Tue, 27 Sep 2022

Package yakmoR (with last version 0.1.1) was removed from CRAN

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

2015-08-04 0.1.1
2015-08-03 0.1.0

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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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Package bootCT updated to version 1.1.1 with previous version 1.1 dated 2022-07-18

Title: Bootstrapping the ARDL Tests for Cointegration
Description: The bootstrap ARDL tests for cointegration is the main functionality of this package. It also acts as a wrapper of the most commond ARDL testing procedures for cointegration: the bound tests of Pesaran, Shin and Smith (PSS; 2001 - <doi:10.1002/jae.616>) and the asymptotic test on the independent variables of Sam, McNown and Goh (SMG: 2019 - <doi:10.1016/j.econmod.2018.11.001>). Bootstrap and bound tests are performed under both the conditional and unconditional ARDL models.
Author: Gianmarco Vacca, Stefano Bertelli
Maintainer: Gianmarco Vacca <gianmarco.vacca@unicatt.it>

Diff between bootCT versions 1.1 dated 2022-07-18 and 1.1.1 dated 2022-09-27

 DESCRIPTION          |   14 +++++++-------
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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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Package tinytex updated to version 0.42 with previous version 0.41 dated 2022-08-16

Title: Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] , RStudio, PBC [cph], Christophe Dervieux [ctb] , Devon Ryan [ctb] , Ethan Heinzen [ctb], Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between tinytex versions 0.41 dated 2022-08-16 and 0.42 dated 2022-09-27

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Package RPresto updated to version 1.4.0 with previous version 1.3.7 dated 2021-09-04

Title: DBI Connector to Presto
Description: Implements a 'DBI' compliant interface to Presto. Presto is an open source distributed SQL query engine for running interactive analytic queries against data sources of all sizes ranging from gigabytes to petabytes: <https://prestodb.io/>.
Author: Onur Ismail Filiz [aut], Sergey Goder [aut], Jarod G.R. Meng [aut, cre], Thomas J. Leeper [ctb], John Myles White [ctb]
Maintainer: Jarod G.R. Meng <jarodm@fb.com>

Diff between RPresto versions 1.3.7 dated 2021-09-04 and 1.4.0 dated 2022-09-27

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Package rocbc updated to version 0.1.1 with previous version 0.1.0 dated 2022-09-20

Title: Statistical Inference for Box-Cox Based Receiver Operating Characteristic Curves
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.
Author: Leonidas Bantis [aut], Benjamin Brewer [cre, ctb], Christos Nakas [ctb], Benjamin Reiser [ctb]
Maintainer: Benjamin Brewer <tennisbenj@gmail.com>

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Package migraph updated to version 0.12.0 with previous version 0.11.3 dated 2022-09-13

Title: Tools for Multimodal Network Analysis
Description: A set of tools for analysing multimodal networks. All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects, and on one-mode, two-mode (bipartite), and sometimes three-mode networks. It includes functions for measuring centrality, centralization, cohesion, closure, and constraint, as well as for network block-modelling and regression. The package is released as a complement to 'Multimodal Political Networks' (2021, ISBN:9781108985000), and includes various datasets used in the book in addition to other network data.
Author: James Hollway [cre, aut, ctb] , Jael Tan [ctb] , Bernhard Bieri [ctb] , Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>

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Package iheiddown updated to version 0.9.5 with previous version 0.9.3 dated 2022-05-13

Title: For Writing Geneva Graduate Institute Documents
Description: A set of tools for writing documents according to Geneva Graduate Institute conventions and regulations. The most common use is for writing and compiling theses or thesis chapters, as drafts or for examination with correct preamble formatting. However, the package also offers users to create HTML presentation slides with 'xaringan', complete problem sets, format posters, and, for course instructors, prepare a syllabus. The package includes additional functions for institutional color palettes, an institutional 'ggplot' theme, a function for counting manuscript words, and a bibliographical analysis toolkit.
Author: James Hollway [aut, cre, cph] , Bernhard Bieri [ctb] , Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>

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Package IDSL.MXP updated to version 1.6 with previous version 1.5 dated 2022-07-07

Title: Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data)
Description: A tiny parser to extract mass spectra data and metadata table of MS acquisition properties from mzML, mzXML and netCDF mass spectrometry files.
Author: Sadjad Fakouri-Baygi [cre, aut] , Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>

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Package IDSL.IPA updated to version 2.3 with previous version 2.2 dated 2022-09-09

Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A sophisticated pipeline for processing LC/HRMS data to extract signals of organic compounds. The package performs isotope pairing, peak detection, alignment, RT correction, gap filling, peak annotation and visualization of extracted ion chromatograms (EIC) and total ion chromatograms (TIC).
Author: Sadjad Fakouri-Baygi [cre, aut] , Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>

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Package EFAtools updated to version 0.4.2 with previous version 0.4.1 dated 2022-04-24

Title: Fast and Flexible Implementations of Exploratory Factor Analysis Tools
Description: Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Author: Markus Steiner [aut, cre], Silvia Grieder [aut], William Revelle [ctb], Max Auerswald [ctb], Morten Moshagen [ctb], John Ruscio [ctb], Brendan Roche [ctb], Urbano Lorenzo-Seva [ctb], David Navarro-Gonzalez [ctb]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>

Diff between EFAtools versions 0.4.1 dated 2022-04-24 and 0.4.2 dated 2022-09-27

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Package shinymanager updated to version 1.0.410 with previous version 1.0.400 dated 2021-06-16

Title: Authentication Management for 'Shiny' Applications
Description: Simple and secure authentification mechanism for single 'Shiny' applications. Credentials are stored in an encrypted 'SQLite' database. Source code of main application is protected until authentication is successful.
Author: Benoit Thieurmel [aut, cre], Victor Perrier [aut]
Maintainer: Benoit Thieurmel <bthieurmel@gmail.com>

Diff between shinymanager versions 1.0.400 dated 2021-06-16 and 1.0.410 dated 2022-09-27

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Package rsprite2 updated to version 0.2.0 with previous version 0.1.0 dated 2021-09-22

Title: Identify Distributions that Match Reported Sample Parameters (SPRITE)
Description: The SPRITE algorithm creates possible distributions of discrete responses based on reported sample parameters, such as mean, standard deviation and range (Heathers et al., 2018, <doi:10.7287/peerj.preprints.26968v1>). This package implements it, drawing heavily on the code for Nick Brown's 'rSPRITE' Shiny app <https://shiny.ieis.tue.nl/sprite/>. In addition, it supports the modeling of distributions based on multi-item (Likert-type) scales and the use of restrictions on the frequency of particular responses.
Author: Lukas Wallrich [aut, cre] , Aurelien Allard [ctb]
Maintainer: Lukas Wallrich <lukas.wallrich@gmail.com>

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Package chameleon updated to version 0.2-3 with previous version 0.2-1 dated 2022-07-13

Title: Automatic Colors for Multi-Dimensional Data
Description: Assign distinct colors to arbitrary multi-dimensional data, considering its structure.
Author: Oren Ben-Kiki [aut, cre], Weizmann Institute of Science [cph]
Maintainer: Oren Ben-Kiki <oren@ben-kiki.org>

Diff between chameleon versions 0.2-1 dated 2022-07-13 and 0.2-3 dated 2022-09-27

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Package AGread (with last version 1.3.2) was removed from CRAN

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

2022-09-13 1.3.2

Permanent link

Mon, 26 Sep 2022

Package rsurveycto updated to version 0.1.0 with previous version 0.0.5 dated 2022-09-08

Title: Interact with Data on 'SurveyCTO'
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.
Author: Jake Hughey [aut, cre], Robert On [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>

Diff between rsurveycto versions 0.0.5 dated 2022-09-08 and 0.1.0 dated 2022-09-26

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Package roger updated to version 1.1-0 with previous version 1.0-0 dated 2022-08-25

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 Frechette [aut], Jean-Christophe Langlois [aut], Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>

Diff between roger versions 1.0-0 dated 2022-08-25 and 1.1-0 dated 2022-09-26

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Package ggcorrplot updated to version 0.1.4 with previous version 0.1.3 dated 2019-05-19

Title: Visualization of a Correlation Matrix using 'ggplot2'
Description: The 'ggcorrplot' package can be used to visualize easily a correlation matrix using 'ggplot2'. It provides a solution for reordering the correlation matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.
Author: Alboukadel Kassambara [aut, cre], Indrajeet Patil [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

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Package relSim updated to version 0.3-4 with previous version 0.3-3 dated 2022-09-15

Title: Relative Simulator
Description: A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved. The package also offers some useful tools for exploring other forensic DNA situations.
Author: James M. Curran
Maintainer: James M. Curran <j.curran@auckland.ac.nz>

Diff between relSim versions 0.3-3 dated 2022-09-15 and 0.3-4 dated 2022-09-26

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Package pagedown updated to version 0.19 with previous version 0.18 dated 2022-04-26

Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] , Romain Lesur [aut, cph] , Brent Thorne [aut] , Xianying Tan [aut] , Christophe Dervieux [ctb] , Atsushi Yasumoto [ctb] , RStudio, PBC [cph], Adam Hyde [ctb] , Min-Zhong Lu [ctb] , Zulko [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between pagedown versions 0.18 dated 2022-04-26 and 0.19 dated 2022-09-26

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Package flextable updated to version 0.8.2 with previous version 0.8.1 dated 2022-09-19

Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'PDF', 'Microsoft Word', 'Microsoft PowerPoint' documents from 'R Markdown' and as 'Grid Graphics' objects. Functions are provided to let users create tables, modify and format their content. It also extends package 'officer' that does not contain any feature for customized tabular reporting.
Author: David Gohel [aut, cre], Clementine Jager [ctb], Panagiotis Skintzos [aut], Quentin Fazilleau [ctb], Maxim Nazarov [ctb] , Titouan Robert [ctb], Michael Barrowman [ctb] , Atsushi Yasumoto [ctb] , Paul Julian [ctb] , Sean Browning [ctb] , Remi Theriaul [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>

Diff between flextable versions 0.8.1 dated 2022-09-19 and 0.8.2 dated 2022-09-26

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Package extrafrail updated to version 1.2 with previous version 1.1 dated 2022-08-06

