Thu, 13 Jan 2022

Package supercompress updated to version 1.1 with previous version 1.0 dated 2021-10-20

Title: Supervised Compression of Big Data
Description: A supervised compression method that incorporates the response for reducing big data to a carefully selected subset. Please see Joseph and Mak (2021) <doi:10.1002/sam.11508>. This research is supported by a U.S. National Science Foundation (NSF) grant CMMI-1921646.
Author: Chaofan Huang [aut, cre], V. Roshan Joseph [aut]
Maintainer: Chaofan Huang <chaofan.huang@gatech.edu>

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Package pedSimulate updated to version 1.3.1 with previous version 1.3.0 dated 2021-12-08

Title: Pedigree, Genetic Merit, Phenotype, and Genotype Simulation
Description: Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females. Genotypes can be simulated for a given pedigree, or an appended pedigree to an existing pedigree with genotypes. Bijma, P. & Rutten, M. (2002) <https://www.wur.nl/en/Research-Results/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genomics-Group/Research/Software.htm>.
Author: Mohammad Ali Nilforooshan [aut, cre] (<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>

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Package ActivePathways updated to version 1.0.4 with previous version 1.0.3 dated 2021-12-03

Title: Integrative Pathway Enrichment Analysis of Multivariate Omics Data
Description: Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The package is part of the following publication: Integrative Pathway Enrichment Analysis of Multivariate Omics Data. Paczkowska M^, Barenboim J^, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group; Reimand J, PCAWG Consortium. Nature Communications (2020) <doi:10.1038/s41467-019-13983-9>.
Author: Juri Reimand [aut, cre], Jonathan Barenboim [aut], Mykhaylo Slobodyanyuk [ctb]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>

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Package tidytable updated to version 0.6.7 with previous version 0.6.6 dated 2021-12-10

Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table' that is 'rlang' compatible, giving users the speed of 'data.table' with the clean syntax of the tidyverse.
Author: Mark Fairbanks [aut, cre], Abdessabour Moutik [ctb], Matt Carlson [ctb], Ivan Leung [ctb], Ross Kennedy [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>

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Package logr updated to version 1.2.8 with previous version 1.2.7 dated 2021-11-16

Title: Creates Log Files
Description: Contains functions to help create log files. The package aims to overcome the difficulty of the base R sink() command. The log_print() function will print to both the console and the file log, without interfering in other write operations.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>

Diff between logr versions 1.2.7 dated 2021-11-16 and 1.2.8 dated 2022-01-13

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Package jab.adverse.reactions updated to version 1.0.1 with previous version 1.0.0 dated 2022-01-12

Title: Possible Adverse Events/Reactions from the Vaccinations/Experimental Gene Therapies
Description: Provides data about the possible adverse events/reactions resulting from being injected with a vaccine/experimental gene therapy. Currently, this data set only includes information from six reference sources. Refer to the CITATION.cff file for the complete citations of the reference sources. For information about vaccination$/immunization$ hazards, visit <https://www.questionuniverse.com/rethink.html#vaccine>, <https://www.ecoccs.com/healing.html#vaccines>, <https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin>, and <https://www.questionuniverse.com/vaccination.html>.
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>

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Package fmcmc updated to version 0.5-1 with previous version 0.5-0 dated 2021-09-03

Title: A friendly MCMC framework
Description: Provides a friendly (flexible) Markov Chain Monte Carlo (MCMC) framework for implementing Metropolis-Hastings algorithm in a modular way allowing users to specify automatic convergence checker, personalized transition kernels, and out-of-the-box multiple MCMC chains using parallel computing. Most of the methods implemented in this package can be found in Brooks et al. (2011, ISBN 9781420079425). Among the methods included, we have: Haario (2001) <doi:10.1007/s11222-011-9269-5> Adaptive Metropolis, Vihola (2012) <doi:10.1007/s11222-011-9269-5> Robust Adaptive Metropolis, and Thawornwattana et al. (2018) <doi:10.1214/17-BA1084> Mirror transition kernels.
Author: George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Fabian Scheipl [rev] (JOSS reviewer, <https://orcid.org/0000-0001-8172-3603>)
Maintainer: George Vega Yon <g.vegayon@gmail.com>

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Package cpsurvsim updated to version 1.2.1 with previous version 1.2.0 dated 2020-01-20

Title: Simulating Survival Data from Change-Point Hazard Distributions
Description: Simulates time-to-event data with type I right censoring using two methods: the inverse CDF method and our proposed memoryless method. The latter method takes advantage of the memoryless property of survival and simulates a separate distribution between change-points. We include two parametric distributions: exponential and Weibull. Inverse CDF method draws on the work of Rainer Walke (2010), <https://www.demogr.mpg.de/papers/technicalreports/tr-2010-003.pdf>.
Author: Camille Hochheimer [aut, cre]
Maintainer: Camille Hochheimer <dochoch19@gmail.com>

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Package fmtr updated to version 1.5.5 with previous version 1.5.4 dated 2021-11-18

Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply formats to data frames or vectors. The package aims to provide to functionality similar to that of SAS® formats. Formats are assigned to the format attribute on data frame columns. Then when the fdata() function is called, a new data frame is created with the column data formatted as specified. The package also contains a value() function to create a user-defined format, similar to a SAS® user-defined format.
Author: David Bosak
Maintainer: David Bosak <dbosak01@gmail.com>

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Package bistablehistory updated to version 1.1.0 with previous version 1.0.0 dated 2021-09-28

