching sizes. This pattern is known as "broadcasting" in 'Python' and "implicit expansion" in 'Matlab' and is explained for example in the article "Array programming with NumPy" by C. R. Harris et al. (2020) <doi:10.1038/s41586-020-2649-2>.
License: MIT + file LICENSE
URL: https://github.com/ManuelHentschel/implicitExpansion
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-12 11:09:58 UTC; Manuel
Author: Manuel Hentschel [aut, cre]
Maintainer: Manuel Hentschel <Manuel.Hentschel@unige.ch>
Repository: CRAN
Date/Publication: 2022-09-13 10:10:11 UTC

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New package historicalborrowlong with initial version 0.0.5
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: 0.0.5
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, 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, StanHeaders
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2022-09-12 16:08:28 UTC; c240390
Author: William Michael Landau [aut, cre] , Albert Man [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-13 10:20:06 UTC

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New package historicalborrow with initial version 1.0.4
Package: historicalborrow
Title: Non-Longitudinal Bayesian Historical Borrowing Models
Description: Historical borrowing in clinical trials can improve precision and operating characteristics. This package supports a hierarchical model and a mixture 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 benchmark models (independent and pooled). Some of the methods are discussed by Viele et al. (2013) <doi:10.1002/pst.1589>.
Version: 1.0.4
License: MIT + file LICENSE
URL: https://wlandau.github.io/historicalborrow/, https://github.com/wlandau/historicalborrow
BugReports: https://github.com/wlandau/historicalborrow/issues
Depends: R (>= 3.5.0)
Imports: dplyr, ggplot2, Matrix, posterior, rjags, rlang, stats, tibble, tidyr, tidyselect, utils
Suggests: knitr, markdown, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-12 12:46:56 UTC; c240390
Author: William Michael Landau [aut, cre] , Albert Man [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-13 10:20:10 UTC

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New package BFF with initial version 1.0.0
Package: BFF
Title: Bayes Factor Functions
Version: 1.0.0
Author: Rachael Shudde [aut, cre], Sandy Pramanik [aut], Valen E. Johnson [aut]
Maintainer: Rachael Shudde <rachael.shudde@gmail.com>
Description: Bayes factors represent the ratio of probabilities assigned to data by competing scientific hypotheses. Drawbacks of Bayes factors are their dependence on prior specifications that define null and alternative hypotheses and difficulties encountered in their computation. To address these problems we define Bayes factor functions (BFF) directly from common test statistics. BFFs depend on a single non-centrality parameter that can be expressed as a function of standardized effect sizes, and plots of BFFs versus effect size provide informative summaries of hypothesis tests that can be easily aggregated across studies. Such summaries eliminate the need for arbitrary bright-line thresholds to determine “statistical significance.” BFFs are available in closed form and can be computed easily from z, t, chi^2, and F statistics.
License: GPL (>= 2)
Encoding: UTF-8
Imports: BSDA, grDevices, graphics
Suggests: testthat (>= 2.1.0), knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-09-12 11:59:26 UTC; rachaelshudde
Repository: CRAN
Date/Publication: 2022-09-13 10:30:05 UTC

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New package besthr with initial version 0.3.0
Package: besthr
Title: Generating Bootstrap Estimation Distributions of HR Data
Version: 0.3.0
Description: Creates plots showing scored HR experiments and plots of distribution of means of ranks of HR score from bootstrapping. Authors (2019) <doi:10.5281/zenodo.3374507>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, ggplot2, ggridges, magrittr, patchwork, rlang, stringr, tibble
Suggests: knitr, rmarkdown, readr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-12 10:37:30 UTC; macleand
Author: Dan MacLean [aut, cre]
Maintainer: Dan MacLean <dan.maclean@tsl.ac.uk>
Repository: CRAN
Date/Publication: 2022-09-13 10:10:14 UTC

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New package admiralonco with initial version 0.1.0
Package: admiralonco
Title: Oncology Extension Package for ADaM in 'R' Asset Library
Version: 0.1.0
Description: Programming oncology specific Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>). The package is an extension package of the 'admiral' package.
Language: en-US
License: Apache License (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5)
Imports: admiral (>= 0.8.0), admiraldev, dplyr (>= 0.8.4), lubridate (>= 1.7.4), magrittr (>= 1.5), rlang (>= 0.4.4), tidyselect (>= 1.0.0)
Suggests: admiral.test, devtools, diffdf, lifecycle, lintr, pkgdown, testthat (>= 3.0.0), knitr, methods, miniUI, rmarkdown, roxygen2, spelling, stringr, styler, tibble, usethis, covr, DT
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-12 09:10:07 UTC; bundfuss
Author: Stefan Bundfuss [aut, cre], Ross Farrugia [aut], Amit Jain [aut], Andrew Smith [aut], Teckla Akinyi [aut], Samia Kabi [aut], Stephen Gormley [aut], Hinal Patel [aut], Karl Kennedy [ctb], Matt Marino [ctb], Gopi Vegesna [ctb], Thomas Neitmann [ctb], A [...truncated...]
Maintainer: Stefan Bundfuss <stefan.bundfuss@roche.com>
Repository: CRAN
Date/Publication: 2022-09-13 10:10:16 UTC

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New package TDboost with initial version 1.4
Package: TDboost
Title: A Boosted Tweedie Compound Poisson Model
Version: 1.4
Date: 2022-09-12
Depends: R (>= 2.12.0), lattice
Description: An implementation of a boosted Tweedie compound Poisson model proposed by Yang, Y., Qian, W. and Zou, H. (2018) <doi:10.1080/07350015.2016.1200981>. It is capable of fitting a flexible nonlinear Tweedie compound Poisson model (or a gamma model) and capturing high-order interactions among predictors. This package is based on the 'gbm' package originally developed by Greg Ridgeway.
LazyData: yes
License: GPL-3
Packaged: 2022-09-12 04:14:15 UTC; jiaozi
NeedsCompilation: yes
Date/Publication: 2022-09-13 10:00:05 UTC
Author: Yi Yang [aut, cre] , Hui Zou [aut] , Wei Qian [aut] , Greg Ridgeway [ctb, cph]
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Repository: CRAN

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New package degday with initial version 0.4.0
Package: degday
Title: Compute Degree Days
Version: 0.4.0
Date: 2022-09-09
Description: Compute degree days from daily min and max temperatures for modeling plant and insect development.
License: GPL (>= 3)
URL: https://github.com/ucanr-igis/degday/
BugReports: https://github.com/ucanr-igis/degday/issues/
Depends: R (>= 3.5)
Imports: crayon, magrittr, methods, zoo
Suggests: cimir, dplyr, knitr, testthat (>= 3.0.0), tidyr, units
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2022-09-12 00:28:50 UTC; Andy
Author: Andy Lyons [aut, cre] , Regents of the University of California [cph]
Maintainer: Andy Lyons <andlyons@ucanr.edu>
Repository: CRAN
Date/Publication: 2022-09-13 10:00:02 UTC

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New package nlive with initial version 0.1.0
Package: nlive
Title: Automated Estimation of Sigmoidal and Piecewise Linear Mixed Models
Version: 0.1.0
Date: 2022-09-12
Maintainer: Maude Wagner <maude_wagner@rush.edu>
Description: Estimation of relatively complex nonlinear mixed-effects models, including the Sigmoidal Mixed Model and the Piecewise Linear Mixed Model with abrupt or smooth transition, through a single intuitive line of code and with automated generation of starting values.
License: MIT + file LICENSE
URL: https://github.com/MaudeWagner/nlive
Encoding: UTF-8
LazyLoad: yes
LazyData: yes
Depends: R (>= 2.10)
Imports: dplyr, nlraa, sqldf, ggplot2, graphics, lcmm, saemix, Rmisc, sitar, stats, knitr
Suggests: rmarkdown, MASS, survival, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-09-12 23:13:15 UTC; Maude W
Author: Maude Wagner [aut, cre] , Ana W. Capuano [aut], Emmanuelle Comets [ctb]
Repository: CRAN
Date/Publication: 2022-09-13 07:30:02 UTC