Title: Estimation and Additional Tools for Alternative Shared Frailty Models
Description: Provide estimation and data generation tools for some new multivariate frailty models. This version includes the gamma, inverse Gaussian and weighted Lindley as the distribution for the frailty terms. For the basal model, it is considered a parametric approach based on the Weibull distribution and a semiparametric approach. For details, see Gallardo and Bourguignon (2022) <arXiv:2206.12973>.
Author: Diego Gallardo [aut, cre], Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>

Diff between extrafrail versions 1.1 dated 2022-08-06 and 1.2 dated 2022-09-26

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Package netrankr updated to version 1.2.0 with previous version 1.1.1 dated 2021-12-21

Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks. While the package includes the possibility to build more than 20 indices, its main focus lies on index-free assessment of centrality via partial rankings obtained by neighborhood-inclusion or positional dominance. These partial rankings can be analyzed with different methods, including probabilistic methods like computing expected node ranks and relative rank probabilities (how likely is it that a node is more central than another?). The methodology is described in depth in the vignettes and in Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre] , Julian Mueller [ctb]
Maintainer: David Schoch <david@schochastics.net>

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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

More information about highs at CRAN
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Package dttr2 updated to version 0.4.2 with previous version 0.4.1 dated 2022-08-26

Title: Manipulate Date, POSIXct and hms Vectors
Description: Manipulates date ('Date'), date time ('POSIXct') and time ('hms') vectors. Date/times are considered discrete and are floored whenever encountered. Times are wrapped and time zones are maintained unless explicitly altered by the user.
Author: Joe Thorley [aut] , Ayla Pearson [aut, cre] , Poisson Consulting [cph, fnd]
Maintainer: Ayla Pearson <ayla@poissonconsulting.ca>

Diff between dttr2 versions 0.4.1 dated 2022-08-26 and 0.4.2 dated 2022-09-26

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Package RCALI updated to version 0.3.4 with previous version 0.3.3 dated 2022-08-12

Title: Calculation of the Integrated Flow of Particles Between Polygons
Description: Calculate the flow of particles between polygons by two integration methods: integration by a cubature method and integration on a grid of points. Annie Bouvier, Kien Kieu, Kasia Adamczyk and Herve Monod (2009) <doi:10.1016/j.envsoft.2008.11.006>.
Author: Annie Bouvier [aut, cph], Kien Kieu [aut, cph], Kasia Adamczyk [aut, cph], Herve Monod [aut, cph], Jean-Francois Rey [cre]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>

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Package multidplyr updated to version 0.1.2 with previous version 0.1.1 dated 2021-12-01

Title: A Multi-Process 'dplyr' Backend
Description: Partition a data frame across multiple worker processes to provide simple multicore parallelism.
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package eatATA updated to version 1.1.0 with previous version 1.0.0 dated 2021-07-06

Title: Create Constraints for Small Test Assembly Problems
Description: Provides simple functions to create constraints for small test assembly problems (e.g. van der Linden (2005, ISBN: 978-0-387-29054-6)) using sparse matrices. Currently, 'GLPK', 'lpSolve', 'Symphony', and 'Gurobi' are supported as solvers. The 'gurobi' package is not available from any mainstream repository; see <https://www.gurobi.com/downloads/>.
Author: Benjamin Becker [aut, cre], Dries Debeer [aut]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>

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Package climatrends updated to version 0.4 with previous version 0.2 dated 2022-02-24

Title: Climate Variability Indices for Ecological Modelling
Description: Supports analysis of trends in climate change, ecological and crop modelling.
Author: Kaue de Sousa [aut, cre] , Jacob van Etten [ctb, ths] , Svein O. Solberg [ctb, ths]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>

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Package basemaps updated to version 0.0.5 with previous version 0.0.4 dated 2022-09-08

Title: Accessing Spatial Basemaps in R
Description: A lightweight package to access spatial basemaps from open sources such as 'OpenStreetMap', 'Carto', 'Mapbox' and others in R.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <dev@schwalb-willmann.de>

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Package webshot updated to version 0.5.4 with previous version 0.5.3 dated 2022-04-14

Title: Take Screenshots of Web Pages
Description: Takes screenshots of web pages, including Shiny applications and R Markdown documents.
Author: Winston Chang [aut, cre], Yihui Xie [ctb], Francois Guillem [ctb], Barret Schloerke [ctb], Nicolas Perriault [ctb]
Maintainer: Winston Chang <winston@rstudio.com>

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Package targets updated to version 0.13.5 with previous version 0.13.4 dated 2022-09-15

Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R, the 'targets' package brings together function-oriented programming and 'Make'-like declarative workflows. It analyzes the dependency relationships among the tasks of a workflow, skips steps that are already up to date, runs the necessary computation with optional parallel workers, abstracts files as R objects, and provides tangible evidence that the results match the underlying code and data. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre] , Matthew T. Warkentin [ctb], Mark Edmondson [ctb] , Samantha Oliver [rev] , Tristan Mahr [rev] , Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package survSpearman updated to version 1.0.1 with previous version 1.0.0 dated 2021-01-29

Title: Nonparametric Spearman's Correlation for Survival Data
Description: Nonparametric estimation of Spearman's rank correlation with bivariate survival (right-censored) data as described in Eden, S.K., Li, C., Shepherd B.E. (2021), Nonparametric Estimation of Spearman's Rank Correlation with Bivariate Survival Data, Biometrics (under revision). The package also provides functions that visualize bivariate survival data and bivariate probability mass function.
Author: Svetlana Eden [aut, cre], Chun Li [aut, anl], Bryan Shepherd [aut, anl]
Maintainer: Svetlana Eden <svetlana.k.eden.1@vumc.org>

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Package SIHR updated to version 1.1.0 with previous version 1.0.1 dated 2022-08-10

Title: Statistical Inference in High Dimensional Regression
Description: Inference procedures in the high-dimensional setting for (1) linear functionals in generalized linear regression ('Cai et al.' (2019) <arXiv:1904.12891>, 'Guo et al.' (2020) <arXiv:2012.07133>, 'Cai et al.' (2021)), (2) individual treatment effects in generalized linear regression, (3) quadratic functionals in generalized linear regression ('Guo et al.' (2019) <arXiv:1909.01503>).
Author: Prabrisha Rakshit, Zhenyu Wang, Tony Cai, Zijian Guo
Maintainer: Zijian Guo <zijguo@stat.rutgers.edu>

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Package shinytest2 updated to version 0.2.0 with previous version 0.1.1 dated 2022-09-06

Title: Testing for Shiny Applications
Description: Automated unit testing of Shiny applications through a headless 'Chromium' browser.
Author: Barret Schloerke [cre, aut] , RStudio [cph, fnd], Winston Chang [ctb] , Gabor Csardi [ctb] , Hadley Wickham [ctb] , Mango Solutions [cph, ccp]
Maintainer: Barret Schloerke <barret@rstudio.com>

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Package reactlog updated to version 1.1.1 with previous version 1.1.0 dated 2020-09-12

Title: Reactivity Visualizer for 'shiny'
Description: Building interactive web applications with R is incredibly easy with 'shiny'. Behind the scenes, 'shiny' builds a reactive graph that can quickly become intertwined and difficult to debug. 'reactlog' (Schloerke 2019) <doi:10.5281/zenodo.2591517> provides a visual insight into that black box of 'shiny' reactivity by constructing a directed dependency graph of the application's reactive state at any time point in a reactive recording.
Author: Barret Schloerke [aut, cre] , Joe Cheng [ctb], RStudio [cph, fnd]
Maintainer: Barret Schloerke <barret@rstudio.com>

Diff between reactlog versions 1.1.0 dated 2020-09-12 and 1.1.1 dated 2022-09-26

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Package micromapST updated to version 2.0.1 with previous version 2.0.0 dated 2022-08-20

Title: Linked Micromap Plots for U. S. and Other Geographic Areas
Description: Provides the users with the ability to quickly create linked micromap plots for a collection of geographic areas. Linked micromap plots are visualizations of geo-referenced data that link statistical graphics to an organized series of small maps or graphic images. The Help description contains examples of how to use the 'micromapST' function. Contained in this package are border group datasets to support creating linked micromap plots for the 50 U.S. states and District of Columbia (51 areas), the U. S. 20 Seer Registries, the 105 counties in the state of Kansas, the 62 counties of New York, the 24 counties of Maryland, the 29 counties of Utah, the 32 administrative areas in China, the 218 administrative areas in the UK and Ireland (for testing only), the 25 districts in the city of Seoul South Korea, and the 52 counties on the Africa continent. A border group dataset contains the boundaries related to the data level areas, a second layer boundaries, a top or third layer boundary, a pa [...truncated...]
Author: Jim Pearson [aut, cre, cph], Dan Carr [aut, cph], Linda Pickle [ctb, cph]
Maintainer: Jim Pearson <jbpearson353@gmail.com>

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Package rdecision updated to version 1.1.3 with previous version 1.1.2 dated 2022-09-07

Title: Decision Analytic Modelling in Health Economics
Description: Classes and functions for modelling health care interventions using decision trees and semi-Markov models. Mechanisms are provided for associating an uncertainty distribution with each source variable and for ensuring transparency of the mathematical relationships between variables. The package terminology follows Briggs "Decision Modelling for Health Economic Evaluation" (2006, ISBN:978-0-19-852662-9).
Author: Andrew Sims [aut, cre] , Kim Fairbairn [aut] , Paola Cognigni [aut]
Maintainer: Andrew Sims <andrew.sims@newcastle.ac.uk>

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Package MCM updated to version 0.1.7 with previous version 0.1.6 dated 2022-09-25

Title: Estimating and Testing Intergenerational Social Mobility Effect
Description: Estimate and test inter-generational social mobility effect on an outcome with cross-sectional or longitudinal data.
Author: Jiahui Xu [aut, cre], Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>

Diff between MCM versions 0.1.6 dated 2022-09-25 and 0.1.7 dated 2022-09-26

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Package fso updated to version 2.1-2 with previous version 2.1-1 dated 2018-06-01

Title: Fuzzy Set Ordination
Description: Fuzzy set ordination is a multivariate analysis used in ecology to relate the composition of samples to possible explanatory variables. While differing in theory and method, in practice, the use is similar to 'constrained ordination.' The package contains plotting and summary functions as well as the analyses.
Author: David W. Roberts <droberts@montana.edu>
Maintainer: David W. Roberts <droberts@montana.edu>