Title: Cumulative History Analysis for Bistable Perception Time Series
Description: Estimates cumulative history for time-series for continuously viewed bistable perceptual rivalry displays. Computes cumulative history via a homogeneous first order differential process. I.e., it assumes exponential growth/decay of the history as a function time and perceptually dominant state, Pastukhov & Braun (2011) <doi:10.1167/11.10.12>. Supports Gamma, log normal, and normal distribution families. Provides a method to compute history directly and example of using the computation on a custom Stan code.
Author: Alexander Pastukhov [aut, cre] (<https://orcid.org/0000-0002-8738-8591>)
Maintainer: Alexander Pastukhov <pastukhov.alexander@gmail.com>

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Package Rcpp updated to version 1.0.8 with previous version 1.0.7 dated 2021-07-07

Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013, <doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018, <doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Inaki Ucar, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between Rcpp versions 1.0.7 dated 2021-07-07 and 1.0.8 dated 2022-01-13

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New package rGhanaCensus with initial version 0.1.0
Package: rGhanaCensus
Title: 2021 Ghana Population and Housing Census Results as Data Frames
Version: 0.1.0
Description: Datasets from the 2021 Ghana Population and Housing Census Results. Users can access results as 'tidyverse' and 'sf'-Ready Data Frames. The data in this package is scraped from pdf reports released by the Ghana Statistical Service website <https://census2021.statsghana.gov.gh/> . The package currently only contains datasets from the literacy and education reports. Namely, school attendance data for respondents aged 3 years and above.
License: MIT + file LICENSE
Encoding: UTF-8
Maintainer: Ama Owusu-Darko <aowusuda@asu.edu>
Depends: R (>= 3.5.0)
LazyData: true
Suggests: dplyr, knitr, magrittr, rmarkdown, sf, tmap
VignetteBuilder: knitr
URL: https://github.com/ktemadarko/rGhanaCensus
BugReports: https://github.com/ktemadarko/rGhanaCensus/issues
NeedsCompilation: no
Packaged: 2022-01-13 11:01:36 UTC; LENOVO
Author: Ama Owusu-Darko [cre, aut]
Repository: CRAN
Date/Publication: 2022-01-13 20:02:43 UTC

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Package renv updated to version 0.15.1 with previous version 0.15.0 dated 2022-01-04

Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre], RStudio, PBC [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>

Diff between renv versions 0.15.0 dated 2022-01-04 and 0.15.1 dated 2022-01-13

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New package PTSR with initial version 0.1.0
Package: PTSR
Date: 2022-01-13
Title: Positive Time Series Regression
Version: 0.1.0
Depends: R (>= 4.0.0)
Imports: extraDistr, SuppDists, actuar, numDeriv
Description: A collection of functions to simulate, estimate and forecast a wide range of regression based dynamic models for positive time series. This package implements the results presented in Prass, T.S.; Carlos, J.H.; Taufemback, C.G. and Pumi, G. (2022). "Positive Time Series Regression" <arXiv:2201.03667>.
License: GPL (>= 3)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-01-13 14:42:24 UTC; Taiane
Author: Taiane Schaedler Prass [aut, cre, com] (<https://orcid.org/0000-0003-3136-909X>), Jonas Hendler Carlos [aut], Cleiton Guollo Taufemback [aut]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Repository: CRAN
Date/Publication: 2022-01-13 20:22:45 UTC

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New package PoissonMultinomial with initial version 1.0
Package: PoissonMultinomial
Title: The Poisson-Multinomial Distribution
Version: 1.0
Date: 2022-01-12
Maintainer: Yili Hong <yilihong@vt.edu>
Description: Implementation of the exact, normal approximation, and simulation-based methods for computing the probability mass function (pmf) and cumulative distribution function (cdf) of the Poisson-Multinomial distribution, together with a random number generator for the distribution. The exact method is based on multi-dimensional fast Fourier transformation (FFT) of the characteristic function of the Poisson-Multinomial distribution. The normal approximation method uses a multivariate normal distribution to approximate the pmf of the distribution based on central limit theorem. The simulation method is based on the law of large numbers. Details about the methods are available in Lin, Wang, and Hong (2022) <arXiv:2201.04237>.
License: GPL (>= 2)
Encoding: UTF-8
Imports: mvtnorm, Rcpp
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: fftw3(>=3.3)
NeedsCompilation: yes
Packaged: 2022-01-13 13:23:10 UTC; yilih
Author: Yili Hong [aut, cre], Zhengzhi Lin [aut, ctb], Yueyao Wang [aut, ctb], Florian Junge [aut, ctb]
Repository: CRAN
Date/Publication: 2022-01-13 20:22:42 UTC

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Package MPSEM updated to version 0.4-1 with previous version 0.3-6 dated 2019-06-03

Title: Modeling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Author: Guillaume Guenard, with contribution from Pierre Legendre
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>

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New package longmixr with initial version 1.0.0
Package: longmixr
Title: Longitudinal Consensus Clustering with 'flexmix'
Version: 1.0.0
Description: An adaption of the consensus clustering approach from 'ConsensusClusterPlus' for longitudinal data. The longitudinal data is clustered with flexible mixture models from 'flexmix', while the consensus matrices are hierarchically clustered as in 'ConsensusClusterPlus'. By using the flexibility from 'flexmix' and 'FactoMineR', one can use mixed data types for the clustering.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
URL: https://cellmapslab.github.io/longmixr/
BugReports: https://github.com/cellmapslab/longmixr/issues
Depends: R (>= 3.5.0)
biocViews:
Imports: checkmate, ConsensusClusterPlus, graphics, grDevices, flexmix, StatMatch, stats, utils
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, ggplot2, ggalluvial, FactoMineR, factoextra, lme4, purrr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-01-13 15:26:02 UTC; jonas_hagenberg
Author: Jonas Hagenberg [aut, cre] (<https://orcid.org/0000-0002-1849-1106>), Matt Wilkerson [aut, cph], Peter Waltman [aut, cph], Max Planck Institute of Psychiatry [cph]
Maintainer: Jonas Hagenberg <jonas_hagenberg@psych.mpg.de>
Repository: CRAN
Date/Publication: 2022-01-13 20:32:42 UTC