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Mon, 12 Sep 2022

New package umbridge with initial version 0.9
Package: umbridge
Title: Integration for the UM-Bridge Protocol
Version: 0.9
Maintainer: Linus Seelinger <mail@linusseelinger.de>
Description: A convenient wrapper for the UM-Bridge protocol. UM-Bridge is a protocol designed for coupling uncertainty quantification (or statistical / optimization) software to numerical models. A model is represented as a mathematical function with optional support for derivatives via Jacobian actions etc.
License: MIT + file LICENSE
Encoding: UTF-8
BugReports: https://github.com/um-bridge
Imports: httr2, jsonlite, magrittr
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-09-10 06:57:02 UTC; linus
Author: Linus Seelinger [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-12 10:00:02 UTC

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New package r2resize with initial version 1.2
Package: r2resize
Title: In-Text Resizing for Images and Data Tables in 'Markdown' and 'Quarto' Documents
Version: 1.2
Author: Obinna Obianom
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Description: Automatic resizing toolbar for images and tables. Most suitable to include resize functionality in 'Markdown', 'Rmarkdown' and 'Quarto' documents.
License: MIT + file LICENSE
URL: https://r2resize.obi.obianom.com/
BugReports: https://github.com/oobianom/r2resize/issues
Depends: R (>= 3.4)
Imports: utils, DT
Suggests: rmarkdown, knitr
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-US
LazyData: false
NeedsCompilation: no
Packaged: 2022-09-11 00:23:33 UTC; in198
Repository: CRAN
Date/Publication: 2022-09-12 10:10:02 UTC

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New package fastrep with initial version 0.7
Package: fastrep
Title: Time-Saving Package for Creating Reports
Version: 0.7
Description: Provides templates for reports in 'rmarkdown' and functions to create tables and summaries of data.
License: GPL
Depends: R (>= 4.1.0)
Imports: dplyr, ggplot2, janitor, kableExtra, lifecycle, magrittr, purrr, tidyr
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
BugReports: https://github.com/AlissonRP/fastrep/issues
NeedsCompilation: no
Packaged: 2022-09-11 16:33:21 UTC; alissonrp
Author: Alisson Rosa [aut, cre]
Maintainer: Alisson Rosa <alirpereira887@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-12 10:42:56 UTC

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New package HeckmanEM with initial version 0.1.3
Package: HeckmanEM
Title: Fit Normal or Student-t Heckman Selection Models
Version: 0.1.3
Author: Marcos Prates [aut, cre, trl], Victor Lachos [aut], Dipak Dey [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Description: Maximum likelihood estimation by an EM algorithm of Heckman-type sample selection Normal or Student-t models. The reference is Lachos, Prates and Dey (2020) <doi:10.1016/j.jmva.2021.104737>.
Imports: mvtnorm (>= 1.1-0), sampleSelection (>= 1.2-6), MomTrunc (>= 5.79), PerformanceAnalytics (>= 2.0.4)
License: GPL (>= 2.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-09 19:05:04 UTC; marcos
Repository: CRAN
Date/Publication: 2022-09-12 09:22:56 UTC

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New package corrtable with initial version 0.1.0
Package: corrtable
Title: Creates and Saves Out a Correlation Table with Significance Levels Indicated
Version: 0.1.0
Description: After using this, a publication-ready correlation table with p-values indicated will be created. The input can be a full data frame; any string and Boolean terms will be dropped as part of functionality. Correlations and p-values are calculated using the 'Hmisc' framework. Output of the correlation_matrix() function is a table of strings; this gets saved out to a '.csv2' with the save_correlation_matrix() function for easy insertion into a paper. For more details about the process, consult <https://paulvanderlaken.com/2020/07/28/publication-ready-correlation-matrix-significance-r/>.
License: GPL-3
Encoding: UTF-8
Imports: Hmisc
Suggests: waldo, withr, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-09-09 23:59:31 UTC; Laura
Author: Paul van der Laken [aut] , Laura Lambert [ctb, cre]
Maintainer: Laura Lambert <laura.lambert.99@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-12 09:52:54 UTC

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New package boussinesq with initial version 1.0.4
Package: boussinesq
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
License: GPL (>= 2)
Title: Analytic Solutions for (Ground-Water) Boussinesq Equation
Depends: R (>= 2.10)
Author: Emanuele Cordano
Description: A collection of R functions were implemented from published and available analytic solutions for the One-Dimensional Boussinesq Equation (ground-water). In particular, the function "beq.lin()" is the analytic solution of the linearized form of Boussinesq Equation between two different head-based boundary (Dirichlet) conditions; "beq.song" is the non-linear power-series analytic solution of the motion of a wetting front over a dry bedrock (Song at al, 2007, see complete reference on function documentation). Bugs/comments/questions/collaboration of any kind are warmly welcomed.
Version: 1.0.4
Repository: CRAN
Date: 2022-09-06
URL: https://agupubs.onlinelibrary.wiley.com/doi/10.1002/wrcr.20072
Packaged: 2022-09-12 08:38:03 UTC; ecor
NeedsCompilation: no
Date/Publication: 2022-09-12 09:12:56 UTC

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New package msda with initial version 1.0.3
Package: msda
Title: Multi-Class Sparse Discriminant Analysis
Version: 1.0.3
Date: 2022-09-12
Author: Qing Mai <mai@stat.fsu.edu>, Yi Yang <yi.yang6@mcgill.ca>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Depends: Matrix, MASS
Imports: methods
Description: Efficient procedures for computing a new Multi-Class Sparse Discriminant Analysis method that estimates all discriminant directions simultaneously. It is an implementation of the work proposed by Mai, Q., Yang, Y., and Zou, H. (2019) <doi:10.5705/ss.202016.0117>.
LazyData: yes
License: GPL-2
URL: https://github.com/emeryyi/msda
Packaged: 2022-09-12 04:50:15 UTC; jiaozi
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2022-09-12 08:00:02 UTC

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New package m5 with initial version 0.1.1
Package: m5
Title: 'M5 Forecasting' Challenges Data
Version: 0.1.1
Description: Contains functions, which facilitate downloading, loading and preparing data from 'M5 Forecasting' challenges (by 'University of Nicosia', hosted on 'Kaggle'). The data itself is set of time series of different product sales in 'Walmart'. The package also includes a ready-to-use built-in M5 subset named 'tiny_m5'. For detailed information about the challenges, see: Makridakis, S. & Spiliotis, E. & Assimakopoulos, V. (2020). <doi:10.1016/j.ijforecast.2021.10.009>.
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/krzjoa/m5/issues
URL: https://github.com/krzjoa/m5, https://krzjoa.github.io/m5/
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Suggests: ggplot2, knitr, testthat (>= 3.0.0), rmarkdown, zeallot
VignetteBuilder: knitr
Imports: data.table, stringi, lubridate
NeedsCompilation: no
Packaged: 2022-09-09 18:28:59 UTC; krzysztof
Author: Krzysztof Joachimiak [aut, cre]
Maintainer: Krzysztof Joachimiak <joachimiak.krzysztof@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-12 08:32:55 UTC

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New package blm with initial version 2022.0.0.1
Package: blm
Title: Binomial Linear Regression
Version: 2022.0.0.1
Date: 2022-09-09
Depends: R (>= 3.0), methods
Imports: stats, stats4
Author: S. Kovalchik
Maintainer: S.Kovalchik <s.a.kovalchik@gmail.com>
Description: Implements regression models for binary data on the absolute risk scale. These models are applicable to cohort and population-based case-control data.
License: GPL (>= 2)
LazyLoad: yes
LazyData: true
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2022-09-12 08:12:56 UTC
Packaged: 2022-09-10 13:40:00 UTC; skovalchik

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New package bionetdata with initial version 1.1
Package: bionetdata
Title: Biological and Chemical Data Networks
Version: 1.1
Date: 2022-09-10
Author: Giorgio Valentini, Matteo Re -- Universita' degli Studi di Milano
Maintainer: Giorgio Valentini<valentini@di.unimi.it>
Description: Data Package that includes several examples of chemical and biological data networks, i.e. data graph structured.
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-09-10 15:43:31 UTC; valenti
Repository: CRAN
Date/Publication: 2022-09-12 08:12:59 UTC