Diff between fso versions 2.1-1 dated 2018-06-01 and 2.1-2 dated 2022-09-26

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Package comorbidity updated to version 1.0.5 with previous version 1.0.3 dated 2022-07-12

Title: Computing Comorbidity Scores
Description: Computing comorbidity indices and scores such as the weighted Charlson score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>) using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>). Australian and Swedish modifications of the Charlson Comorbidity Index are available as well (Sundararajan, 2004 <doi:10.1016/j.jclinepi.2004.03.012> and Ludvigsson, 2021 <doi:10.2147/CLEP.S282475>).
Author: Alessandro Gasparini [aut, cre] , Hojjat Salmasian [ctb] , Jonathan Williman [ctb] , Sing Yi Chia [ctb] , Edmund Teo [ctb]
Maintainer: Alessandro Gasparini <alessandro@ellessenne.xyz>

Diff between comorbidity versions 1.0.3 dated 2022-07-12 and 1.0.5 dated 2022-09-26

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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

More information about tmod at CRAN
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Package shorts updated to version 2.1.0 with previous version 2.0.0 dated 2022-07-07

Title: Short Sprints
Description: Create short sprint (<6sec) profiles using the split times or the radar gun data. Mono-exponential equation is used to estimate maximal sprinting speed (MSS), relative acceleration (TAU), and other parameters such us maximal acceleration (MAC) and maximal relative power (PMAX). These parameters can be used to predict kinematic and kinetics variables and to compare individuals. The modeling method utilized in this package is based on the works of Chelly SM, Denis C. (2001) <doi: 10.1097/00005768-200102000-00024>, Clark KP, Rieger RH, Bruno RF, Stearne DJ. (2017) <doi: 10.1519/JSC.0000000000002081>, Furusawa K, Hill AV, Parkinson JL (1927) <doi: 10.1098/rspb.1927.0035>, Greene PR. (1986) <doi: 10.1016/0025-5564(86)90063-5>, and Samozino P. (2018) <doi: 10.1007/978-3-319-05633-3_11>.
Author: Mladen Jovanović [aut, cre], Jason D. Vescovi [dtc]
Maintainer: Mladen Jovanović <coach.mladen.jovanovic@gmail.com>

Diff between shorts versions 2.0.0 dated 2022-07-07 and 2.1.0 dated 2022-09-26

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More information about shorts at CRAN
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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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Package colorDF updated to version 0.1.7 with previous version 0.1.5 dated 2022-09-25

Title: Colorful Data Frames in R Terminal
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.
Author: January Weiner [aut, cre]
Maintainer: January Weiner <january.weiner@gmail.com>

Diff between colorDF versions 0.1.5 dated 2022-09-25 and 0.1.7 dated 2022-09-26

 DESCRIPTION           |    6 +++---
 MD5                   |   19 ++++++++++---------
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 inst/doc/colorDF.html |   50 ++++++++++++++++++++------------------------------
 vignettes/colorDF.Rmd |   29 -----------------------------
 11 files changed, 59 insertions(+), 121 deletions(-)

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Package ACEt updated to version 1.8.2 with previous version 1.8.1 dated 2020-10-21

Title: Estimating Dynamic Heritability and Twin Model Comparison
Description: Twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.
Author: Liang He
Maintainer: Liang He <lianghe@health.sdu.dk>

Diff between ACEt versions 1.8.1 dated 2020-10-21 and 1.8.2 dated 2022-09-26

 DESCRIPTION         |   30 ++++++++++++++----------------
 MD5                 |   31 +++++++++++++++++++------------
 NAMESPACE           |    3 ++-
 R/acetp_mcmc.R      |   15 +++++++++------
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 src/AtCtEtp.cpp     |   48 ++++++++++++++++--------------------------------
 src/AtEtp.cpp       |   48 ++++++++++++++++--------------------------------
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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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Package rgl updated to version 0.110.2 with previous version 0.109.6 dated 2022-07-08

Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre], Daniel Adler [aut], Oleg Nenadic [ctb], Simon Urbanek [ctb], Ming Chen [ctb], Albrecht Gebhardt [ctb], Ben Bolker [ctb], Gabor Csardi [ctb], Adam Strzelecki [ctb], Alexander Senger [ctb], The R Core Team [ctb, cph], Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>

Diff between rgl versions 0.109.6 dated 2022-07-08 and 0.110.2 dated 2022-09-26

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 rgl-0.110.2/rgl/R/enum.R                                      |   10 
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 rgl-0.110.2/rgl/R/persp3d.R                                   |    2 
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 rgl-0.110.2/rgl/R/r3d.rgl.R                                   |    7 
 rgl-0.110.2/rgl/R/rglwidget.R                                 |    4 
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 rgl-0.110.2/rgl/man/Buffer.Rd                                 |  150 +++--
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 rgl-0.110.2/rgl/man/polygon3d.Rd                              |    5 
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 rgl-0.110.2/rgl/man/rglwidget.Rd                              |    7 
 rgl-0.110.2/rgl/src/BBoxDeco.cpp                              |    5 
 rgl-0.110.2/rgl/src/Material.cpp                              |   18 
 rgl-0.110.2/rgl/src/Material.h                                |    1 
 rgl-0.110.2/rgl/src/Texture.cpp                               |    6 
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 rgl-0.110.2/rgl/src/api.h                                     |    2 
 rgl-0.110.2/rgl/src/geom.cpp                                  |   21 
 rgl-0.110.2/rgl/src/gui.cpp                                   |    3 
 rgl-0.110.2/rgl/src/init.cpp                                  |    3 
 rgl-0.110.2/rgl/src/subscene.cpp                              |    8 
 rgl-0.110.2/rgl/src/x11gui.cpp                                |    5 
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 54 files changed, 800 insertions(+), 540 deletions(-)

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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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Package dsfa updated to version 1.0.0 with previous version 0.0.3 dated 2022-09-07

Title: Distributional Stochastic Frontier Analysis
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>.
Author: Rouven Schmidt [aut, cre]
Maintainer: Rouven Schmidt <rouven.schmidt@tu-clausthal.de>

Diff between dsfa versions 0.0.3 dated 2022-09-07 and 1.0.0 dated 2022-09-26

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 45 files changed, 1374 insertions(+), 942 deletions(-)

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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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Package IDSL.UFAx updated to version 1.6 with previous version 1.5 dated 2022-09-09

Title: Exhaustive Chemical Enumeration for United Formula Annotation
Description: A pipeline to annotate a number of peaks from the IDSL.IPA peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Se, Si, N, H, As, F, I, Na, O, and P.
Author: Sadjad Fakouri-Baygi [cre, aut] , Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>

Diff between IDSL.UFAx versions 1.5 dated 2022-09-09 and 1.6 dated 2022-09-26

 DESCRIPTION                          |    6 ++--
 MD5                                  |    9 +++---
 R/UFAx_score_coefficient_corrector.R |   46 +++++++++++++++++++++--------------
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 6 files changed, 39 insertions(+), 29 deletions(-)

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Package ggOceanMaps updated to version 1.3.4 with previous version 1.3.0 dated 2022-09-20

Title: Plot Data on Oceanographic Maps using 'ggplot2'
Description: Allows plotting data on bathymetric maps using 'ggplot2'. Plotting oceanographic spatial data is made as simple as feasible, but also flexible for custom modifications. Data that contain geographic information from anywhere around the globe can be plotted on maps generated by the basemap() or qmap() functions using 'ggplot2' layers separated by the '+' operator. The package uses spatial shapefiles stored in the 'ggOceanMapsData' package, geospatial packages for R to manipulate, and the 'ggspatial' package to help to plot these shapefiles. High-resolution shapefiles for detailed maps are stored on GitHub and downloaded automatically when needed.
Author: Mikko Vihtakari [aut, cre] , Yves Reecht [ctb] , Hadley Wickham [ctb], Simon O'Hanlon [ctb], Roger Bivand [ctb]
Maintainer: Mikko Vihtakari <mikko.vihtakari@hi.no>

Diff between ggOceanMaps versions 1.3.0 dated 2022-09-20 and 1.3.4 dated 2022-09-26

 DESCRIPTION            |    8 ++++----
 MD5                    |   30 +++++++++++++++---------------
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 R/reorder_layers.R     |    2 ++
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 man/fdir_sub_areas.Rd  |    2 ++
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 16 files changed, 85 insertions(+), 50 deletions(-)

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Package calculus updated to version 1.0.0 with previous version 0.3.4 dated 2022-08-20

Title: High Dimensional Numerical and Symbolic Calculus
Description: Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2022) <doi:10.18637/jss.v104.i05>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Author: Emanuele Guidotti [aut, cre]
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>

Diff between calculus versions 0.3.4 dated 2022-08-20 and 1.0.0 dated 2022-09-26

 DESCRIPTION                          |    8 -
 MD5                                  |  155 +++++++++++++++++------------------
 NEWS.md                              |    4 
 R/contraction.R                      |    2 
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Package tidytree updated to version 0.4.1 with previous version 0.4.0 dated 2022-08-13

Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph] , Bradley Jones [ctb], Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between tidytree versions 0.4.0 dated 2022-08-13 and 0.4.1 dated 2022-09-26

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Package Rogue updated to version 2.1.3 with previous version 2.1.2 dated 2022-08-16

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] , Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

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Package mnormt updated to version 2.1.1 with previous version 2.1.0 dated 2022-06-07

Title: The Multivariate Normal and t Distributions, and Their Truncated Versions
Description: Functions are provided for computing the density and the distribution function of d-dimensional normal and "t" random variables, possibly truncated (on one side or two sides), and for generating random vectors sampled from these distributions, except sampling from the truncated "t". Moments of arbitrary order of a multivariate truncated normal are computed, and converted to cumulants up to order 4. Probabilities are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d=3, d>3, if d denotes the dimensionality.
Author: Adelchi Azzalini [aut, cre], Alan Genz [aut] , Alan Miller [ctb] , Michael J. Wichura [ctb] , G. W. Hill [ctb] , Yihong Ge [ctb] .
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

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Package intensitynet updated to version 1.3.1 with previous version 1.3.0 dated 2022-05-16

Title: Intensity Analysis of Spatial Point Patterns on Complex Networks
Description: Tools to analyze point patterns in space occurring over planar network structures derived from graph-related intensity measures for undirected, directed, and mixed networks. This package is based on the following research: Eckardt and Mateu (2018) <doi:10.1080/10618600.2017.1391695>. Eckardt and Mateu (2021) <doi:10.1007/s11749-020-00720-4>.
Author: Pol Llagostera [aut, cre], Matthias Eckardt [aut]
Maintainer: Pol Llagostera <pol.llagostera@udl.cat>