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New package TSLSTM with initial version 0.1.0
Package: TSLSTM
Title: Long Short Term Memory (LSTM) Model for Time Series Forecasting
Version: 0.1.0
Author: Dr. Ranjit Kumar Paul [aut, cre], Dr. Md Yeasin [aut]
Maintainer: Dr. Ranjit Kumar Paul <ranjitstat@gmail.com>
Description: The LSTM (Long Short-Term Memory) model is a Recurrent Neural Network (RNN) based architecture that is widely used for time series forecasting. Min-Max transformation has been used for data preparation. Here, we have used one LSTM layer as a simple LSTM model and a Dense layer is used as the output layer. Then, compile the model using the loss function, optimizer and metrics. This package is based on Keras and TensorFlow modules and the algorithm of Paul and Garai (2021) <doi:10.1007/s00500-021-06087-4>.
License: GPL-3
Encoding: UTF-8
Imports: keras, tensorflow, tsutils, stats
NeedsCompilation: no
Packaged: 2022-01-10 07:16:32 UTC; YEASIN
Repository: CRAN
Date/Publication: 2022-01-13 19:12:41 UTC

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Package pkgdown updated to version 2.0.2 with previous version 2.0.1 dated 2021-12-03

Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Jay Hesselberth [aut] (<https://orcid.org/0000-0002-6299-179X>), Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package ecce updated to version 1.0.8 with previous version 1.0.7 dated 2020-06-29

Title: Translate English Words into Chinese, or Translate Chinese Words into English
Description: If translate English words into Chinese, there is a faster way for R user. 'RYoudaoTranslate' package provides interface to 'Youdao' <http://youdao.com/> translation open API for R user. 'entcn' package also provides similar features. But it does not support Chinese words translation into English, I have made some improvements on the basis of this software. You can pass in a words or a vector consisting of multiple words, ecce package support both English and Chinese translation. It also support browse translation results in website.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>

Diff between ecce versions 1.0.7 dated 2020-06-29 and 1.0.8 dated 2022-01-13

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More information about ecce at CRAN
Permanent link

New package CondiS with initial version 0.1.1
Package: CondiS
Title: Censored Data Imputation for Direct Modeling
Version: 0.1.1
Description: Impute the survival times for censored observations based on their conditional survival distributions derived from the Kaplan-Meier estimator. 'CondiS' can replace the censored observations with the best approximations from the statistical model, allowing for direct application of machine learning-based methods. When covariates are available, 'CondiS' is extended by incorporating the covariate information through machine learning-based regression modeling ('CondiS_X'), which can further improve the imputed survival time.
License: GPL-2
Encoding: UTF-8
Depends: R (>= 3.6)
Imports: caret, survival, kernlab, purrr, tidyverse, survminer
NeedsCompilation: no
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Packaged: 2022-01-13 07:32:40 UTC; YWang70
Author: Yizhuo Wang [aut, cre] (<https://orcid.org/0000-0002-1870-0019>), Ziyi Li [aut], Xuelin Huang [aut], Christopher Flowers [ctb]
Maintainer: Yizhuo Wang <ywang70@mdanderson.org>
Repository: CRAN
Date/Publication: 2022-01-13 19:32:44 UTC

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Package PlaneGeometry updated to version 1.3.1 with previous version 1.3.0 dated 2021-12-23

Title: Plane Geometry
Description: An extensive set of plane geometry routines. Provides R6 classes representing triangles, circles, circular arcs, ellipses, elliptical arcs and lines, and their plot methods. Also provides R6 classes representing transformations: rotations, reflections, homotheties, scalings, general affine transformations, inversions, Möbius transformations.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

Diff between PlaneGeometry versions 1.3.0 dated 2021-12-23 and 1.3.1 dated 2022-01-13

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Permanent link

New package intRinsic with initial version 0.2.0
Package: intRinsic
Title: Likelihood-Based Intrinsic Dimension Estimators
Version: 0.2.0
Maintainer: Francesco Denti <francescodenti.personal@gmail.com>
Description: Provides functions to estimate the intrinsic dimension of a dataset via likelihood-based approaches. Specifically, the package implements the 'TWO-NN' and 'Gride' estimators and the 'Hidalgo' Bayesian mixture model. References: Allegra et al. (2020, <doi:10.1038/s41598-020-72222-0>); Denti et al. (2022+, <arXiv:2104.13832>); Facco et al. (2017, <doi:10.1038/s41598-017-11873-y>); Santos-Fernandez et al. (2021, <arXiv:1902.10459>).
License: MIT + file LICENSE
URL: https://github.com/Fradenti/intRinsic
Depends: R (>= 3.6.0)
Imports: dplyr, FNN, ggplot2, knitr, MCMCpack, pheatmap, Rcpp, reshape2, rlang, salso, stats, utils
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
ByteCompile: true
Encoding: UTF-8
Packaged: 2022-01-13 04:50:14 UTC; francescodenti
Author: Francesco Denti [aut, cre, cph] (<https://orcid.org/0000-0003-2978-4702>), Andrea Gilardi [aut] (<https://orcid.org/0000-0002-9424-7439>)
Repository: CRAN
Date/Publication: 2022-01-13 18:52:42 UTC