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New package WOTPLY with initial version 0.1.0
Package: WOTPLY
Title: Plot Connectivity Between Cells from Different Time Points
Version: 0.1.0
Description: It shows the connections between selected clusters from the latest time point and the clusters from all the previous time points. The transition matrices between time point t and t+1 are obtained from Waddington-OT analysis <https://github.com/ScialdoneLab/WOTPLY>.
License: GPL-3
Depends: R (>= 4.0)
Imports: network, GGally, sna
Suggests: testthat, knitr
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-09 09:31:08 UTC; gabriele.lubatti
Author: Gabriele Lubatti [aut, cre, cph]
Maintainer: Gabriele Lubatti <gabriele.lubatti@helmholtz-muenchen.de>
Repository: CRAN
Date/Publication: 2022-09-12 07:43:01 UTC

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New package scPloidy with initial version 0.3.0
Package: scPloidy
Title: Infer Ploidy of Single Cells
Version: 0.3.0
Description: Compute ploidy of single cells (or nuclei) based on single-cell (or single-nucleus) ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data <https://github.com/fumi-github/scPloidy>.
BugReports: https://github.com/fumi-github/scPloidy/issues
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, GenomicRanges, magrittr, matrixStats, mixtools, rlang, Rsamtools, utils
Suggests: IRanges, knitr, readr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-09 07:45:55 UTC; fumi
Author: Fumihiko Takeuchi [aut, cre]
Maintainer: Fumihiko Takeuchi <fumihiko@takeuchi.name>
Repository: CRAN
Date/Publication: 2022-09-12 07:40:02 UTC

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New package queryup with initial version 1.0.0
Package: queryup
Title: Query the 'UniProtKB' REST API
Version: 1.0.0
Maintainer: Guillaume Voisinne <voisinne@gmail.com>
Description: Retrieve protein information from the 'UniProtKB' REST API (see <https://www.uniprot.org/help/api_queries>).
License: GPL-3
URL: https://github.com/VoisinneG/queryup
BugReports: https://github.com/VoisinneG/queryup/issues
Depends: R (>= 2.10)
Imports: jsonlite, RCurl, utils
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-09 09:53:46 UTC; rstudio
Author: Guillaume Voisinne [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-12 07:40:04 UTC

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New package HQM with initial version 0.1.0
Package: HQM
Title: Superefficient Estimation of Future Conditional Hazards Based on Marker Information
Version: 0.1.0
Maintainer: Alex Isakson <alex.isakson@bayes.city.ac.uk>
Description: Provides a nonparametric smoothed kernel density estimator for the future conditional hazard when time-dependent covariates are present. It also provides pointwise and uniform confidence bands and a bandwidth selection.
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: stats, utils
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-09-09 11:43:03 UTC; Alex
Author: Alex Isakson [aut, cre], Dimitrios Bagkavos [ctb], Enno Mammen [ctb], Jens Nielsen [ctb], Cecile Proust-Lima [ctb]
Repository: CRAN
Date/Publication: 2022-09-12 07:52:55 UTC

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New package BoundEdgeworth with initial version 0.1.1
Package: BoundEdgeworth
Title: Bound on the Error of the First-Order Edgeworth Expansion
Version: 0.1.1
Description: Computes uniform bounds on the distance between the cumulative distribution function of a standardized sum of random variables and its first-order Edgeworth expansion, following the article Derumigny, Girard, Guyonvarch (2021) <arXiv:2101.05780>.
License: GPL-3
Encoding: UTF-8
Imports: expint, mathjaxr
BugReports: https://github.com/AlexisDerumigny/BoundEdgeworth/issues
NeedsCompilation: no
Packaged: 2022-09-09 08:19:00 UTC; Alexis
Author: Alexis Derumigny [aut, cre] , Lucas Girard [aut], Yannick Guyonvarch [aut]
Maintainer: Alexis Derumigny <a.f.f.derumigny@tudelft.nl>
Repository: CRAN
Date/Publication: 2022-09-12 07:43:07 UTC

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Fri, 09 Sep 2022

New package truncnormbayes with initial version 0.0.2
Package: truncnormbayes
Title: Estimates Moments for a Truncated Normal Distribution using 'Stan'
Version: 0.0.2
Description: Finds the posterior modes for the mean and standard deviation for a truncated normal distribution with one or two known truncation points. The method used extends Bayesian methods for parameter estimation for a singly truncated normal distribution under the Jeffreys prior (see Zhou X, Giacometti R, Fabozzi FJ, Tucker AH (2014). "Bayesian estimation of truncated data with applications to operational risk measurement". <doi:10.1080/14697688.2012.752103>). This package additionally allows for a doubly truncated normal distribution.
URL: https://github.com/leonkt/truncnormbayes
BugReports: https://github.com/leonkt/truncnormbayes/issues
License: GPL (>= 3)
Encoding: UTF-8
Biarch: true
Depends: R (>= 3.4.0)
Imports: methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), Rdpack, rstan (>= 2.18.1), rstantools (>= 2.2.0), stats
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests: testthat (>= 3.0.0), truncnorm (>= 1.0), withr (>= 2.5.0)
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2022-09-08 02:37:09 UTC; mbraginsky
Author: Mika Braginsky [aut, cre], Leon Tran [aut], Maya Mathur [ctb]
Maintainer: Mika Braginsky <mika.br@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-09 10:30:02 UTC

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New package wordbankr with initial version 1.0.0
Package: wordbankr
Title: Accessing the Wordbank Database
Description: Connecting to Wordbank, an open repository for developmental vocabulary data. For more information on the underlying data, see <http://wordbank.stanford.edu>.
Version: 1.0.0
Depends: R (>= 4.0)
License: GPL-3
URL: https://langcog.github.io/wordbankr/, https://github.com/langcog/wordbankr/
BugReports: https://github.com/langcog/wordbankr/issues/
Imports: assertthat (>= 0.2.1), DBI (>= 1.1.3), dbplyr (>= 2.2.1), dplyr (>= 1.0.9), glue (>= 1.6.2), jsonlite (>= 1.8.0), lifecycle (>= 1.0.1), purrr (>= 0.3.4), quantregGrowth (>= 1.4), rlang (>= 1.0.4), RMySQL (>= 0.10.23), robustbase (>= 0.95), stringr (>= 1.4.0), tidyr (>= 1.2.0)
Suggests: ggplot2, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-08 19:00:01 UTC; mbraginsky
Author: Mika Braginsky [aut, cre], Daniel Yurovsky [ctb], Michael Frank [ctb], Danielle Kellier [ctb], Alvin Tan [ctb]
Maintainer: Mika Braginsky <mika.br@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-09 08:10:02 UTC

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New package sqlstrings with initial version 1.0.0
Package: sqlstrings
Title: Map 'SQL' Code to R Lists
Version: 1.0.0
Description: Provides a helper function, to bulk read 'SQL' code from separate files and load it into an 'R' list, where the list elements contain the individual statements and queries as strings. This works by annotating the 'SQL' code with a name comment, which also will be the name of the list element.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Imports: fs, readr, stringr
NeedsCompilation: no
Packaged: 2022-09-08 18:36:59 UTC; Admin
Author: Dejan Prvulovic [aut, cre]
Maintainer: Dejan Prvulovic <dejan.prv@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-09 08:10:05 UTC

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New package moose with initial version 0.0.1
Package: moose
Title: Mean Squared Out-of-Sample Error Projection
Version: 0.0.1
Description: Projects mean squared out-of-sample error for a linear regression based upon the methodology developed in Rohlfs (2022) <doi:10.48550/arXiv.2209.01493>. It consumes as inputs the lm object from an estimated OLS regression (based on the "training sample") and a data.frame of out-of-sample cases (the "test sample") that have non-missing values for the same predictors. The test sample may or may not include data on the outcome variable; if it does, that variable is not used. The aim of the exercise is to project what what mean squared out-of-sample error can be expected given the predictor values supplied in the test sample. Output consists of a list of three elements: the projected mean squared out-of-sample error, the projected out-of-sample R-squared, and a vector of out-of-sample "hat" or "leverage" values, as defined in the paper.
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-09 00:07:54 UTC; chris
Author: Chris Rohlfs [aut, cre]
Maintainer: Chris Rohlfs <car2228@columbia.edu>
Repository: CRAN
Date/Publication: 2022-09-09 08:20:02 UTC