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Package rcdk updated to version 3.7.0 with previous version 3.6.0 dated 2021-10-17

Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph], Zachary Charlop-Powers [cre], Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>

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Package hmm.discnp updated to version 3.0-9 with previous version 3.0-7 dated 2022-02-08

Title: Hidden Markov Models with Discrete Non-Parametric Observation Distributions
Description: Fits hidden Markov models with discrete non-parametric observation distributions to data sets. The observations may be univariate or bivariate. Simulates data from such models. Finds most probable underlying hidden states, the most probable sequences of such states, and the log likelihood of a collection of observations given the parameters of the model. Auxiliary predictors are accommodated in the univariate setting.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

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Package HistDAWass updated to version 1.0.7 with previous version 1.0.6 dated 2021-06-22

Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new approach to the statistical analysis of multi-valued data, we consider histogram-valued data, i.e., data described by univariate histograms. The methods and the basic statistics for histogram-valued data are mainly based on the L2 Wasserstein metric between distributions, i.e., the Euclidean metric between quantile functions. The package contains unsupervised classification techniques, least square regression and tools for histogram-valued data and for histogram time series. An introducing paper is Irpino A. Verde R. (2015) <doi: 10.1007/s11634-014-0176-4>.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unicampania.it>

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Package Bergm updated to version 5.0.5 with previous version 5.0.4 dated 2022-08-15

Title: Bayesian Exponential Random Graph Models
Description: Bayesian analysis for exponential random graph models using advanced computational algorithms. More information can be found at: <https://acaimo.github.io/Bergm/>.
Author: Alberto Caimo [aut, cre], Lampros Bouranis [aut], Robert Krause [aut] Nial Friel [ctb]
Maintainer: Alberto Caimo <alberto.caimo@tudublin.ie>

Diff between Bergm versions 5.0.4 dated 2022-08-15 and 5.0.5 dated 2022-09-26

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Package mlim updated to version 0.2.0 with previous version 0.0.9 dated 2022-09-07

Title: Multiple Imputation with Automated Machine Learning
Description: Machine learning algorithms have been used for performing single missing data imputation and most recently, multiple imputations. However, this is the first attempt for using automated machine learning algorithms for performing both single and multiple imputation. Automated machine learning is a procedure for fine-tuning the model automatic, performing a random search for a model that results in less error, without overfitting the data. The main idea is to allow the model to set its own parameters for imputing each variable seperately instead of setting fixed predefined parameters to impute all variables of the dataset. 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 (from one or a combination of other supported algorithms) for imputing the missing observations. This procedure has been implemented for the first time by this package [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@uio.no>

Diff between mlim versions 0.0.9 dated 2022-09-07 and 0.2.0 dated 2022-09-26

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Package actilifecounts updated to version 1.1.0 with previous version 1.0.0 dated 2022-05-30

Title: Generate Activity Counts from Raw Accelerometer Data
Description: A tool to obtain activity counts, originally a translation of the 'python' package 'agcounts' <https://github.com/actigraph/agcounts>. This tool allows the processing of data from any accelerometer brand, with a more flexible approach to handle different sampling frequencies.
Author: Jairo Hidalgo Migueles
Maintainer: Jairo Hidalgo Migueles <jairo.hidalgo.migueles@gmail.com>

Diff between actilifecounts versions 1.0.0 dated 2022-05-30 and 1.1.0 dated 2022-09-26

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Package workflows updated to version 1.1.0 with previous version 1.0.0 dated 2022-07-05

Title: Modeling Workflows
Description: Managing both a 'parsnip' model and a preprocessor, such as a model formula or recipe from 'recipes', can often be challenging. The goal of 'workflows' is to streamline this process by bundling the model alongside the preprocessor, all within the same object.
Author: Davis Vaughan [aut], Simon Couch [aut, cre] , RStudio [cph, fnd]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>

Diff between workflows versions 1.0.0 dated 2022-07-05 and 1.1.0 dated 2022-09-26

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 16 files changed, 280 insertions(+), 44 deletions(-)

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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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Package riskRegression updated to version 2022.09.23 with previous version 2022.09.13 dated 2022-09-17

Title: Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis. Risk regression models for survival endpoints also in the presence of competing risks are fitted using binomial regression based on a time sequence of binary event status variables. A formula interface for the Fine-Gray regression model and an interface for the combination of cause-specific Cox regression models. A toolbox for assessing and comparing performance of risk predictions (risk markers and risk prediction models). Prediction performance is measured by the Brier score and the area under the ROC curve for binary possibly time-dependent outcome. Inverse probability of censoring weighting and pseudo values are used to deal with right censored data. Lists of risk markers and lists of risk models are assessed simultaneously. Cross-validation repeatedly splits the data, trains the risk prediction models on one part of each split and then summarizes and compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre], Johan Sebastian Ohlendorff [aut], Paul Blanche [ctb], Rikke Mortensen [ctb], Marvin Wright [ctb], Nikolaj Tollenaar [ctb], John Muschelli [ctb], Ulla Brasch Mogensen [ctb], Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>

Diff between riskRegression versions 2022.09.13 dated 2022-09-17 and 2022.09.23 dated 2022-09-26

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Package RGBM updated to version 1.0-10 with previous version 1.0-9 dated 2022-08-11

Title: LS-TreeBoost and LAD-TreeBoost for Gene Regulatory Network Reconstruction
Description: Provides an implementation of Regularized LS-TreeBoost & LAD-TreeBoost algorithm for Regulatory Network inference from any type of expression data (Microarray/RNA-seq etc).
Author: Raghvendra Mall [aut, cre], Khalid Kunji [aut], Melissa O'Neill [ctb]
Maintainer: Raghvendra Mall <raghvendra5688@gmail.com>

Diff between RGBM versions 1.0-9 dated 2022-08-11 and 1.0-10 dated 2022-09-26

 DESCRIPTION                    |    8 ++++----
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Package golem updated to version 0.3.4 with previous version 0.3.3 dated 2022-07-13

Title: A Framework for Robust Shiny Applications
Description: An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.
Author: Colin Fay [cre, aut] , Vincent Guyader [aut] , Sebastien Rochette [aut] , Cervan Girard [aut] , Novica Nakov [ctb], David Granjon [ctb], Arthur Breant [ctb], Antoine Languillaume [ctb], ThinkR [cph]
Maintainer: Colin Fay <contact@colinfay.me>

Diff between golem versions 0.3.3 dated 2022-07-13 and 0.3.4 dated 2022-09-26

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Package ggridges updated to version 0.5.4 with previous version 0.5.3 dated 2021-01-08

Title: Ridgeline Plots in 'ggplot2'
Description: Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Author: Claus O. Wilke [aut, cre]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>

Diff between ggridges versions 0.5.3 dated 2021-01-08 and 0.5.4 dated 2022-09-26

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Package conos updated to version 1.4.8 with previous version 1.4.7 dated 2022-09-04

Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut], Nikolas Barkas [aut], Peter Kharchenko [aut], Weiliang Qiu [ctb], Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

Diff between conos versions 1.4.7 dated 2022-09-04 and 1.4.8 dated 2022-09-26

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Sun, 25 Sep 2022

Package leidenAlg updated to version 1.0.4 with previous version 1.0.3 dated 2022-04-11

Title: Implements the Leiden Algorithm via an R Interface
Description: An R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory). The original implementation was constructed as a python interface "leidenalg" found here: <https://github.com/vtraag/leidenalg>. The algorithm was originally described in Traag, V.A., Waltman, L. & van Eck, N.J. "From Louvain to Leiden: guaranteeing well-connected communities". Sci Rep 9, 5233 (2019) <doi:10.1038/s41598-019-41695-z>.
Author: Peter Kharchenko [aut], Viktor Petukhov [aut], V.A. Traag [ctb], Gabor Csardi [ctb], Tamas Nepusz [ctb], Minh Van Nguyen [ctb], Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

Diff between leidenAlg versions 1.0.3 dated 2022-04-11 and 1.0.4 dated 2022-09-25

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Package MCM updated to version 0.1.6 with previous version 0.1.5 dated 2022-01-04

Title: Estimating and Testing Intergenerational Social Mobility Effect
Description: Estimate and test inter-generational social mobility effect on an outcome with cross-sectional or longitudinal data.
Author: Jiahui Xu [aut, cre], Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>

Diff between MCM versions 0.1.5 dated 2022-01-04 and 0.1.6 dated 2022-09-25

 DESCRIPTION              |    8 ++++----
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Package Exact updated to version 3.2 with previous version 3.1 dated 2021-11-26

Title: Unconditional Exact Test
Description: Performs unconditional exact tests and power calculations for 2x2 contingency tables. For comparing two independent proportions, performs Barnard's test (1945) <doi:10.1038/156177a0> using the original CSM test (Barnard, 1947 <doi:10.1093/biomet/34.1-2.123>), using Fisher's p-value referred to as Boschloo's test (1970) <doi:10.1111/j.1467-9574.1970.tb00104.x>, or using a Z-statistic (Suissa and Shuster, 1985, <doi:10.2307/2981892>). For comparing two binary proportions, performs unconditional exact test using McNemar's Z-statistic (Berger and Sidik, 2003, <doi:10.1191/0962280203sm312ra>), using McNemar's conditional p-value, using McNemar's Z-statistic with continuity correction, or using CSM test. Calculates confidence intervals for the difference in proportion. This package interacts with pre-computed data available through the ExactData R package, which is available in a 'drat' repository. Install the ExactData R package from GitHub at <https://pcal [...truncated...]
Author: Peter Calhoun [aut, cre]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>

Diff between Exact versions 3.1 dated 2021-11-26 and 3.2 dated 2022-09-25

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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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Package rcdklibs updated to version 2.8 with previous version 2.3 dated 2020-03-08

Title: The CDK Libraries Packaged for R
Description: An R interface to the Chemistry Development Kit, a Java library for chemoinformatics. Given the size of the library itself, this package is not expected to change very frequently. To make use of the CDK within R, it is suggested that you use the 'rcdk' package. Note that it is possible to directly interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more idiomatic way. The CDK library itself is released as LGPL and the sources can be obtained from <https://github.com/cdk/cdk>.
Author: Rajarshi Guha [aut], Zachary Charlop-Powers [cre], CDK Project [ctb, cph]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>