More information about intRinsic at CRAN
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New package inlpubs with initial version 1.0.2
Package: inlpubs
Title: USGS INL Project Office Publications
Version: 1.0.2
Description: Contains bibliographic information for the U.S. Geological Survey (USGS) Idaho National Laboratory (INL) Project Office.
Depends: R (>= 3.6.0)
Imports: checkmate, stats, tm
Suggests: covr, DT, graphics, inlmisc, kableExtra, knitr, pkgdown, rmarkdown, RWeka, stringi, textutils, testthat, tools, usethis, utils
License: CC0
URL: https://code.usgs.gov/inl/inlpubs
BugReports: https://code.usgs.gov/inl/inlpubs/-/issues
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits
Encoding: UTF-8
VignetteBuilder: knitr
SystemRequirements: Package vignettes require pandoc (https://pandoc.org/) and phantomjs (https://phantomjs.org/). Text mining using n-grams requires Amazon Corretto (https://aws.amazon.com/corretto/).
BuildVignettes: true
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2022-01-13 03:15:51 UTC; jfisher
Author: Jason C. Fisher [aut, cre] (<https://orcid.org/0000-0001-9032-8912>)
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Repository: CRAN
Date/Publication: 2022-01-13 18:52:46 UTC

More information about inlpubs at CRAN
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New package gnrprod with initial version 1.0.0
Package: gnrprod
Title: Estimates Gross Output Functions
Version: 1.0.0
Author: David Jin [aut, cre]
Maintainer: David Jin <djin6817@gmail.com>
Description: Estimation of gross output production functions and productivity in the presence of numerous fixed (nonflexible) and a single flexible input using the nonparametric identification strategy specified in Gandhi, Navarro, and Rivers (2020) <doi:10.1086/707736>. Monte Carlo evidence from the paper demonstrates high performance in estimating production function elasticities.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: base, data.table, stats
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-01-12 22:10:29 UTC; David Jin
Repository: CRAN
Date/Publication: 2022-01-13 18:42:43 UTC

More information about gnrprod at CRAN
Permanent link

Package mlt.docreg updated to version 1.1-3 with previous version 1.1-2 dated 2021-12-16

Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt.docreg versions 1.1-2 dated 2021-12-16 and 1.1-3 dated 2022-01-13

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More information about mlt.docreg at CRAN
Permanent link

Package mixKernel updated to version 0.8 with previous version 0.7 dated 2021-06-15

Title: Omics Data Integration Using Kernel Methods
Description: Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel aims at providing methods to combine kernel for unsupervised exploratory analysis. Different solutions are provided to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view. Functions to assess and display important variables are also provided in the package. Ref: Jerome Mariette and Nathalie Villa-Vialaneix (2018) <doi:10.1093/bioinformatics/btx682>.
Author: Jerome Mariette [aut, cre], Celine Brouard [aut], Remi Flamary [aut], Nathalie Vialaneix [aut]
Maintainer: Jerome Mariette <jerome.mariette@inrae.fr>

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Package zCompositions updated to version 1.4.0 with previous version 1.3.4 dated 2020-03-04

Title: Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
Description: Principled methods for the imputation of zeros, left-censored and missing data in compositional data sets (Palarea-Albaladejo and Martin-Fernandez (2015) <doi:10.1016/j.chemolab.2015.02.019>).
Author: Javier Palarea-Albaladejo [cre, aut] (<https://orcid.org/0000-0003-0162-669X>), Josep Antoni Martin-Fernandez [aut] (<https://orcid.org/0000-0003-2366-1592>)
Maintainer: Javier Palarea-Albaladejo <javier.palarea@udg.edu>

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Package SEMID updated to version 0.4.0 with previous version 0.3.2 dated 2019-05-21

Title: Identifiability of Linear Structural Equation Models
Description: Provides routines to check identifiability or non-identifiability of linear structural equation models as described in Drton, Foygel, and Sullivant (2011) <doi:10.1214/10-AOS859>, Foygel, Draisma, and Drton (2012) <doi:10.1214/12-AOS1012>, and other works. The routines are based on the graphical representation of structural equation models.
Author: Rina Foygel Barber [aut], Mathias Drton [aut], Luca Weihs [aut], Nils Sturma [cre, aut]
Maintainer: Nils Sturma <nils.sturma@tum.de>

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Package nngeo updated to version 0.4.5 with previous version 0.4.4 dated 2021-09-06

Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C code from 'GeographicLib' for lon-lat point layers, (2) function knn() from package 'nabor' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers. The package also includes several other utility functions for spatial analysis.
Author: Michael Dorman [aut, cre], Johnathan Rush [ctb], Ian Hough [ctb], Dominic Russel [ctb], Luigi Ranghetti [ctb], Attilio Benini [ctb], Arnaud Tarroux [ctb], Charles F.F Karney [ctb, cph] (Author of included C code from 'GeographicLib' for geodesic distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>

Diff between nngeo versions 0.4.4 dated 2021-09-06 and 0.4.5 dated 2022-01-13

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Permanent link

Package bpp updated to version 1.0.4 with previous version 1.0.3 dated 2021-11-30

Title: Computations Around Bayesian Predictive Power
Description: Implements functions to update Bayesian Predictive Power Computations after not stopping a clinical trial at an interim analysis. Such an interim analysis can either be blinded or unblinded. Code is provided for Normally distributed endpoints with known variance, with a prominent example being the hazard ratio.
Author: Kaspar Rufibach, Paul Jordan, Markus Abt
Maintainer: Kaspar Rufibach <kaspar.rufibach@roche.com>

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Package bliss updated to version 1.0.3 with previous version 1.0.2 dated 2021-05-17

Title: Bayesian Functional Linear Regression with Sparse Step Functions
Description: A method for the Bayesian functional linear regression model (scalar-on-function), including two estimators of the coefficient function and an estimator of its support. A representation of the posterior distribution is also available. Grollemund P-M., Abraham C., Baragatti M., Pudlo P. (2019) <doi:10.1214/18-BA1095>.
Author: Paul-Marie Grollemund [aut, cre], Isabelle Sanchez [ctr], Meili Baragatti [ctr]
Maintainer: Paul-Marie Grollemund <paul.marie.grollemund@gmail.com>