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New package macrocol with initial version 0.1.0
Package: macrocol
Title: Colombian Macro-Financial Time Series Generator
Version: 0.1.0
Maintainer: Pedro Alejandro Cabra-Acela <jando2797@gmail.com>
Description: This repository aims to contribute to the econometric models' production with Colombian data, by providing a set of web-scrapping functions of some of the main macro-financial indicators. All the sources are public and free, but the advantage of these functions is that they directly download and harmonize the information in R's environment. No need to import or download additional files. You only need an internet connection!
License: Apache License 2.0
Encoding: UTF-8
Imports: openxlsx,httr,lubridate,readxl,stats,utils,R.utils
URL: <https://github.com/pedroCabraAcela/Scrapping-Colombian-Macrodata>
NeedsCompilation: no
Packaged: 2022-09-08 18:16:16 UTC; pc5297
Author: Pedro Alejandro Cabra-Acela [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-09 08:13:01 UTC

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New package figuRes2 with initial version 1.0.0
Package: figuRes2
Title: Support for a Variety of Figure Production Tasks
Version: 1.0.0
Date: 2022-08-29
URL: https://github.com/gcicc/figures2
Maintainer: Greg Cicconetti <greg.cicconetti@gmail.com>
Description: We view a figure as a collection of graphs/tables assembled on a page and optionally annotated with metadata (titles, headers and footers). Functions and supporting documentation are offered to streamline a variety of figure production task.
License: GPL-2
Encoding: UTF-8
LazyLoad: no
Depends: R (>= 3.5.0)
Imports: survival, ggplot2, scales, stringr, plyr, grid, gridExtra, gtable, reshape2, grDevices, utils
Suggests: RColorBrewer, knitr, rmarkdown, tidyverse, latex2exp
ByteCompile: TRUE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-08 15:30:45 UTC; eri7441
Author: Greg Cicconetti [aut, cre] , David Wade [aut]
Repository: CRAN
Date/Publication: 2022-09-09 08:02:55 UTC

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New package EvidenceSynthesis with initial version 0.3.0
Package: EvidenceSynthesis
Title: Synthesizing Causal Evidence in a Distributed Research Network
Version: 0.3.0
Date: 2022-09-02
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Description: Routines for combining causal effect estimates and study diagnostics across multiple data sites in a distributed study, without sharing patient-level data. Allows for normal and non-normal approximations of the data-site likelihood of the effect parameter.
SystemRequirements: Java version 8 or higher (https://www.java.com/)
Depends: survival, R (>= 3.5.0)
Imports: ggplot2, gridExtra, meta, EmpiricalCalibration, rJava, BeastJar, Cyclops (>= 3.1.0), HDInterval, coda, rlang, methods
Suggests: knitr, rmarkdown, testthat, sn
License: Apache License 2.0
URL: https://ohdsi.github.io/EvidenceSynthesis/, https://github.com/OHDSI/EvidenceSynthesis
BugReports: https://github.com/OHDSI/EvidenceSynthesis/issues
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-09 05:22:39 UTC; mschuemi
Author: Martijn Schuemie [aut, cre], Marc A. Suchard [aut], Observational Health Data Science and Informatics [cph]
Repository: CRAN
Date/Publication: 2022-09-09 08:22:58 UTC

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New package DBIsqldf with initial version 0.9.9-2
Package: DBIsqldf
Version: 0.9.9-2
Date: 2022-09-07
Title: Manipulate R Data Frames Using SQL
Author: Neal Fultz <nfultz@gmail.com> and G. Grothendieck <ggrothendieck@gmail.com>
Maintainer: Neal Fultz <nfultz@gmail.com>
Description: Helper function sqldf() transparently initializes a database, imports data frames into it, and executes a query or other statement. This supports all DBI drivers to some degree, and parameterized queries.
ByteCompile: true
Imports: DBI
Suggests: RSQLite
License: GPL-2
BugReports: https://github.com/nfultz/DBIsqldf/issues
URL: https://github.com/nfultz/DBIsqldf
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-08 20:03:13 UTC; nfultz
Repository: CRAN
Date/Publication: 2022-09-09 08:13:04 UTC

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New package TSdeeplearning with initial version 0.1.0
Package: TSdeeplearning
Title: Deep Learning Model for Time Series Forecasting
Version: 0.1.0
Maintainer: Ronit Jaiswal <ronitjaiswal2912@gmail.com>
Description: RNNs are preferred for sequential data like time series, speech, text, etc. but when dealing with long range dependencies, vanishing gradient problems account for their poor performance. LSTM and GRU are effective solutions which are nothing but RNN networks with the abilities of learning both short-term and long-term dependencies. Their structural makeup enables them to remember information for a long period without any difficulty. LSTM consists of one cell state and three gates, namely, forget gate, input gate and output gate whereas GRU comprises only two gates, namely, reset gate and update gate. This package consists of three different functions for the application of RNN, LSTM and GRU to any time series data for its forecasting. For method details see Jaiswal, R. et al. (2022). <doi:10.1007/s00521-021-06621-3>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: keras, tensorflow, reticulate, tsutils, BiocGenerics, utils, graphics, magrittr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-09-08 11:50:23 UTC; kapil
Author: Ronit Jaiswal [aut, cre], Girish Kumar Jha [aut, ths, ctb], Rajeev Ranjan Kumar [aut, ctb], Kapil Choudhary [aut, ctb]
Repository: CRAN
Date/Publication: 2022-09-09 07:33:00 UTC

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New package latentFactoR with initial version 0.0.2
Package: latentFactoR
Title: Data Simulation Based on Latent Factors
Version: 0.0.2
Date: 2022-09-08
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Description: Generates data based on latent factor models. Data can be continuous, polytomous, dichotomous, or mixed. Skews, cross-loadings, wording effects, population errors, and local dependencies can be added. All parameters can be manipulated. Data categorization is based on Garrido, Abad, and Ponsoda (2011) <doi:10.1177/0013164410389489>.
Depends: R (>= 3.6.0)
License: GPL (>= 3.0)
Imports: methods, mvtnorm, psych, rstudioapi
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-08 12:38:48 UTC; chria12
Author: Alexander Christensen [aut, cre] , Maria Dolores Nieto Canaveras [aut], Hudson Golino [aut] , Luis Eduardo Garrido [aut]
Repository: CRAN
Date/Publication: 2022-09-09 07:32:55 UTC

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New package ExpGenetic with initial version 0.1.0
Package: ExpGenetic
Title: Non-Additive Expression Analysis of Hybrid Offspring
Version: 0.1.0
Description: Three functional modules, including genetic features, differential expression analysis and non-additive expression analysis were integrated into the package. And the package is suitable for RNA-seq and small RNA sequencing data. Besides, two methods of non-additive expression analysis were provided. One is the calculation of the additive (a) and dominant (d), the other is the evaluation of expression level dominance by comparing the total expression of the gene in hybrid offspring with the expression level in parents. For non-additive expression analysis of RNA-seq data, it is only applicable to hybrid offspring (including two sub-genomes) species for the time being.
License: AGPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: DESeq2 (>= 1.34.0), futile.logger (>= 1.4.3), ggplot2 (>= 3.3.6), ggsci (>= 2.9), plyr (>= 1.8.7), VennDiagram (>= 1.7.3)
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-09-08 08:27:24 UTC; wuyuqing
Author: Yuqing Wu [aut, cre]
Maintainer: Yuqing Wu <wuyuqing0104@163.com>
Repository: CRAN
Date/Publication: 2022-09-09 07:13:01 UTC

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New package binfunest with initial version 0.1.0
Package: binfunest
Title: Estimates Parameters of Functions Driving Binomial Random Variables
Version: 0.1.0
Maintainer: Philip Shea <philshea@gmail.com>
Description: Provides maximum likelihood estimates of the performance parameters that drive a binomial distribution of observed errors, and takes full advantage of zero error observations. High performance communications systems typically have inherent noise sources and other performance limitations that need to be estimated. Measurements made at high signal to noise ratios typically result in zero errors due to limitation in available measurement time. Package includes theoretical performance functions for common modulation schemes (Proakis, "Digital Communications" (1995, <ISBN:0-07-051726-6>)), polarization shifted QPSK (Agrell & Karlsson (2009, <DOI:10.1109/JLT.2009.2029064>)), and utility functions to work with the performance functions.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Imports: pracma, stats, stats4
URL: https://github.com/PhilShea/binfunest
BugReports: https://github.com/PhilShea/binfunest/issues
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-09-08 13:14:30 UTC; phils
Author: Philip Shea [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-09 07:32:57 UTC