Diff between rcdklibs versions 2.3 dated 2020-03-08 and 2.8 dated 2022-09-25

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Package osfr updated to version 0.2.9 with previous version 0.2.8 dated 2020-02-17

Title: Interface to the 'Open Science Framework' ('OSF')
Description: An interface for interacting with 'OSF' (<https://osf.io>). 'osfr' enables you to access open research materials and data, or create and manage your own private or public projects.
Author: Aaron Wolen [aut, cre] , Chris Hartgerink [aut] , Timothy York [ctb] , Ryan Hafen [ctb], Brian Richards [ctb], Courtney Soderberg [ctb] , Carl Boettiger [rev] , Heidi Seibold [rev]
Maintainer: Aaron Wolen <aaron@wolen.com>

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Package graphql updated to version 1.5.1 with previous version 1.5 dated 2018-12-01

Title: A GraphQL Query Parser
Description: Bindings to the 'libgraphqlparser' C++ library. Parses GraphQL syntax and exports the AST in JSON format.
Author: Jeroen Ooms [cre, aut], Barret Schloerke [ctb], Scott Wolchok [ctb], Facebook, Inc [aut, cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package bibtex updated to version 0.5.0 with previous version 0.4.2.3 dated 2020-09-19

Title: Bibtex Parser
Description: Utility to parse a bibtex file.
Author: Romain Francois [aut, cph] , James Joseph Balamuta [ctb, cre] , Diego Hernangomez [aut] , Scott Chamberlain [ctb] , Kurt Hornik [ctb] , Brian Ripley [ctb] , Michael Koohafkan [ctb], Mathew W. McLean [ctb]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package unittest updated to version 1.5-3 with previous version 1.5-1 dated 2022-09-07

Title: TAP-Compliant Unit Testing
Description: Concise TAP <http://testanything.org/> compliant unit testing package. Authored tests can be run using CMD check with minimal implementation overhead.
Author: Jamie Lentin [aut, cre], Anthony Hennessey [aut]
Maintainer: Jamie Lentin <jm@ravingmantis.com>

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Package ichimoku updated to version 1.4.1 with previous version 1.4.0 dated 2022-09-08

Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as 'cloud charts'. Static and interactive visualizations with tools for creating, backtesting and development of quantitative 'ichimoku' strategies. As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement on candlestick charting, originating from Japan and now in widespread use in technical analysis worldwide. Translating as 'one-glance equilibrium chart', it allows the price action and market structure of financial securities to be determined 'at-a-glance'. Incorporates an interface with the OANDA fxTrade API <https://developer.oanda.com/> for retrieving historical and live streaming price data for major currencies, metals, commodities, government bonds and stock indices.
Author: Charlie Gao [aut, cre] , Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>

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Package psychTools updated to version 2.2.9 with previous version 2.2.5 dated 2022-05-10

Title: Tools to Accompany the 'psych' Package for Psychological Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as one vignette. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre]
Maintainer: William Revelle <revelle@northwestern.edu>

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Package lvplot updated to version 0.2.1 with previous version 0.2.0 dated 2016-05-01

Title: Letter Value 'Boxplots'
Description: Implements the letter value 'boxplot' which extends the standard 'boxplot' to deal with both larger and smaller number of data points by dynamically selecting the appropriate number of letter values to display.
Author: Hadley Wickham [aut, cre], Heike Hofmann [aut]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package httr2 updated to version 0.2.2 with previous version 0.2.1 dated 2022-05-10

Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then performing them and processing the results. 'httr2' is a modern re-imagining of 'httr' that uses a pipe-based interface and solves more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package fastGLCM updated to version 1.0.2 with previous version 1.0.1 dated 2022-09-04

Title: 'GLCM' Texture Features
Description: Two 'Gray Level Co-occurrence Matrix' ('GLCM') implementations are included: The first is a fast 'GLCM' feature texture computation based on 'Python' 'Numpy' arrays ('Github' Repository, <https://github.com/tzm030329/GLCM>). The second is a fast 'GLCM' 'RcppArmadillo' implementation which is parallelized (using 'OpenMP') with the option to return all 'GLCM' features at once. For more information, see "Artifact-Free Thin Cloud Removal Using Gans" by Toizumi Takahiro, Zini Simone, Sagi Kazutoshi, Kaneko Eiji, Tsukada Masato, Schettini Raimondo (2019), IEEE International Conference on Image Processing (ICIP), pp. 3596-3600, <doi:10.1109/ICIP.2019.8803652>.
Author: Lampros Mouselimis [aut, cre] , Takahiro Toizumi [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

Diff between fastGLCM versions 1.0.1 dated 2022-09-04 and 1.0.2 dated 2022-09-25

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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

More information about popEpi at CRAN
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Package onmaRg updated to version 0.1.2 with previous version 0.1.1 dated 2022-09-18

Title: Import Public Health Ontario's Ontario Marginalization Index
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>.
Author: William Conley [aut, cre]
Maintainer: William Conley <william@cconley.ca>

Diff between onmaRg versions 0.1.1 dated 2022-09-18 and 0.1.2 dated 2022-09-25

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Package nflreadr updated to version 1.3.1 with previous version 1.3.0 dated 2022-08-06

Title: Download 'nflverse' Data
Description: A minimal package for downloading data from 'GitHub' repositories of the 'nflverse' project.
Author: Tan Ho [aut, cre, cph] , Sebastian Carl [aut], John Edwards [ctb], Ben Baldwin [ctb], Thomas Mock [ctb], Lee Sharpe [ctb], Pranav Rajaram [ctb]
Maintainer: Tan Ho <tan@tanho.ca>

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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

More information about bfsMaps at CRAN
Permanent link

Package ngramr updated to version 1.8.3 with previous version 1.8.2 dated 2022-09-20

Title: Retrieve and Plot Google n-Gram Data
Description: Retrieve and plot word frequencies through time from the "Google Ngram Viewer" <https://books.google.com/ngrams>.
Author: Sean Carmody [aut, cre, cph]
Maintainer: Sean Carmody <seancarmody@gmail.com>

Diff between ngramr versions 1.8.2 dated 2022-09-20 and 1.8.3 dated 2022-09-25

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Package GENEAclassify updated to version 1.5.3 with previous version 1.5.2 dated 2021-01-05

Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://activinsights.com/technology/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing. Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut], Aimee Gott [aut], Joss Langford [aut], Charles Sweetland [aut, cre], Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@springhead-data.com>

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Package epiR updated to version 2.0.52 with previous version 2.0.50 dated 2022-07-01

Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>

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Package edecob updated to version 1.2.0 with previous version 1.1.0 dated 2022-05-27

Title: Event Detection Using Confidence Bounds
Description: Detects sustained change in digital bio-marker data using simultaneous confidence bands. Accounts for noise using an auto-regressive model. Based on Buehlmann (1998) "Sieve bootstrap for smoothing in nonstationary time series" <doi:10.1214/aos/1030563978>.
Author: Zheng Chen Man [aut, cre]
Maintainer: Zheng Chen Man <zheng.chen.man@alumni.ethz.ch>

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Package cld2 updated to version 1.2.2 with previous version 1.2.1 dated 2020-12-15

Title: Google's Compact Language Detector 2
Description: Bindings to Google's C++ library Compact Language Detector 2 (see <https://github.com/cld2owners/cld2#readme> for more information). Probabilistically detects over 80 languages in plain text or HTML. For mixed-language input it returns the top three detected languages and their approximate proportion of the total classified text bytes (e.g. 80% English and 20% French out of 1000 bytes). There is also a 'cld3' package on CRAN which uses a neural network model instead.
Author: Jeroen Ooms [aut, cre] , Dirk Sites [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between cld2 versions 1.2.1 dated 2020-12-15 and 1.2.2 dated 2022-09-25

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Package phase updated to version 1.2.2 with previous version 1.2.1 dated 2021-08-16

Title: Analyse Biological Time-Series Data
Description: Compiles functions to trim, bin, visualise, and analyse activity/sleep time-series data collected from the Drosophila Activity Monitor (DAM) system (Trikinetics, USA). The following methods were used to compute periodograms - Chi-square periodogram: Sokolove and Bushell (1978) <doi:10.1016/0022-5193(78)90022-X>, Lomb-Scargle periodogram: Lomb (1976) <doi:10.1007/BF00648343>, Scargle (1982) <doi:10.1086/160554> and Ruf (1999) <doi:10.1076/brhm.30.2.178.1422>, and Autocorrelation: Eijzenbach et al. (1986) <doi:10.1111/j.1440-1681.1986.tb00943.x>. Identification of activity peaks is done after using a Savitzky-Golay filter (Savitzky and Golay (1964) <doi:10.1021/ac60214a047>) to smooth raw activity data. Three methods to estimate anticipation of activity are used based on the following papers - Slope method: Fernandez et al. (2020) <doi:10.1016/j.cub.2020.04.025>, Harrisingh method: Harrisingh et al. (2007) <doi:10.1523/JNEUROSCI.3680-07.2007&g [...truncated...]
Author: Lakshman Abhilash [aut, cre]
Maintainer: Lakshman Abhilash <labhilash@gc.cuny.edu>

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Package openair updated to version 2.11 with previous version 2.10-0 dated 2022-06-21

Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Author: David Carslaw [aut, cre], Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>

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Package datawizard updated to version 0.6.1 with previous version 0.6.0 dated 2022-09-15

Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to easily manipulate, clean, transform, and prepare your data for analysis. It also forms the data wrangling backend for the packages in the 'easystats' ecosystem.
Author: Indrajeet Patil [aut, cre] , Dominique Makowski [aut] , Daniel Luedecke [aut] , Mattan S. Ben-Shachar [aut] , Brenton M. Wiernik [aut] , Etienne Bacher [aut] , Remi Theriault [ctb]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package metamisc updated to version 0.4.0 with previous version 0.2.5 dated 2021-09-20