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Package mapsapi updated to version 0.5.3 with previous version 0.5.0 dated 2021-09-06

Title: 'sf'-Compatible Interface to 'Google Maps' APIs
Description: Interface to the 'Google Maps' APIs: (1) routing directions based on the 'Directions' API, returned as 'sf' objects, either as single feature per alternative route, or a single feature per segment per alternative route; (2) travel distance or time matrices based on the 'Distance Matrix' API; (3) geocoded locations based on the 'Geocode' API, returned as 'sf' objects, either points or bounds; (4) map images using the 'Maps Static' API, returned as 'stars' objects.
Author: Michael Dorman [aut, cre], Tom Buckley [ctb], Alex Dannenberg [ctb], Mihir Bhaskar [ctb], Juan P. Fonseca-Zamora [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>

Diff between mapsapi versions 0.5.0 dated 2021-09-06 and 0.5.3 dated 2022-01-13

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Package terra updated to version 1.5-12 with previous version 1.4-22 dated 2021-11-24

Title: Spatial Data Analysis
Description: Methods for spatial data analysis with raster and vector data. Raster methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is very similar to the 'raster' package; but 'terra' can do more, is easier to use, and it is faster.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>), Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>), Jacob van Etten [ctb] (<https://orcid.org/0000-0001-7554-2558>), Karl Forner [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

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Package Rogue updated to version 2.1.0 with previous version 2.0.0 dated 2021-09-13

Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between Rogue versions 2.0.0 dated 2021-09-13 and 2.1.0 dated 2022-01-13

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Package RClickhouse updated to version 0.6.0 with previous version 0.5.2 dated 2020-03-06

Title: A 'DBI' Interface to the 'Yandex Clickhouse' Database Providing Basic 'dplyr' Support
Description: 'Yandex Clickhouse' (<https://clickhouse.com/>) is a high-performance relational column-store database to enable big data exploration and 'analytics' scaling to petabytes of data. Methods are provided that enable working with 'Yandex Clickhouse' databases via 'DBI' methods and using 'dplyr'/'dbplyr' idioms.
Author: Christian Hotz-Behofsits [aut, cre], Daniel Winkler [aut], Luca Rauchenberger [aut], Peter Knaus [aut], Clemens Danninger [aut], Simon Stiebellehner [aut], Dan Egnor [aut], Vlad Losev [aut], Keith Ray [aut], Zhanyong Wan [aut], Markus Heule [aut], Oliver Flasch [aut], Google [cph], Yann Collet [cph]
Maintainer: Christian Hotz-Behofsits <christian.hotz-behofsits@wu.ac.at>

Diff between RClickhouse versions 0.5.2 dated 2020-03-06 and 0.6.0 dated 2022-01-13

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Package nlme updated to version 3.1-155 with previous version 3.1-153 dated 2021-09-07

Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>

Diff between nlme versions 3.1-153 dated 2021-09-07 and 3.1-155 dated 2022-01-13

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Package mlr3measures updated to version 0.4.1 with previous version 0.4.0 dated 2021-09-26

Title: Performance Measures for 'mlr3'
Description: Implements multiple performance measures for supervised learning. Includes over 40 measures for regression and classification. Additionally, meta information about the performance measures can be queried, e.g. what the best and worst possible performances scores are.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Martin Binder [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3measures versions 0.4.0 dated 2021-09-26 and 0.4.1 dated 2022-01-13

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More information about mlr3measures at CRAN
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Package foreign updated to version 0.8-82 with previous version 0.8-81 dated 2020-12-22

Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre], Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Michael Nelson [ctb], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>

Diff between foreign versions 0.8-81 dated 2020-12-22 and 0.8-82 dated 2022-01-13

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Package deaR updated to version 1.2.5 with previous version 1.2.4 dated 2021-11-16

Title: Conventional and Fuzzy Data Envelopment Analysis
Description: Set of functions for Data Envelopment Analysis. It runs both classic and fuzzy DEA models.See: Banker, R.; Charnes, A.; Cooper, W.W. (1984). <doi:10.1287/mnsc.30.9.1078>, Charnes, A.; Cooper, W.W.; Rhodes, E. (1978). <doi:10.1016/0377-2217(78)90138-8> and Charnes, A.; Cooper, W.W.; Rhodes, E. (1981). <doi:10.1287/mnsc.27.6.668>.
Author: Vicente Coll-Serrano, Vicente Bolos, Rafael Benitez Suarez <rabesua@uv.es>
Maintainer: Vicente Bolos <vicente.bolos@uv.es>

Diff between deaR versions 1.2.4 dated 2021-11-16 and 1.2.5 dated 2022-01-13

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Package chirps updated to version 0.1.4 with previous version 0.1.2 dated 2020-07-13

Title: API Client for CHIRPS and CHIRTS
Description: API Client for the Climate Hazards Center 'CHIRPS' and 'CHIRTS'. The 'CHIRPS' data is a quasi-global (50°S – 50°N) high-resolution (0.05 arc-degrees) rainfall data set, which incorporates satellite imagery and in-situ station data to create gridded rainfall time series for trend analysis and seasonal drought monitoring. 'CHIRTS' is a quasi-global (60°S – 70°N), high-resolution data set of daily maximum and minimum temperatures. For more details on 'CHIRPS' and 'CHIRTS' data please visit its official home page <https://www.chc.ucsb.edu/data>.
Author: Kauê de Sousa [aut, cre] (<https://orcid.org/0000-0002-7571-7845>), Adam H. Sparks [aut] (<https://orcid.org/0000-0002-0061-8359>), Aniruddha Ghosh [aut] (<https://orcid.org/0000-0003-3667-8019>), Pete Peterson [ctb] (API Client implementation), William Ashmall [ctb] (API Client implementation), Jacob van Etten [ths] (<https://orcid.org/0000-0001-7554-2558>), Svein Ø. Solberg [ths] (<https://orcid.org/0000-0002-4491-4483>)
Maintainer: Kauê de Sousa <kaue.desousa@inn.no>