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New package allhomes with initial version 0.3.0
Package: allhomes
Title: Extract Past Sales Data from Allhomes.com.au
Version: 0.3.0
Description: Extract past sales data for specific suburb(s) and year(s) from the Australian property website <https://www.allhomes.com.au>. Allhomes data include the address and property details, date and price of the sale, block size and unimproved value of properties mainly in the ACT and NSW.
Language: en-AU
License: MIT + file LICENSE
Depends: R (>= 4.0)
Imports: dplyr, htmltab, httr, jsonlite, magrittr, purrr, readr, rlang, tibble, tidyr, stringr
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
URL: https://mevers.github.io/allhomes/
NeedsCompilation: no
Packaged: 2022-09-08 11:34:46 UTC; maurits
Author: Maurits Evers [aut, cre]
Maintainer: Maurits Evers <maurits.evers@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-09 07:23:00 UTC

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Thu, 08 Sep 2022

New package mglasso with initial version 0.1.2
Package: mglasso
Title: Multiscale Graphical Lasso
Version: 0.1.2
Description: Inference of Multiscale graphical models with neighborhood selection approach. The method is based on solving a convex optimization problem combining a Lasso and fused-group Lasso penalties. This allows to infer simultaneously a conditional independence graph and a clustering partition. The optimization is based on the Continuation with Nesterov smoothing in a Shrinkage-Thresholding Algorithm solver (Hadj-Selem et al. 2018) <doi:10.1109/TMI.2018.2829802> implemented in python.
License: MIT + file LICENSE
Imports: corpcor, ggplot2, ggrepel, gridExtra, Matrix, methods, R.utils, reticulate (>= 1.25), rstudioapi
Suggests: knitr, mvtnorm, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
ByteCompile: true
Config/reticulate: list( packages = list( list(package = "scipy", version = "1.7.1"), list(package = "numpy", version = "1.22.4"), list(package = "matplotlib"), list(package = "scikit-learn"), list(package = "six"), list(package = "pylearn-parsimony", version = "0.3.1", pip = TRUE) ) )
Encoding: UTF-8
URL: https://desanou.github.io/mglasso/
NeedsCompilation: no
Packaged: 2022-09-05 22:06:02 UTC; doedm
Author: Edmond Sanou [aut, cre], Tung Le [ctb], Christophe Ambroise [ths], Genevieve Robin [ths]
Maintainer: Edmond Sanou <doedmond.sanou@univ-evry.fr>
Repository: CRAN
Date/Publication: 2022-09-08 13:12:55 UTC

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New package protti with initial version 0.4.0
Package: protti
Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
Version: 0.4.0
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: rlang, dplyr, stringr, magrittr, data.table, janitor, progress, purrr, tidyr, ggplot2, forcats, tibble, plotly, ggrepel, utils, grDevices, curl, readr, lifecycle, httr, methods, R.utils, stats
Suggests: testthat, covr, knitr, rmarkdown, shiny, r3dmol, proDA, limma, dendextend, pheatmap, heatmaply, furrr, future, parallel, seriation, drc, igraph, stringi, STRINGdb, iq
Depends: R (>= 4.0)
URL: https://github.com/jpquast/protti, https://jpquast.github.io/protti/
BugReports: https://github.com/jpquast/protti/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-02 12:18:12 UTC; jan-philippquast
Author: Jan-Philipp Quast [aut, cre] , Dina Schuster [aut] , ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Repository: CRAN
Date/Publication: 2022-09-08 11:00:18 UTC

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New package WormTensor with initial version 0.1.0
Package: WormTensor
Title: A Clustering Method for Time-Series Whole-Brain Activity Data of 'C. elegans'
Version: 0.1.0
Maintainer: Kentaro Yamamoto <yamaken37.the.answer@gmail.com>
Description: A toolkit to detect clusters from distance matrices. The distance matrices are assumed to be calculated between the cells of multiple animals ('Caenorhabditis elegans') from input time-series matrices. Some functions for generating distance matrices, performing clustering, evaluating the clustering, and visualizing the results of clustering and evaluation are available. We're also providing the download function to retrieve the calculated distance matrices from 'figshare' <https://figshare.com>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/rikenbit/WormTensor
BugReports: https://github.com/rikenbit/WormTensor/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 4.1.0)
Imports: rTensor, usedist, dtwclust, clusterSim, clValid, aricode, cluster, ggplot2, Rtsne, uwot, factoextra, ggrepel, cowplot, methods
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-08 05:19:16 UTC; rstudio
Author: Kentaro Yamamoto [aut, cre], Koki Tsuyuzaki [aut], Itoshi Nikaido [aut]
Repository: CRAN
Date/Publication: 2022-09-08 09:22:58 UTC

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New package seqimpute with initial version 1.7
Package: seqimpute
Title: Imputation of Missing Data in Sequence Analysis
Version: 1.7
Date: 2022-09-06
Description: Multiple imputation of missing data present in a dataset through the prediction based on either a random forest or a multinomial regression model. Covariates and time-dependant covariates can be included in the model. The prediction of the missing values is based on the method of Halpin (2012) <https://ulir.ul.ie/handle/10344/3639>.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: Amelia, rms, stringr, TraMineR, cluster, swfscMisc, plyr, dplyr, dfidx, mice, foreach, parallel, doRNG, doSNOW, ranger, mlr, nnet
Author: Andre Berchtold [aut, cre], Anthony Guinchard [aut], Kevin Emery [aut], Kamyar Taher [aut]
Maintainer: Andre Berchtold <andre.berchtold@unil.ch>
Repository: CRAN
Repository/R-Forge/Project: seqimpute
Repository/R-Forge/Revision: 92
Repository/R-Forge/DateTimeStamp: 2022-09-06 06:53:41
Date/Publication: 2022-09-08 09:00:02 UTC
NeedsCompilation: no
Packaged: 2022-09-06 07:12:07 UTC; rforge
Depends: R (>= 3.5.0)

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New package OneArmTTE with initial version 1.0
Package: OneArmTTE
Title: One-Arm Clinical Trial Designs for Time-to-Event Endpoint
Version: 1.0
Maintainer: Heng Zhou <heng.zhou@merck.com>
Description: Get operating characteristics of one-arm clinical trial designs for time-to-event endpoint through simulation and perform analysis with time-to-event data.
Imports: tibble, dplyr, tidyr, survival
Depends: R (>= 3.6)
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-08 02:52:23 UTC; zhouheng
Author: Heng Zhou [aut, cre], Keaven Anderson [aut], Linda Sun [aut], Meihua Wang [aut]
Repository: CRAN
Date/Publication: 2022-09-08 09:23:01 UTC

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New package mmpca with initial version 2.0.2
Package: mmpca
Title: Integrative Analysis of Several Related Data Matrices
Version: 2.0.2
Description: A generalization of principal component analysis for integrative analysis. The method finds principal components that describe single matrices or that are common to several matrices. The solutions are sparse. Rank of solutions is automatically selected using cross validation. The method is described in Kallus et al. (2019) <arXiv:1911.04927>.
Depends: R (>= 3.3.0)
Imports: digest (>= 0.6.0), Rcpp (>= 1.0.8)
LinkingTo: Rcpp, RcppEigen, RcppGSL
SystemRequirements: C++11
Biarch: true
NeedsCompilation: yes
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/cyianor/mmpca
BugReports: https://github.com/cyianor/mmpca/issues
Packaged: 2022-09-08 06:40:35 UTC; hefelix
Author: Jonatan Kallus [aut], Felix Held [ctb, cre]
Maintainer: Felix Held <felix.held@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-08 09:20:02 UTC

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New package AmoudSurv with initial version 0.1.0
Package: AmoudSurv
Title: Tractable Parametric Odds-Based Regression Models
Version: 0.1.0
Maintainer: Abdisalam Hassan Muse <abdisalam.h.muse@gmail.com>
Description: Fits tractable fully parametric odds-based regression models for survival data, including proportional odds (PO), accelerated failure time (AFT), accelerated odds (AO), and General Odds (GO) models in overall survival frameworks. Given at least an R function specifying the survivor, hazard rate and cumulative distribution functions, any user-defined parametric distribution can be fitted. We applied and evaluated a minimum of seventeen (17) various baseline distributions that can handle different failure rate shapes for each of the four different proposed odds-based regression models. For more information see Bennet et al., (1983) <doi:10.1002/sim.4780020223>, and Muse et al., (2022) <doi:10.1016/j.aej.2022.01.033>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: AHSurv, flexsurv, pracma, stats, stats4
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-09-07 22:05:23 UTC; Admin
Author: Abdisalam Hassan Muse [aut, cre] , Samuel Mwalili [aut, ctb], Oscar Ngesa [aut, ctb], Christophe Chesneau [aut, ctb]
Repository: CRAN
Date/Publication: 2022-09-08 09:12:56 UTC