Title: Meta-Analysis of Diagnosis and Prognosis Research Studies
Description: Facilitate frequentist and Bayesian meta-analysis of diagnosis and prognosis research studies. It includes functions to summarize multiple estimates of prediction model discrimination and calibration performance (Debray et al., 2019) <doi:10.1177/0962280218785504>. It also includes functions to evaluate funnel plot asymmetry (Debray et al., 2018) <doi:10.1002/jrsm.1266>. Finally, the package provides functions for developing multivariable prediction models from datasets with clustering (de Jong et al., 2021) <doi:10.1002/sim.8981>.
Author: Thomas Debray [aut, cre] , Valentijn de Jong [aut]
Maintainer: Thomas Debray <thomas.debray@gmail.com>

Diff between metamisc versions 0.2.5 dated 2021-09-20 and 0.4.0 dated 2022-09-25

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Package WDI updated to version 2.7.8 with previous version 2.7.7 dated 2022-07-16

Title: World Development Indicators and Other World Bank Data
Description: Search and download data from over 40 databases hosted by the World Bank, including the World Development Indicators ('WDI'), International Debt Statistics, Doing Business, Human Capital Index, and Sub-national Poverty indicators.
Author: Vincent Arel-Bundock [aut, cre] , Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

Diff between WDI versions 2.7.7 dated 2022-07-16 and 2.7.8 dated 2022-09-25

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Package owidR updated to version 1.4.0 with previous version 1.3.1 dated 2022-08-07

Title: Import Data from Our World in Data
Description: Search and download the data used in over 3,000 Our World in Data charts.
Author: Piers York
Maintainer: Piers York <piersyork@gmail.com>

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Package marginaleffects updated to version 0.7.1 with previous version 0.7.0 dated 2022-08-06

Title: Marginal Effects, Marginal Means, Predictions, and Contrasts
Description: Compute and plot adjusted predictions, contrasts, marginal effects, and marginal means for over 65 classes of statistical models in R. Conduct linear and non-linear hypothesis tests using the delta method.
Author: Vincent Arel-Bundock [aut, cre, cph] , Marcio Augusto Diniz [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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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

More information about colorDF at CRAN
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Package cat2cat updated to version 0.4.5 with previous version 0.4.4 dated 2022-08-31

Title: Handling an Inconsistently Coded Categorical Variable in a Panel Dataset
Description: Unifying of an inconsistently coded categorical variable between two different time points in accordance with a mapping table. The main rule is to replicate the observation if it could be assign to a few categories. Then using simple frequencies or statistical methods to approximate probabilities of being assign to each of them. This procedure was invented and implemented in the paper by (Nasinski, Majchrowska and Broniatowska (2020) <doi:10.24425/cejeme.2020.134747>).
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>

Diff between cat2cat versions 0.4.4 dated 2022-08-31 and 0.4.5 dated 2022-09-25

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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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Package MRH (with last version 2.2) was removed from CRAN

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

2016-02-26 2.2
2015-09-04 2.1
2015-01-13 2.0
2014-10-23 1.1
2014-10-17 1.0

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Package survivoR updated to version 2.0.1 with previous version 2.0 dated 2022-09-21

Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out. Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre], Carly Levitz [ctb], Dario Mavec [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>

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Package openCR updated to version 2.2.5 with previous version 2.2.4 dated 2022-07-01

Title: Open Population Capture-Recapture
Description: Non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

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Package mapfit (with last version 0.9.9) was removed from CRAN

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

2022-05-30 0.9.9
2015-03-24 0.9.7
2015-03-19 0.9.6

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Sat, 24 Sep 2022

Package TidyMultiqc updated to version 1.0.3 with previous version 1.0.2 dated 2022-02-10

Title: Converts 'MultiQC' Reports into Tidy Data Frames
Description: Provides the means to convert 'multiqc_data.json' files, produced by the wonderful 'MultiQC' tool, into tidy data frames for downstream analysis in R. This analysis might involve cohort analysis, quality control visualisation, change-point detection, statistical process control, clustering, or any other type of quality analysis.
Author: Michael Milton
Maintainer: Michael Milton <michael.r.milton@gmail.com>

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Package BayesianMediationA updated to version 1.0.1 with previous version 1.0 dated 2022-08-18

Title: Bayesian Mediation Analysis
Description: We perform general mediation analysis in the Bayesian setting using the methods described in Yu and Li (2022, ISBN:9780367365479). With the package, the mediation analysis can be performed on different types of outcomes (e.g., continuous, binary, categorical, or time-to-event), with default or user-defined priors and predictive models. The Bayesian estimates and credible sets of mediation effects are reported as analytic results.
Author: Qingzhao Yu [aut, cre, cph], Bin Li [aut]
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>

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Package ssh updated to version 0.8.1 with previous version 0.8.0 dated 2021-05-03

Title: Secure Shell (SSH) Client for R
Description: Connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package clickR updated to version 0.8.3 with previous version 0.8.0 dated 2021-08-10

Title: Semi-Automatic Preprocessing of Messy Data with Change Tracking for Dataset Cleaning
Description: Tools for assessing data quality, performing exploratory analysis, and semi-automatic preprocessing of messy data with change tracking for integral dataset cleaning.
Author: David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>

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Package reclin2 updated to version 0.2.0 with previous version 0.1.1 dated 2022-01-07

Title: Record Linkage Toolkit
Description: Functions to assist in performing probabilistic record linkage and deduplication: generating pairs, comparing records, em-algorithm for estimating m- and u-probabilities (I. Fellegi & A. Sunter (1969) <doi:10.1080/01621459.1969.10501049>, T.N. Herzog, F.J. Scheuren, & W.E. Winkler (2007), "Data Quality and Record Linkage Techniques", ISBN:978-0-387-69502-0), forcing one-to-one matching. Can also be used for pre- and post-processing for machine learning methods for record linkage. Focus is on memory, CPU performance and flexibility.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>

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Package mbRes updated to version 0.1.5 with previous version 0.1.4 dated 2022-08-24

Title: Exploration of Multiple Biomarker Responses using Effect Size
Description: Summarize multiple biomarker responses of aquatic organisms to contaminants using Cliff’s delta, as described in Pham & Sokolova (2022) <doi:10.1002/ieam.4676>.
Author: Duy Nghia Pham [aut, cre] , Inna M. Sokolova [ths]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>

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Package sportyR updated to version 2.0.1 with previous version 2.0.0 dated 2022-08-15

Title: Plot Scaled 'ggplot' Representations of Sports Playing Surfaces
Description: Create scaled 'ggplot' representations of playing surfaces. Playing surfaces are drawn pursuant to rule-book specifications. This package should be used as a baseline plot for displaying any type of tracking data.
Author: Ross Drucker [aut, cre]
Maintainer: Ross Drucker <ross.a.drucker@gmail.com>

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Package robis updated to version 2.11.3 with previous version 2.8.2 dated 2021-10-13

Title: Ocean Biodiversity Information System (OBIS) Client
Description: Client for the Ocean Biodiversity Information System (<https://obis.org>).
Author: Pieter Provoost [cre, aut], Samuel Bosch [aut], Ward Appeltans [ctb], OBIS [cph]
Maintainer: Pieter Provoost <pieterprovoost@gmail.com>

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Package dtwclust updated to version 5.5.11 with previous version 5.5.10 dated 2022-04-14

Title: Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance
Description: Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>

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Package PLSiMCpp updated to version 1.0.4 with previous version 1.0.3 dated 2022-08-20

Title: Methods for Partial Linear Single Index Model
Description: Estimation, hypothesis tests, and variable selection in partially linear single-index models. Please see H. (2010) at <doi:10.1214/10-AOS835> for more details.
Author: Shunyao Wu, Qi Zhang, Zhiruo Li, Hua Liang
Maintainer: Shunyao Wu <wushunyao@qdu.edu.cn>

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Package iotables updated to version 0.9.1 with previous version 0.9 dated 2022-02-10

Title: Reproducible Input-Output Economics Analysis, Economic and Environmental Impact Assessment with Empirical Data
Description: Pre-processing and basic analytical tasks related to working with Eurostat's symmetric input-output tables and provide basic input-output economics calculations. The package is part of rOpenGov <http://ropengov.github.io/> to open source open government initiatives.
Author: Daniel Antal [aut, cre] , Kasia Kulma [ctb] , Pyry Kantanen [ctb]
Maintainer: Daniel Antal <daniel.antal@dataobservatory.eu>

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Package rlang updated to version 1.0.6 with previous version 1.0.5 dated 2022-08-31

Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], mikefc [cph] , Yann Collet [cph] , RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>

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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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Package pins updated to version 1.0.3 with previous version 1.0.2 dated 2022-08-23

Title: Pin, Discover and Share Resources
Description: Publish data sets, models, and other R objects, making it easy to share them across projects and with your colleagues. You can pin objects to a variety of "boards", including local folders (to share on a networked drive or with 'DropBox'), 'RStudio' connect, Amazon S3, and more.
Author: Julia Silge [cre, aut] , Hadley Wickham [aut] , Javier Luraschi [aut], RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>

Diff between pins versions 1.0.2 dated 2022-08-23 and 1.0.3 dated 2022-09-24

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 28 files changed, 144 insertions(+), 82 deletions(-)

More information about pins at CRAN
Permanent link

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

More information about httk at CRAN
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Package adw updated to version 0.2.1 with previous version 0.2.0 dated 2022-09-22

Title: Angular Distance Weighting Interpolation
Description: The irregularly-spaced data are interpolated onto regular latitude-longitude grids by weighting each station according to its distance and angle from the center of a search radius.
Author: Panfeng Zhang [aut, cre]
Maintainer: Panfeng Zhang <zhangpanfeng@cug.edu.cn>

Diff between adw versions 0.2.0 dated 2022-09-22 and 0.2.1 dated 2022-09-24

 DESCRIPTION |    8 ++++----
 MD5         |    9 +++++----
 NEWS.md     |    5 +++++
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 6 files changed, 16 insertions(+), 10 deletions(-)

More information about adw at CRAN
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Package blogdown updated to version 1.13 with previous version 1.12 dated 2022-09-15

Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] , Christophe Dervieux [aut] , Alison Presmanes Hill [aut] , Amber Thomas [ctb], Beilei Bian [ctb], Brandon Greenwell [ctb], Brian Barkley [ctb], Deependra Dhakal [ctb], Eric Nantz [ctb], Forest Fang [ctb], Garrick Aden-Buie [ctb] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between blogdown versions 1.12 dated 2022-09-15 and 1.13 dated 2022-09-24