Diff between chirps versions 0.1.2 dated 2020-07-13 and 0.1.4 dated 2022-01-13

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Package tabshiftr updated to version 0.3.2 with previous version 0.3.0 dated 2021-07-01

Title: Reshape Disorganised Messy Data
Description: Helps the user to build and register schema descriptions of disorganised (messy) tables. Disorganised tables are tables that are not in a topologically coherent form, where packages such as 'tidyr' could be used for reshaping. The schema description documents the arrangement of input tables and is used to reshape them into a standardised (tidy) output format.
Author: Steffen Ehrmann [aut, cre] (<https://orcid.org/0000-0002-2958-0796>), Carsten Meyer [aut] (<https://orcid.org/0000-0003-3927-5856>), Abdualmaged Alhemiary [ctb], Amelie Haas [ctb], Annika Ertel [ctb], Arne Rümmler [ctb] (<https://orcid.org/0000-0001-8637-9071>), Caroline Busse [ctb], Tsvetelina Tomova [ctb]
Maintainer: Steffen Ehrmann <steffen@funroll-loops.de>

Diff between tabshiftr versions 0.3.0 dated 2021-07-01 and 0.3.2 dated 2022-01-13

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Package ReDaMoR updated to version 0.5.2 with previous version 0.4.3 dated 2020-12-14

Title: Relational Data Modeler
Description: The aim of this package is to manipulate relational data models in R. It provides functions to create, modify and export data models in json format. It also allows importing models created with 'MySQL Workbench' (<https://www.mysql.com/products/workbench/>). These functions are accessible through a graphical user interface made with 'shiny'. Constraints such as types, keys, uniqueness and mandatory fields are automatically checked and corrected when editing a model. Finally, real data can be confronted to a model to check their compatibility.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>

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Package htmldf updated to version 0.5.0 with previous version 0.4.0 dated 2021-08-17

Title: Simple Scraping and Tidy Webpage Summaries
Description: Simple tools for scraping webpages, extracting common html tags and parsing contents to a tidy, tabular format. Tools help with extraction of page titles, links, images, rss feeds, social media handles and page metadata.
Author: Alastair Rushworth
Maintainer: Alastair Rushworth <alastairmrushworth@gmail.com>

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Package highfrequency updated to version 0.9.2 with previous version 0.9.1 dated 2021-11-02

Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency trades and quotes data, calculate various liquidity measures, estimate and forecast volatility, detect price jumps and investigate microstructure noise and intraday periodicity.
Author: Kris Boudt [aut, cre] (<https://orcid.org/0000-0002-1000-5142>), Jonathan Cornelissen [aut], Scott Payseur [aut], Giang Nguyen [ctb], Onno Kleen [aut] (<https://orcid.org/0000-0003-4731-4640>), Emil Sjoerup [aut]
Maintainer: Kris Boudt <kris.boudt@ugent.be>

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Package dataverse updated to version 0.3.10 with previous version 0.3.9 dated 2021-07-26

Title: Client for Dataverse 4+ Repositories
Description: Provides access to Dataverse APIs <https://dataverse.org/> (versions 4-5), enabling data search, retrieval, and deposit. For Dataverse versions <= 3.0, use the archived 'dvn' package <https://cran.r-project.org/package=dvn>.
Author: Shiro Kuriwaki [aut, cre] (<https://orcid.org/0000-0002-5687-2647>), Will Beasley [aut] (<https://orcid.org/0000-0002-5613-5006>), Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>), Philip Durbin [aut] (<https://orcid.org/0000-0002-9528-9470>), Sebastian Karcher [aut] (<https://orcid.org/0000-0001-8249-7388>), Jan Kanis [ctb], Edward Jee [ctb]
Maintainer: Shiro Kuriwaki <shirokuriwaki@gmail.com>

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Package NNS updated to version 0.8.4.1 with previous version 0.8.4 dated 2022-01-12

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

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Package modelbased updated to version 0.7.1 with previous version 0.7.0 dated 2021-06-06

Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), used in the computation of marginal means, contrast analysis and predictions.
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>, @Dom_Makowski), Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>, @strengejacke), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>, @mattansb), Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

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Package hibayes updated to version 1.0.1 with previous version 1.0.0 dated 2021-12-10

Title: Individual-Level, Summary-Level and Single-Step Bayesian Regression Model
Description: A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including: (1) fixed effects and coefficients of covariates, (2) environmental random effects, and its corresponding variance, (3) genetic variance, (4) residual variance, (5) heritability, (6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals, (7) SNP effect size, (8) phenotype/genetic variance explained (PVE) for single or multiple SNPs, (9) posterior probability of association of the genomic window (WPPA), (10) posterior inclusive probability (PIP). The functions are not limited, we will keep on going in enriching it with more features. References: Meuwissen et al. (2001) <doi:10.1093/genetics/157.4.1819>; Gustavo et al. (2013) <doi:10.1534/genetics.112.143313>; Habier et al. (2011) <doi:10.1186/1471-2105-12-186>; Yi et al. (2008) <doi:10.1534/genetics.107.085589>; Zhou et al. (2013) <doi:10.1371/journal.pgen.1003264>; Moser et al. (2015) <doi:10.1371/journal.pgen.1004969>; Lloyd-Jones et al. (2019) <doi:10.1038/s41467-019-12653-0>; Henderson (1976) <doi:10.2307/2529339>; Fernando et al. (2014) <doi:10.1186/1297-9686-46-50>.
Author: Lilin Yin [aut, cre, cph], Haohao Zhang [aut, cph], Xiaolei Liu [aut, cph]
Maintainer: Lilin Yin <ylilin@163.com>