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New package rsurveycto with initial version 0.0.5
Package: rsurveycto
Title: Interact with Data on 'SurveyCTO'
Version: 0.0.5
Description: 'SurveyCTO' is a platform for mobile data collection in offline settings. The 'rsurveycto' R package uses the 'SurveyCTO' REST API <https://docs.surveycto.com/05-exporting-and-publishing-data/05-api-access/01.api-access.html> to read datasets and forms from a 'SurveyCTO' server into R as 'data.table's and to download file attachments. The package also has limited support to write datasets to a server.
URL: https://youth-impact.github.io/rsurveycto/, https://github.com/youth-impact/rsurveycto
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1)
Imports: checkmate (>= 2.1.0), curl (>= 4.3.2), data.table (>= 1.14.2), glue (>= 1.6.2), httr (>= 1.4.3), jsonlite (>= 1.8.0), withr (>= 2.5.0)
Suggests: knitr, rmarkdown, testthat (>= 3.1.4)
NeedsCompilation: no
Packaged: 2022-09-07 20:43:18 UTC; jakehughey
Author: Jake Hughey [aut, cre], Robert On [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-08 06:50:02 UTC

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New package onmaRg with initial version 0.1.0
Package: onmaRg
Title: Import Public Health Ontario's Ontario Marginalization Index
Version: 0.1.0
Description: The Ontario Marginalization Index is a socioeconomic model that is built on Statistics Canada census data. The model consists of four dimensions: Residential Instability, Material Deprivation, Dependency and Ethnic Concentration. Each of these dimensions are imported for a variety of geographic levels (DA, CD, etc.) for both the 2011 and 2016 administrations of the census (2021 pending). These data sets contribute to community analysis of equity with respect to Ontario's Anti-Racism Act. The Ontario Marginalization Index data is retrieved from the Public Health Ontario website: <https://www.publichealthontario.ca/en/data-and-analysis/health-equity/ontario-marginalization-index>. The shapefile data is retrieved from the Statistics Canada website: <https://www12.statcan.gc.ca/census-recensement/2011/geo/bound-limit/bound-limit-eng.cfm>.
License: GPL-3
Encoding: UTF-8
Depends: dplyr, httr, readxl, sf, stringr, utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-07 19:59:40 UTC; willi
Author: William Conley [aut, cre]
Maintainer: William Conley <william@cconley.ca>
Repository: CRAN
Date/Publication: 2022-09-08 06:40:02 UTC

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New package IterativeHardThresholding with initial version 1.0.2
Package: IterativeHardThresholding
Title: Iterative Hard Thresholding Extensions to Cyclops
Version: 1.0.2
Date: 2022-9-7
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Description: Fits large-scale regression models with a penalty that restricts the maximum number of non-zero regression coefficients to a prespecified value. While Chu et al (2020) <doi:10.1093/gigascience/giaa044> describe the basic algorithm, this package uses Cyclops for an efficient implementation.
License: Apache License 2.0
Depends: R (>= 3.2.2), Cyclops (>= 1.3.0)
Imports: ParallelLogger
Suggests: testthat, knitr, rmarkdown
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-07 19:01:28 UTC; msuchard
Author: Marc A. Suchard [aut, cre], Patrick Ryan [aut], Observational Health Data Sciences and Informatics [cph]
Repository: CRAN
Date/Publication: 2022-09-08 06:42:59 UTC

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Wed, 07 Sep 2022

New package xhaz with initial version 2.0.0
Package: xhaz
Title: Excess Hazard Modelling Considering Inappropriate Mortality Rates
Version: 2.0.0
Description: Fits relative survival regression models with or without proportional excess hazards and with the additional possibility to correct for background mortality by one or more parameter(s). These models are relevant when the observed mortality in the studied group is not comparable to that of the general population or in population-based studies where the available life tables used for net survival estimation are insufficiently stratified. In the latter case, the proposed model by Touraine et al. (2020) <doi:10.1177/0962280218823234> can be used. The user can also fit a model that relax the proportional expected hazards assumption considered in the Touraine et al. excess hazard model. This extension was proposed by Mba et al. (2020) <doi:10.1186/s12874-020-01139-z> to allow non-proportional effects of the additional variable on the general population mortality. In non-population-based studies, researchers can identify non-comparability source of bias in terms of expected mortal [...truncated...]
License: AGPL (>= 3)
Depends: R (>= 3.5.0), statmod, stats, survival
Imports: gtools, numDeriv, optimParallel, splines, stringr, survexp.fr
Suggests: knitr, rmarkdown, spelling, testthat (>= 2.1.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
Language: en-US
NeedsCompilation: no
Packaged: 2022-09-07 09:22:17 UTC; juste.goungounga
Author: Juste Goungounga [aut, cre] , Darlin Mba [aut] , Nathalie Graffeo [aut] , Roch Giorgi [aut]
Maintainer: Juste Goungounga <juste.goungounga@univ-amu.fr>
Repository: CRAN
Date/Publication: 2022-09-07 18:40:02 UTC

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New package RKorAPClient with initial version 0.7.5
Package: RKorAPClient
Title: 'KorAP' Web Service Client Package
Version: 0.7.5
Description: A client package that makes the 'KorAP' web service API accessible from R. The corpus analysis platform 'KorAP' has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo' or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code, as a programmatic alternative to the 'KorAP' web user-interface. You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Depends: R (>= 3.5.0)
Language: en-US
License: BSD_2_clause + file LICENSE
URL: https://github.com/KorAP/RKorAPClient/, https://korap.ids-mannheim.de/, https://www.ids-mannheim.de/digspra/kl/projekte/korap
BugReports: https://github.com/KorAP/RKorAPClient/issues
Encoding: UTF-8
Imports: R.cache, broom, ggplot2, tibble, magrittr, tidyr, dplyr, lubridate, highcharter, jsonlite, keyring, utils, httr, curl, methods, PTXQC, purrr, stringr, urltools
Suggests: lifecycle, testthat
NeedsCompilation: no
Packaged: 2022-09-07 09:15:49 UTC; kupietz
Author: Marc Kupietz [aut, cre], Nils Diewald [ctb], Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Repository: CRAN
Date/Publication: 2022-09-07 18:40:09 UTC

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New package flexsiteboard with initial version 0.0.6
Package: flexsiteboard
Title: Breaks Single Page Applications from 'flexdashboard' in Multiple Files
Version: 0.0.6
Description: A drop-in replacement for 'flexdashboard' 'Rmd' documents, which implements an after-knit-hook to split the generated single page application in one document per main section to reduce rendering load in the web browser displaying the document. Put all 'JavaScript' stuff needed in all sections before the first headline featuring navigation menu attributes. This package is experimental and maybe replaced by a solution inside 'flexdashboard'.
License: BSD_2_clause + file LICENSE
Encoding: UTF-8
Imports: flexdashboard, htmltools, htmlwidgets, jsonlite, knitr, rmarkdown, stats, yaml
SystemRequirements: pandoc (>= 2.4) - http://pandoc.org
VignetteBuilder: knitr
Suggests: withr, testthat (>= 3.0.0), spelling
Language: en-US
NeedsCompilation: no
Packaged: 2022-09-07 08:55:27 UTC; struckmanns
Author: University Medicine Greifswald [cph], Stephan Struckmann [aut, cre]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Repository: CRAN
Date/Publication: 2022-09-07 18:40:06 UTC