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Permanent link

Package inTextSummaryTable (with last version 3.1.1) was removed from CRAN

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

2022-02-22 3.1.1
2021-09-28 3.1.0
2021-07-13 3.0.1
2021-06-10 3.0.0

Permanent link
Package devtoolbox (with last version 0.2.0) was removed from CRAN

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

2022-07-08 0.2.0
2021-09-07 0.1.0

Permanent link

Fri, 23 Sep 2022

Package rmoo updated to version 0.2.0 with previous version 0.1.8 dated 2022-08-11

Title: Multi-Objective Optimization in R
Description: The 'rmoo' package is a framework for multi- and many-objective optimization, which allows researchers and users versatility in parameter configuration, as well as tools for analysis, replication and visualization of results. The 'rmoo' package was built as a fork of the 'GA' package by Luca Scrucca(2017) <DOI:10.32614/RJ-2017-008> and implementing the Non-Dominated Sorting Genetic Algorithms proposed by K. Deb's.
Author: Francisco Benitez [aut, cre], Diego Pinto Roa [aut]
Maintainer: Francisco Benitez <benitezfj94@gmail.com>

Diff between rmoo versions 0.1.8 dated 2022-08-11 and 0.2.0 dated 2022-09-23

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 45 files changed, 1001 insertions(+), 292 deletions(-)

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Package extras updated to version 0.4.0 with previous version 0.3.0 dated 2022-06-08

Title: Helper Functions for Bayesian Analyses
Description: Functions to 'numericise' 'R' objects (coerce to numeric objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and calculate deviance residuals as well as 'R' translations of some 'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.
Author: Joe Thorley [aut, cre] , Kirill Mueller [ctb] , Nadine Hussein [ctb] , Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between extras versions 0.3.0 dated 2022-06-08 and 0.4.0 dated 2022-09-23

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 21 files changed, 174 insertions(+), 20 deletions(-)

More information about extras at CRAN
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Package mixture updated to version 2.0.5 with previous version 2.0.4 dated 2021-04-19

Title: Mixture Models for Clustering and Classification
Description: An implementation of 14 parsimonious mixture models for model-based clustering or model-based classification. Gaussian, Student's t, generalized hyperbolic, variance-gamma or skew-t mixtures are available. All approaches work with missing data. Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>, Browne and McNicholas (2014) <doi:10.1007/s11634-013-0139-1>, Browne and McNicholas (2015) <doi:10.1002/cjs.11246>.
Author: Nik Pocuca [aut] , Ryan P. Browne [aut] , Paul D. McNicholas [aut, cre]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>

Diff between mixture versions 2.0.4 dated 2021-04-19 and 2.0.5 dated 2022-09-23

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 33 files changed, 1794 insertions(+), 898 deletions(-)

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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

More information about spcov at CRAN
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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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Package tokenizers updated to version 0.2.3 with previous version 0.2.1 dated 2018-03-29

Title: Fast, Consistent Tokenization of Natural Language Text
Description: Convert natural language text into tokens. Includes tokenizers for shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs, characters, shingled characters, lines, tweets, Penn Treebank, regular expressions, as well as functions for counting characters, words, and sentences, and a function for splitting longer texts into separate documents, each with the same number of words. The tokenizers have a consistent interface, and the package is built on the 'stringi' and 'Rcpp' packages for fast yet correct tokenization in 'UTF-8'.
Author: Lincoln Mullen [aut, cre] , Os Keyes [ctb] , Dmitriy Selivanov [ctb], Jeffrey Arnold [ctb] , Kenneth Benoit [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>

Diff between tokenizers versions 0.2.1 dated 2018-03-29 and 0.2.3 dated 2022-09-23

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Package NNS updated to version 0.9.2 with previous version 0.9.1 dated 2022-08-22

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 [aut, cre], Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

Diff between NNS versions 0.9.1 dated 2022-08-22 and 0.9.2 dated 2022-09-23

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Package broom.helpers updated to version 1.9.0 with previous version 1.8.0 dated 2022-07-05

Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model 'broom::tidy()' tibbles. The suite includes functions to group regression model terms by variable, insert reference and header rows for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] , Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>

Diff between broom.helpers versions 1.8.0 dated 2022-07-05 and 1.9.0 dated 2022-09-23

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Package WeMix updated to version 3.2.2 with previous version 3.2.1 dated 2021-12-07

Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Emmanuel Sikali [pdr], Paul Bailey [aut, cre], Claire Kelley [aut], Trang Nguyen [aut], Huade Huo [aut], Eric Buehler [ctb], Christian Kjeldsen [ctb]
Maintainer: Paul Bailey <pbailey@air.org>

Diff between WeMix versions 3.2.1 dated 2021-12-07 and 3.2.2 dated 2022-09-23

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Package tidytable updated to version 0.9.0 with previous version 0.8.1 dated 2022-08-17

Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table', giving users the speed of 'data.table' while using tidyverse-like syntax.
Author: Mark Fairbanks [aut, cre], Abdessabour Moutik [ctb], Matt Carlson [ctb], Ivan Leung [ctb], Ross Kennedy [ctb], Robert On [ctb], Alexander Sevostianov [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>

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Package sgo updated to version 0.9.2 with previous version 0.9.1 dated 2021-12-11

Title: Simple Geographical Operations (with OSGB36)
Description: Methods focused in performing the OSGB36/ETRS89 transformation (Great Britain and the Isle of Man only) by using the Ordnance Survey's OSTN15/OSGM15 transformation model. Calculation of distances and areas from sets of points defined in any of the supported Coordinated Systems is also available.
Author: Carlos Lozano Ruiz [aut, cre]
Maintainer: Carlos Lozano Ruiz <carloslozanoruiz@outlook.com>

Diff between sgo versions 0.9.1 dated 2021-12-11 and 0.9.2 dated 2022-09-23

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Package gosset updated to version 0.5 with previous version 0.4 dated 2022-06-28

Title: Tools for Data Analysis in Experimental Agriculture
Description: Toolkit for a workflow to analyse experimental agriculture data, from data synthesis to model selection and visualisation. The package is named after W.S. Gosset aka ‘Student’, a pioneer of modern statistics in small sample experimental design and analysis.
Author: Kaue de Sousa [aut, cre] , Jacob van Etten [aut] , David Brown [aut] , Jonathan Steinke [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>

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Package EnrichIntersect updated to version 0.4 with previous version 0.3 dated 2022-09-14

Title: Enrichment Analysis and Intersecting Sankey Diagram
Description: A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al. (2022) <doi:10.1016/j.isci.2022.104767>) or similar methods.
Author: Zhi Zhao [aut, cre], Manuela Zucknick [aut], Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>

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Package EdSurvey updated to version 3.0.0 with previous version 2.7.1 dated 2021-10-05

Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education S [...truncated...]
Author: Paul Bailey [aut, cre], Ahmad Emad [aut], Huade Huo [aut], Michael Lee [aut], Yuqi Liao [aut], Alex Lishinski [aut], Trang Nguyen [aut], Qingshu Xie [aut], Jiao Yu [aut], Ting Zhang [aut], Eric Buehler [aut], person, person), Jeppe Bundsgaard [ctb], [...truncated...]
Maintainer: Paul Bailey <pbailey@air.org>

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Permanent link

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

More information about oews2020 at CRAN
Permanent link

Package funrar updated to version 1.5.0 with previous version 1.4.1 dated 2020-04-20

Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity. 'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Author: Matthias Grenie [aut, cre] , Pierre Denelle [aut] , Caroline Tucker [aut] , Francois Munoz [ths] , Cyrille Violle [ths]
Maintainer: Matthias Grenie <matthias.grenie@gmail.com>

Diff between funrar versions 1.4.1 dated 2020-04-20 and 1.5.0 dated 2022-09-23

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Package DrDimont updated to version 0.1.4 with previous version 0.1.3 dated 2022-05-17

Title: Drug Response Prediction from Differential Multi-Omics Networks
Description: While it has been well established that drugs affect and help patients differently, personalized drug response predictions remain challenging. Solutions based on single omics measurements have been proposed, and networks provide means to incorporate molecular interactions into reasoning. However, how to integrate the wealth of information contained in multiple omics layers still poses a complex problem. We present a novel network analysis pipeline, DrDimont, Drug response prediction from Differential analysis of multi-omics networks. It allows for comparative conclusions between two conditions and translates them into differential drug response predictions. DrDimont focuses on molecular interactions. It establishes condition-specific networks from correlation within an omics layer that are then reduced and combined into heterogeneous, multi-omics molecular networks. A novel semi-local, path-based integration step ensures integrative conclusions. Differential predictions are derived fro [...truncated...]
Author: Katharina Baum [cre] , Pauline Hiort [aut] , Julian Hugo [aut] , Spoorthi Kashyap [aut] , Nataniel Mueller [aut] , Justus Zeinert [aut]
Maintainer: Katharina Baum <katharina.baum@hpi.de>

Diff between DrDimont versions 0.1.3 dated 2022-05-17 and 0.1.4 dated 2022-09-23

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More information about DrDimont at CRAN
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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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Package wdnr.gis updated to version 0.1.4 with previous version 0.1.3 dated 2022-03-17

Title: Pull Spatial Layers from 'WDNR ArcGIS REST API'
Description: Functions for finding and pulling data from the 'Wisconsin Department of Natural Resources ArcGIS REST APIs' <https://dnrmaps.wi.gov/arcgis/rest/services> and <https://dnrmaps.wi.gov/arcgis2/rest/services>.
Author: Paul Frater [aut, cre] , Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>

Diff between wdnr.gis versions 0.1.3 dated 2022-03-17 and 0.1.4 dated 2022-09-23

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Package memoiR updated to version 1.2-2 with previous version 1.2-1 dated 2022-08-14

Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem. 'memoiR' makes it easy. It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>

Diff between memoiR versions 1.2-1 dated 2022-08-14 and 1.2-2 dated 2022-09-23

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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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Package desla updated to version 0.2.0 with previous version 0.1.0 dated 2021-11-11

Title: Desparsified Lasso Inference for Time Series
Description: Calculates the desparsified lasso as originally introduced in van de Geer et al. (2014) <doi:10.1214/14-AOS1221>, and provides inference suitable for high-dimensional time series, based on the long run covariance estimator in Adamek et al. (2020) <arXiv:2007.10952>. Also estimates high-dimensional local projections by the desparsified lasso, as described in Adamek et al. (2022) <arXiv:2209.03218>.
Author: Robert Adamek [cre, aut], Stephan Smeekes [aut], Ines Wilms [aut]
Maintainer: Robert Adamek <robertadamek94@gmail.com>