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Package roger updated to version 0.99-2 with previous version 0.99-1 dated 2021-10-20

Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R scripts. This is the R component of Roger the Omni Grader, an automated grading system for computer programming projects based on Unix shell scripts; see <https://gitlab.com/roger-project>. The package also provides an R interface to the shell scripts. Inspired by the lintr package.
Author: Vincent Goulet [aut, cre], Samuel Fréchette [aut], Jean-Christophe Langlois [aut], Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>

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Package CMplot updated to version 4.0.0 with previous version 3.7.0 dated 2021-10-20

Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out. Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>

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Package spatial updated to version 7.3-15 with previous version 7.3-14 dated 2021-05-03

Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph], Roger Bivand [ctb], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package sctransform updated to version 0.3.3 with previous version 0.3.2 dated 2020-12-16

Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction. See Hafemeister and Satija (2019) <doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2021) <doi:10.1101/2021.07.07.451498> for more details.
Author: Christoph Hafemeister [aut] (<https://orcid.org/0000-0001-6365-8254>), Saket Choudhary [aut, cre] (<https://orcid.org/0000-0001-5202-7633>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)
Maintainer: Saket Choudhary <schoudhary@nygenome.org>

Diff between sctransform versions 0.3.2 dated 2020-12-16 and 0.3.3 dated 2022-01-13

 DESCRIPTION                     |   37 ++-
 MD5                             |   46 ++--
 NAMESPACE                       |   13 +
 NEWS.md                         |   32 ++
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More information about sctransform at CRAN
Permanent link

New package powerjoin with initial version 0.0.1
Package: powerjoin
Title: Extensions of 'dplyr' and 'fuzzyjoin' Join Functions
Version: 0.0.1
Description: Extensions of 'dplyr' and 'fuzzyjoin' join functions. Packed with features to preprocess the data, apply various data checks, and deal with conflicting columns.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, generics, glue, rlang, tidyselect, vctrs, purrr, magrittr, lifecycle, tibble, tidyr, cli, methods
URL: https://github.com/moodymudskipper/powerjoin
BugReports: https://github.com/moodymudskipper/powerjoin/issues
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-01-13 00:28:11 UTC; Antoine
Author: Antoine Fabri [aut, cre], Hadley Wickham [ctb] (aut/cre of dplyr, <https://orcid.org/0000-0003-4757-117X>), Romain François [ctb] (aut of dplyr, <https://orcid.org/0000-0002-2444-4226>), David Robinson [ctb] (aut of fuzzyjoin), RStudio [cph, fnd] (cph/fnd dplyr)
Maintainer: Antoine Fabri <antoine.fabri@gmail.com>
Repository: CRAN
Date/Publication: 2022-01-13 08:52:43 UTC

More information about powerjoin at CRAN
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Package pomp updated to version 4.1 with previous version 3.6 dated 2021-09-03

Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre], Edward L. Ionides [aut], Carles Breto [aut], Stephen P. Ellner [ctb], Matthew J. Ferrari [ctb], Sebastian Funk [ctb], Steven G. Johnson [ctb], Bruce E. Kendall [ctb], Michael Lavine [ctb], Dao Nguyen [ctb], Eamon B. O'Dea [ctb], Daniel C. Reuman [ctb], Helen Wearing [ctb], Simon N. Wood [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>

Diff between pomp versions 3.6 dated 2021-09-03 and 4.1 dated 2022-01-13

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 143 files changed, 1857 insertions(+), 659 deletions(-)

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Package nnet updated to version 7.3-17 with previous version 7.3-16 dated 2021-05-03

Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between nnet versions 7.3-16 dated 2021-05-03 and 7.3-17 dated 2022-01-13

 DESCRIPTION |    8 +++----
 MD5         |    4 +--
 src/nnet.c  |   62 ++++++++++++++++++++++++++++++------------------------------
 3 files changed, 37 insertions(+), 37 deletions(-)

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Package neptune updated to version 0.2.0 with previous version 0.1.2 dated 2021-01-11

Title: Interface to 'Neptune' Experiment Tracking and Management Tool
Description: Interface to 'Neptune', experiment tracking tool that helps you organize your machine learning experiments. You can log your hyperparameter, metrics, model binaries and performance charts, organize them with tags and names and share everything easily in the app. For more information see <https://neptune.ai/>.
Author: Mateusz Dominiak [aut], Rafal Jankowski [aut, cre]
Maintainer: Rafal Jankowski <rafal.jankowski@neptune.ai>

Diff between neptune versions 0.1.2 dated 2021-01-11 and 0.2.0 dated 2022-01-13

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Package MASS updated to version 7.3-55 with previous version 7.3-54 dated 2021-05-03

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between MASS versions 7.3-54 dated 2021-05-03 and 7.3-55 dated 2022-01-13

 DESCRIPTION                      |   10 +++++-----
 MD5                              |   14 +++++++-------
 R/area.R                         |    2 +-
 build/partial.rdb                |binary
 inst/po/de/LC_MESSAGES/R-MASS.mo |binary
 po/R-de.po                       |    8 ++++----
 src/MASS.c                       |   36 ++++++++++++++++++------------------
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 8 files changed, 37 insertions(+), 36 deletions(-)