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New package vapour with initial version 0.8.82
Package: vapour
Title: Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Version: 0.8.82
Description: Provides low-level access to 'GDAL' functionality. 'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats that presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable developing further tools.
Depends: R (>= 3.3.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: jsonlite, Rcpp, utils
Suggests: testthat, knitr, markdown, rmarkdown, spelling
SystemRequirements: GDAL (>= 2.2.3), PROJ (>= 4.8.0), C++11
VignetteBuilder: knitr
URL: https://github.com/hypertidy/vapour
BugReports: https://github.com/hypertidy/vapour/issues
Language: en-US
NeedsCompilation: yes
Packaged: 2022-09-06 09:28:00 UTC; mdsumner
Author: Michael Sumner [aut, cre] , Simon Wotherspoon [ctb] , Mark Padgham [ctb] ), Edzer Pebesma [ctb] , Roger Bivand [ctb] , Jim Hester [ctb, cph] , Timothy Keitt [ctb] , Jeroen Ooms [ctb] , Dale Maschette [ctb] , Joseph Stachelek [ctb], Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-07 17:50:02 UTC

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New package SAEforest with initial version 1.0.0
Package: SAEforest
Title: Mixed Effect Random Forests for Small Area Estimation
Version: 1.0.0
Description: Mixed Effects Random Forests (MERFs) are a data-driven, nonparametric alternative to current methods of Small Area Estimation (SAE). 'SAEforest' provides functions for the estimation of regionally disaggregated linear and nonlinear indicators using survey sample data. Included procedures facilitate the estimation of domain-level economic and inequality metrics and assess associated uncertainty. Emphasis lies on straightforward interpretation and visualization of results. From a methodological perspective, the package builds on approaches discussed in Krennmair and Schmid (2022) <arXiv:2201.10933v2> and Krennmair et al. (2022) <arXiv:2204.10736>.
License: GPL (>= 2)
URL: https://github.com/krennpa/SAEforest, https://krennpa.github.io/SAEforest/
Depends: R (>= 4.1.0)
Imports: caret, dplyr, ggplot2, haven, ineq, lme4, maptools, pbapply, pdp, ranger, reshape2, stats, vip
Suggests: R.rsp, sp, rgeos, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2022-09-06 11:37:18 UTC; Patrick
Author: Patrick Krennmair [aut, cre]
Maintainer: Patrick Krennmair <patrick.krennmair@fu-berlin.de>
Repository: CRAN
Date/Publication: 2022-09-07 17:50:06 UTC

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New package IsoCor with initial version 0.1.40
Package: IsoCor
Title: Analyze Isotope Ratios in a 'Shiny'-App
Version: 0.1.40
Date: 2022-09-06
Description: Analyzing Inductively Coupled Plasma - Mass Spectrometry (ICP-MS) measurement data to evaluate isotope ratios (IRs) is a complex process. The 'IsoCor' package facilitates this process and renders it reproducible by providing a function to run a 'Shiny'-App locally in any web browser. In this App the user can upload data files of various formats, select ion traces, apply peak detection and perform calculation of IRs and delta values. Results are provided as figures and tables and can be exported. The App, therefore, facilitates data processing of ICP-MS experiments to quickly obtain optimal processing parameters compared to traditional 'Excel' worksheet based approaches. A more detailed description can be found in the corresponding article "Data processing made easy: standalone tool for automated calculation of isotope ratio from transient signals – IsoCor" by Tukhmetova et al. in Journal of Analytical Atomic Spectrometry (JAAS). The most recent version of 'IsoCor' can be tested online [...truncated...]
URL: https://jali.shinyapps.io/isocor
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.50)
Imports: bsplus, DT, golem, htmltools, MALDIquant, markdown, plyr, rmarkdown, shiny, shinyalert, shinyjs
Suggests: config, pkgload, rsconnect, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-09-06 11:13:45 UTC; jlisec
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Repository: CRAN
Date/Publication: 2022-09-07 18:00:07 UTC

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New package h2otools with initial version 0.0.1
Package: h2otools
Title: Machine Learning Model Evaluation for 'h2o' Package
Version: 0.0.1
Depends: R (>= 3.5.0)
Description: Several functions are provided that simplify using 'h2o' package. Currently, a function for extracting the AutoML model parameter is provided, alongside a function for computing F-Measure statistics at any given threshold. For more information about 'h2o' package see <https://h2o.ai/>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: h2o (>= 3.34.0.0), curl
URL: https://github.com/haghish/h2otools, https://www.sv.uio.no/psi/english/people/aca/haghish/
BugReports: https://github.com/haghish/h2otools/issues
NeedsCompilation: no
Packaged: 2022-09-06 12:01:11 UTC; OJO
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@uio.no>
Repository: CRAN
Date/Publication: 2022-09-07 18:00:05 UTC

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New package remaCor with initial version 0.0.9
Package: remaCor
Title: Random Effects Meta-Analysis for Correlated Test Statistics
Version: 0.0.9
Date: 2022-09-06
Description: Meta-analysis is widely used to summarize estimated effects sizes across multiple statistical tests. Standard fixed and random effect meta-analysis methods assume that the estimated of the effect sizes are statistically independent. Here we relax this assumption and enable meta-analysis when the correlation matrix between effect size estimates is known. Fixed effect meta-analysis uses the method of Lin and Sullivan (2009) <doi:10.1016/j.ajhg.2009.11.001>, and random effects meta-analysis uses the method of Han, et al. <doi:10.1093/hmg/ddw049>.
License: Artistic-2.0
URL: https://github.com/GabrielHoffman/remaCor
BugReports: https://github.com/GabrielHoffman/remaCor/issues
Suggests: knitr, metafor
Depends: R (>= 3.6.0), RUnit, clusterGeneration, ggplot2, grid, reshape2, methods
Imports: mvtnorm, compiler, Rdpack, stats
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-06 13:55:04 UTC; gabrielhoffman
Author: Gabriel Hoffman [aut, cre]
Maintainer: Gabriel Hoffman <gabriel.hoffman@mssm.edu>
Repository: CRAN
Date/Publication: 2022-09-07 08:30:02 UTC

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New package OneArm2stage with initial version 1.1.4
Package: OneArm2stage
Title: Optimal One-Arm Two-Stage Phase II Design with Survival Endpoint
Version: 1.1.4
Description: The proposed two-stage design can be used for single-arm phase II trial designs with time-to-event endpoints, which is desirable for clinical trials on immunotherapies among cancer patients. There're two advantages of the proposed approach: 1) It provides flexible choices of four underlying survival distributions and 2) the power of the design is more accurately calculated using exact variance in one-sample log-rank test. The package can be used for 1) planning the sample size; 2) conducting the interim and final analyses for the Go/No-go decisions. More details about the design method can be found in the paper: Wu, J, Chen L, Wei J, Weiss H, Chauhan A. (2020). <doi:10.1002/pst.1983>.
NeedsCompilation: no
Encoding: UTF-8
Repository: CRAN
Imports: survival, utils, flexsurv, IPDfromKM
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
License: GPL (>= 3)
Depends: R (>= 3.5.0)
Packaged: 2022-09-06 19:42:02 UTC; xyuan86
Author: Xiaomeng Yuan [aut, cre], Haitao Pan [aut], Jianrong Wu [aut]
Maintainer: Xiaomeng Yuan <xiaomeng.yuan@stjude.org>
Date/Publication: 2022-09-07 08:40:02 UTC

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New package dsfa with initial version 0.0.3
Package: dsfa
Title: Distributional Stochastic Frontier Analysis
Version: 0.0.3
Description: Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see Schmidt R, Kneib T (2022) <doi:10.48550/arXiv.2208.10294>.
Imports: mgcv, sn, gratia, graphics, stats, copula, numDeriv, Rdpack
NeedsCompilation: yes
SystemRequirements: C++11
License: MIT + file LICENSE
Encoding: UTF-8
Packaged: 2022-09-06 14:56:08 UTC; admin
Author: Rouven Schmidt [aut, cre]
Maintainer: Rouven Schmidt <rouven.schmidt@tu-clausthal.de>
Repository: CRAN
Date/Publication: 2022-09-07 08:30:08 UTC

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New package rwarrior with initial version 0.4.1
Package: rwarrior
Title: R Warrior - An AI Programming Game
Version: 0.4.1
Description: A port of Ruby Warrior. Teaches R programming in a fun and interactive way.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: methods, R6, glue, cli, dplyr, tibble, checkmate, stringr
Suggests: covr, knitr, rmarkdown, purrr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-06 07:04:03 UTC; tankard.r
Author: Rick M Tankard [cre, aut]
Maintainer: Rick M Tankard <rickmtankard@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-07 07:40:02 UTC

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New package oceanexplorer with initial version 0.0.1
Package: oceanexplorer
Title: Explore Our Planet's Oceans with NOAA
Version: 0.0.1
Description: Provides tools for easy exploration of the world ocean atlas of the US agency National Oceanic and Atmospheric Administration (NOAA). It includes functions to extract NetCDF data from the repository and code to visualize several physical and chemical parameters of the ocean. A Shiny app further allows interactive exploration of the data. The methods for data collecting and quality checks are described in several papers, which can be found here: <https://www.ncei.noaa.gov/products/world-ocean-atlas>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: cffr, covr, curl, devtools (>= 2.4.3), diffviewer (>= 0.1.1), globals (>= 0.14.0), knitr, rmarkdown, roxygen2, shinytest (>= 1.5.1), spelling, testthat (>= 3.1.2), tibble, vdiffr (>= 1.0.2)
Imports: stars (>= 0.5.5), shiny (>= 1.7.1), ggplot2 (>= 3.3.5), sf (>= 1.0.5), waiter (>= 0.2.5), bslib (>= 0.3.1), thematic (>= 0.1.2.1), shinyFeedback (>= 0.4.0), purrr (>= 0.3.4), miniUI (>= 0.1.1.1), rstudioapi (>= 0.13), DT (>= 0.20), fs (>= 1.5.2), glue (>= 1.6.0), shinyjs (>= 2.1.0), rlang (>= 0.4.11), maps (>= 3.4.0), ncmeta (>= 0.3.0), RNetCDF (>= 2.6.1), dplyr (>= 1.0.9)
VignetteBuilder: knitr
Depends: R (>= 4.1.0)
URL: https://utrechtuniversity.github.io/oceanexplorer/, https://utrecht-university.shinyapps.io/oceanexplorer/, https://www.ncei.noaa.gov/products/world-ocean-atlas
BugReports: https://github.com/UtrechtUniversity/oceanexplorer/issues
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2022-09-06 07:53:33 UTC; maria
Author: Martin Schobben [aut, cre, cph] , Peter Bijl [ctb]
Maintainer: Martin Schobben <schobbenmartin@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-07 07:40:05 UTC

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New package mlim with initial version 0.0.9
Package: mlim
Title: Multiple Imputation with Automated Machine Learning
Version: 0.0.9
Depends: R (>= 3.5.0)
Description: Using automated machine learning, the package fine-tunes an Elastic Net (default) or Gradient Boosting, Random Forest, Deep Learning, Extreme Gradient Boosting, or Stacked Ensemble machine learning model for imputing the missing observations of each variable. This procedure has been implemented for the first time by this package and is expected to outperform other packages for imputing missing data that do not fine-tune their models. The main idea is to allow the model to set its own parameters for imputing each variable instead of setting fixed predefined parameters to impute all variables of the dataset.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: h2o (>= 3.34.0.0), curl (>= 4.3.0), mice, missRanger, memuse, md.log (>= 0.2.0)
LazyData: true
URL: https://github.com/haghish/mlim, https://www.sv.uio.no/psi/english/people/aca/haghish/
BugReports: https://github.com/haghish/mlim/issues
NeedsCompilation: no
Packaged: 2022-09-06 09:19:02 UTC; OJO
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@uio.no>
Repository: CRAN
Date/Publication: 2022-09-07 07:50:08 UTC

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New package mccca with initial version 0.1.1
Package: mccca
Title: Visualizing Class Specific Heterogeneous Tendencies in Categorical Data
Version: 0.1.1
Author: Mariko Takagishi [aut, cre]
Maintainer: Mariko Takagishi <m.takagishi0728@gmail.com>
Description: Performing multiple-class cluster correspondence analysis(MCCCA). The main functions are create.MCCCAdata() to create a list to be applied to MCCCA, MCCCA() to apply MCCCA, and plot.mccca() for visualizing MCCCA result. Methods used in the package refers to Mariko Takagishi and Michel van de Velden (2022)<doi:10.1080/10618600.2022.2035737>.
License: GPL (>= 2)
Depends: R (>= 4.1.0)
Imports: magic, stringr, ggplot2, wordcloud, RColorBrewer, stats, utils, grDevices
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2022-09-06 07:35:12 UTC; takagishimariko
Repository: CRAN
Date/Publication: 2022-09-07 07:40:08 UTC

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New package eHDPrep with initial version 1.2.1
Package: eHDPrep
Title: Quality Control and Semantic Enrichment of Datasets
Version: 1.2.1
Maintainer: Ian Overton <I.Overton@qub.ac.uk>
Description: A tool for the preparation and enrichment of health datasets for analysis. Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: ggplot2 (>= 3.3.3), dplyr (>= 1.0.3), forcats (>= 0.5.0), stringr (>= 1.4.0), purrr (>= 0.3.4), tidyr (>= 1.1.2), kableExtra (>= 1.3.1), magrittr (>= 2.0.1), tibble (>= 3.0.5), scales (>= 1.1.1), rlang (>= 0.4.10), quanteda (>= 2.1.2), tm (>= 0.7-8), pheatmap (>= 1.0.12), igraph (>= 1.2.6), tidygraph (>= 1.2.0), readr (>= 1.4.0), readxl (>= 1.3.1), knitr (>= 1.31)
VignetteBuilder: knitr
Depends: R (>= 3.6.0)
Suggests: testthat (>= 2.1.0), ggraph (>= 2.0.5)
NeedsCompilation: no
Packaged: 2022-09-06 10:47:07 UTC; tom
Author: Tom Toner [aut] , Ian Overton [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-07 07:50:14 UTC

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New package BFS with initial version 0.4.3
Package: BFS
Title: Get Data from the Swiss Statistical Office
Version: 0.4.3
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Description: Search and download data from the Swiss Federal Statistical Office (BFS) <https://www.bfs.admin.ch/>.
License: MIT + file LICENSE
Depends: R (>= 3.0.1)
Imports: pxweb, jsonlite, xml2, rvest, tibble, magrittr, janitor, lifecycle, tidyRSS
Encoding: UTF-8
URL: https://felixluginbuhl.com/BFS/, https://github.com/lgnbhl/BFS/
BugReports: https://github.com/lgnbhl/BFS/issues
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-09-06 08:50:54 UTC; Admin
Author: Felix Luginbuhl [aut, cre]
Repository: CRAN
Date/Publication: 2022-09-07 07:50:21 UTC

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Tue, 06 Sep 2022

New package meconetcomp with initial version 0.1.0
Package: meconetcomp
Title: Compare Microbial Networks of 'trans_network' Class of 'microeco' Package
Version: 0.1.0
Author: Chi Liu [aut, cre], Minjie Yao [ctb], Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Description: Compare microbial co-occurrence networks created from 'trans_network' class of 'microeco' package <https://github.com/ChiLiubio/microeco>. This package is the extension of 'trans_network' class of 'microeco' package and especially useful when different networks are constructed and analyzed simultaneously.
URL: https://github.com/ChiLiubio/meconetcomp
Depends: R (>= 3.5.0)
Imports: microeco, magrittr, dplyr, igraph, reshape2
Suggests: rgexf, ape, file2meco
License: GPL-3
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-09-06 04:27:05 UTC; Chi
Repository: CRAN
Date/Publication: 2022-09-06 07:30:02 UTC

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New package luz with initial version 0.3.1
Package: luz
Title: Higher Level 'API' for 'torch'
Version: 0.3.1
Description: A high level interface for 'torch' providing utilities to reduce the the amount of code needed for common tasks, abstract away torch details and make the same code work on both the 'CPU' and 'GPU'. It's flexible enough to support expressing a large range of models. It's heavily inspired by 'fastai' by Howard et al. (2020) <arXiv:2002.04688>, 'Keras' by Chollet et al. (2015) and 'PyTorch Lightning' by Falcon et al. (2019) <doi:10.5281/zenodo.3828935>.
License: MIT + file LICENSE
URL: https://mlverse.github.io/luz/, https://github.com/mlverse/luz
Encoding: UTF-8
Imports: torch (>= 0.5.0), magrittr, zeallot, rlang, coro, glue, progress, R6, generics, purrr, ellipsis, fs, prettyunits, cli
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), covr, Metrics, withr, vdiffr, ggplot2, dplyr, torchvision
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-05 20:27:39 UTC; dfalbel
Author: Daniel Falbel [aut, cre, cph], RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Repository: CRAN
Date/Publication: 2022-09-06 07:10:02 UTC

More information about luz at CRAN
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