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New package gittargets with initial version 0.0.1
Package: gittargets
Title: Data Version Control for the Targets Package
Description: Pipelines with the 'targets' R package (2021, <doi:10.21105/joss.02959>) skip steps that are up to already date. Although this behavior reduces the runtime of subsequent runs, it comes at the cost of overwriting previous results. So if the pipeline source code is under version control, and if you revert to a previous commit or branch, the data will no longer be up to date with the code you just checked out. Ordinarily, you would need to rerun the pipeline in order to recover the targets you had before. However, 'gittargets' preserves historical output, creating version control snapshots of data store. Each data snapshot remembers the contemporaneous Git commit of the pipeline source code, so you can recover the right data when you navigate the Git history. In other words, 'gittargets' makes it possible to switch commits or branches without invalidating the pipeline. You can simply check out the up-to-date targets from the past instead of taking the time to recompute them from scratch.
Version: 0.0.1
License: MIT + file LICENSE
URL: https://docs.ropensci.org/gittargets/, https://github.com/ropensci/gittargets
BugReports: https://github.com/ropensci/gittargets/issues
Depends: R (>= 3.5.0)
Imports: cli (>= 3.1.0), data.table (>= 1.12.8), gert (>= 1.0.0), processx (>= 3.0.0), stats, targets (>= 0.6.0), tibble (>= 3.0.0), utils, uuid (>= 0.1.4)
Suggests: knitr (>= 1.30), markdown (>= 1.1), rmarkdown (>= 2.4), testthat (>= 3.0.0)
SystemRequirements: Git (>= 2.0.0)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-01-12 15:16:25 UTC; c240390
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Saras Windecker [rev], David Neuzerling [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Repository: CRAN
Date/Publication: 2022-01-13 08:32:46 UTC

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Package class updated to version 7.3-20 with previous version 7.3-19 dated 2021-05-03

Title: Functions for Classification
Description: Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between class versions 7.3-19 dated 2021-05-03 and 7.3-20 dated 2022-01-13

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 src/class.c |   26 +++++++++++++-------------
 3 files changed, 19 insertions(+), 19 deletions(-)

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New package casabourse with initial version 0.1.0
Package: casabourse
Title: Casablanca Stock Exchange Data
Version: 0.1.0
Description: It provides real-time data from the Casablanca Stock Exchange. The objective is to facilitate access to data for all users of the R programming language. It includes a variety of data accessible just by function call.
License: GPL-2
URL: https://github.com/AODiakite, https://rpubs.com/AODiakite/casabourse
Encoding: UTF-8
Imports: gsheet, httr
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-01-12 22:01:26 UTC; abdouloudoussdiakite
Author: Abdoul Oudouss Diakité [aut, cre]
Maintainer: Abdoul Oudouss Diakité <abdouloudoussdiakite@gmail.com>
Repository: CRAN
Date/Publication: 2022-01-13 08:42:42 UTC

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New package acca with initial version 0.1
Package: acca
Version: 0.1
Date: 2022-01-01
Title: A Canonical Correlation Analysis with Inferential Guaranties
Author: Livio Finos
Maintainer: livio finos <livio.finos@unipd.it>
Description: It performs Canonical Correlation Analysis and provides inferential guaranties on the correlation components. The p-values are computed following the resampling method developed in Winkler, A. M., Renaud, O., Smith, S. M., & Nichols, T. E. (2020). Permutation inference for canonical correlation analysis. NeuroImage, <doi:10.1016/j.neuroimage.2020.117065>. Furthermore, it provides plotting tools to visualize the results.
Encoding: UTF-8
License: GPL (>= 2)
Imports: methods, stats, ggplot2, plyr
NeedsCompilation: no
Packaged: 2022-01-12 21:18:33 UTC; livio
Repository: CRAN
Date/Publication: 2022-01-13 08:42:45 UTC

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Package ufRisk updated to version 1.0.1 with previous version 1.0.0 dated 2022-01-11

Title: Risk Measure Calculation in Financial TS
Description: Enables the user to calculate Value at Risk (VaR) and Expected Shortfall (ES) by means of various parametric and semiparametric GARCH-type models. For the latter the estimation of the nonparametric scale function is carried out by means of a data-driven smoothing approach. Model quality, in terms of forecasting VaR and ES, can be assessed by means of various backtesting methods such as the traffic light test for VaR and a newly developed traffic light test for ES. The approaches implemented in this package are described in e.g. Feng Y., Beran J., Letmathe S. and Ghosh S. <https://ideas.repec.org/p/pdn/ciepap/137.html> as well as Letmathe S., Feng Y. and Uhde A. (2021) <https://ideas.repec.org/p/pdn/ciepap/141.html>.
Author: Yuanhua Feng [aut] (Paderborn University, Germany), Xuehai Zhang [aut] (Ernst & Young, Germany), Christian Peitz [aut] (Paderborn University, Germany), Dominik Schulz [aut] (Paderborn University, Germany), Shujie Li [aut] (Paderborn Universtiy, Germany), Sebastian Letmathe [aut, cre] (Paderborn University, Germany)
Maintainer: Sebastian Letmathe <sebastian.letmathe@uni-paderborn.de>

Diff between ufRisk versions 1.0.0 dated 2022-01-11 and 1.0.1 dated 2022-01-13

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Package FunWithNumbers updated to version 1.1 with previous version 1.0 dated 2020-10-05

Title: Fun with Fractions and Number Sequences
Description: A collection of toys to do things like generate Collatz sequences, convert a fraction to "continued fraction" form, calculate a fraction which is a close approximation to some value (e.g., 22/7 or 355/113 for pi), and so on.
Author: Carl Witthoft
Maintainer: Carl Witthoft <carl@witthoft.com>

Diff between FunWithNumbers versions 1.0 dated 2020-10-05 and 1.1 dated 2022-01-13

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Package glacierSMBM (with last version 0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2017-09-28 0.1

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Package efts (with last version 0.9-0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-04-26 0.9-0

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Package ClimDown (with last version 1.0.8) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-06-25 1.0.8
2016-12-02 1.0.2

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