Diff between desla versions 0.1.0 dated 2021-11-11 and 0.2.0 dated 2022-09-23

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Package volcano3D updated to version 2.0.8 with previous version 2.0.0 dated 2022-07-05

Title: 3D Volcano Plots and Polar Plots for Three-Class Data
Description: Generates interactive plots for analysing and visualising three-class high dimensional data. It is particularly suited to visualising differences in continuous attributes such as gene/protein/biomarker expression levels between three groups. Differential gene/biomarker expression analysis between two classes is typically shown as a volcano plot. However, with three groups this type of visualisation is particularly difficult to interpret. This package generates 3D volcano plots and 3-way polar plots for easier interpretation of three-class data.
Author: Katriona Goldmann [aut, cre] , Myles Lewis [aut]
Maintainer: Katriona Goldmann <k.goldmann@qmul.ac.uk>

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Package cffr updated to version 0.3.0 with previous version 0.2.3 dated 2022-08-15

Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0 <doi:10.5281/zenodo.5171937> is a human and machine readable file format which provides citation metadata for software. This package provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph] , Joao Martins [rev] , Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>

Diff between cffr versions 0.2.3 dated 2022-08-15 and 0.3.0 dated 2022-09-23

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Package tidyterra updated to version 0.2.1 with previous version 0.2.0 dated 2022-06-21

Title: 'tidyverse' Methods and 'ggplot2' Utils for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of the 'terra' package. It includes also new 'geom_' functions that provide a convenient way of visualizing 'terra' objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph] , Dewey Dunnington [ctb] , ggplot2 authors [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>

Diff between tidyterra versions 0.2.0 dated 2022-06-21 and 0.2.1 dated 2022-09-23

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Package this.path updated to version 1.0.1 with previous version 1.0.0 dated 2022-09-21

Title: Get Executing Script's Path, from 'RStudio', 'Rgui', 'VSCode', 'Rscript' (Shells Including Windows Command-Line / / Unix Terminal), and 'source'
Description: Determine the full path of the executing script. Works when running a line or selection from a script in 'RStudio', 'Rgui', and 'VSCode', when using 'source', 'sys.source', 'debugSource' in 'RStudio', and 'testthat::source_file', and when running from a shell.
Author: Andrew Simmons
Maintainer: Andrew Simmons <akwsimmo@gmail.com>

Diff between this.path versions 1.0.0 dated 2022-09-21 and 1.0.1 dated 2022-09-23

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Package Require updated to version 0.1.2 with previous version 0.0.13 dated 2021-05-31

Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that makes rerun-tolerant versions of 'install.packages' and `require` for CRAN packages, packages no longer on CRAN (i.e., archived), specific versions of packages, and GitHub packages. This approach is developed to create reproducible workflows that are flexible and fast enough to use while in development stages, while able to build snapshots once a stable package collection is found. As with other functions in a reproducible workflow, this package emphasizes functions that return the same result whether it is the first or subsequent times running the function, with subsequent times being sufficiently fast that they can be run every time without undue waiting burden on the user or developer.
Author: Eliot J B McIntire [aut, cre] , Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>

Diff between Require versions 0.0.13 dated 2021-05-31 and 0.1.2 dated 2022-09-23

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Package h2o updated to version 3.38.0.1 with previous version 3.36.1.2 dated 2022-05-27

Title: R Interface for the 'H2O' Scalable Machine Learning Platform
Description: R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Author: Erin LeDell [aut, cre], Navdeep Gill [aut], Spencer Aiello [aut], Anqi Fu [aut], Arno Candel [aut], Cliff Click [aut], Tom Kraljevic [aut], Tomas Nykodym [aut], Patrick Aboyoun [aut], Michal Kurka [aut], Michal Malohlava [aut], Ludi Rehak [ctb], Eric [...truncated...]
Maintainer: Erin LeDell <erin@h2o.ai>

Diff between h2o versions 3.36.1.2 dated 2022-05-27 and 3.38.0.1 dated 2022-09-23

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Package DatabaseConnector updated to version 5.1.0 with previous version 5.0.4 dated 2022-06-28

Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server', 'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', and 'SQLite'). Also includes support for fetching data as 'Andromeda' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases (except SQLite).
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut], Observational Health Data Science and Informatics [cph], Microsoft Inc. [cph] , PostgreSQL Global Development Group [cph] , Oracle Inc. [cph] , Amazon Inc. [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

Diff between DatabaseConnector versions 5.0.4 dated 2022-06-28 and 5.1.0 dated 2022-09-23

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Package cli updated to version 3.4.1 with previous version 3.4.0 dated 2022-09-08

Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.
Author: Gabor Csardi [aut, cre], Hadley Wickham [ctb], Kirill Mueller [ctb], RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between cli versions 3.4.0 dated 2022-09-08 and 3.4.1 dated 2022-09-23

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Package vglmer updated to version 1.0.2 with previous version 1.0.1 dated 2022-09-17

Title: Variational Inference for Hierarchical Generalized Linear Models
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.
Author: Max Goplerud [aut, cre]
Maintainer: Max Goplerud <mgoplerud@pitt.edu>

Diff between vglmer versions 1.0.1 dated 2022-09-17 and 1.0.2 dated 2022-09-23

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Package Rgff updated to version 0.1.5 with previous version 0.1.4 dated 2022-09-19

Title: R Utilities for GFF Files
Description: R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.
Author: Juan Antonio Garcia-Martin [cre, aut] , Juan Carlos Oliveros [aut, ctb] , Rafael Torres-Perez [aut, ctb]
Maintainer: Juan Antonio Garcia-Martin <ja.garcia@cnb.csic.es>

Diff between Rgff versions 0.1.4 dated 2022-09-19 and 0.1.5 dated 2022-09-23

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Package fbst updated to version 1.9 with previous version 1.7 dated 2022-03-08

Title: The Full Bayesian Evidence Test, Full Bayesian Significance Test and the e-Value
Description: Provides access to a range of functions for computing and visualizing the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative, and the Full Bayesian Evidence Test (FBET) and the (generalized) Bayesian evidence value for testing a composite (or interval) hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>

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Package cvCovEst updated to version 1.1.1 with previous version 1.1.0 dated 2022-05-04

Title: Cross-Validated Covariance Matrix Estimation
Description: An efficient cross-validated approach for covariance matrix estimation, particularly useful in high-dimensional settings. This method relies upon the theory of loss-based estimator selection to identify the optimal estimator of the covariance matrix from among a prespecified set of candidates.
Author: Philippe Boileau [aut, cre, cph] , Nima Hejazi [aut] , Brian Collica [aut] , Jamarcus Liu [ctb], Mark van der Laan [ctb, ths] , Sandrine Dudoit [ctb, ths]
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>

Diff between cvCovEst versions 1.1.0 dated 2022-05-04 and 1.1.1 dated 2022-09-23

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Package CommKern updated to version 1.0.1 with previous version 1.0.0 dated 2022-09-20

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).
Author: Alexandria Jensen [aut, cre] , Peter DeWitt [ctb] , Debashis Ghosh [ths]
Maintainer: Alexandria Jensen <alexandria.jensen@cuanschutz.edu>

Diff between CommKern versions 1.0.0 dated 2022-09-20 and 1.0.1 dated 2022-09-23

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Package autostsm updated to version 3.0.3 with previous version 3.0.2 dated 2022-09-02

Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components, plus optionality for structural interpolation, using the Kalman filter. Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models" <doi:10.1093/oxfordhb/9780195398649.013.0006>. 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/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>

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Package strvalidator updated to version 2.4.0 with previous version 2.3.0 dated 2020-07-10

Title: Process Control and Validation of Forensic STR Kits
Description: An open source platform for validation and process control. Tools to analyze data from internal validation of forensic short tandem repeat (STR) kits are provided. The tools are developed to provide the necessary data to conform with guidelines for internal validation issued by the European Network of Forensic Science Institutes (ENFSI) DNA Working Group, and the Scientific Working Group on DNA Analysis Methods (SWGDAM). A front-end graphical user interface is provided. More information about each function can be found in the respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>

Diff between strvalidator versions 2.3.0 dated 2020-07-10 and 2.4.0 dated 2022-09-23

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Package hBayesDM updated to version 1.2.1 with previous version 1.2.0 dated 2022-09-10

Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of various computational models with a single line of coding (Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: Woo-Young Ahn [aut, cre], Nate Haines [aut], Lei Zhang [aut], Harhim Park [ctb], Jaeyeong Yang [ctb], Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>

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Package umbridge updated to version 1.0 with previous version 0.9 dated 2022-09-12

Title: Integration for the UM-Bridge Protocol
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.
Author: Linus Seelinger [aut, cre]
Maintainer: Linus Seelinger <mail@linusseelinger.de>

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Package anndata updated to version 0.7.5.5 with previous version 0.7.5.4 dated 2022-08-23

Title: 'anndata' for R
Description: A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format.
Author: Philipp Angerer [ccp] , Alex Wolf [ccp] , Isaac Virshup [ccp] , Sergei Rybakov [ccp] , Robrecht Cannoodt [aut, cre, cph]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package AlphaPart updated to version 0.9.7 with previous version 0.9.5 dated 2022-07-07

Title: Partition/Decomposition of Breeding Values by Paths of Information
Description: A software that implements a method for partitioning genetic trends to quantify the sources of genetic gain in breeding programmes. The partitioning method is described in Garcia-Cortes et al. (2008) <doi:10.1017/S175173110800205X>. The package includes the main function AlphaPart for partitioning breeding values and auxiliary functions for manipulating data and summarizing, visualizing, and saving results.
Author: Gregor Gorjanc [aut, cre] , Jana Obsteter [aut] , Thiago de Paula Oliveira [aut]
Maintainer: Gregor Gorjanc <highlander.research.lab@gmail.com>

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Package GillespieSSA2 updated to version 0.2.10 with previous version 0.2.8 dated 2021-05-18

Title: Gillespie's Stochastic Simulation Algorithm for Impatient People
Description: A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended. Cannoodt and Saelens et al. (2020) <doi:10.1101/2020.02.06.936971>.
Author: Robrecht Cannoodt [aut, cre] , Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package hadron (with last version 3.2.0) was removed from CRAN

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

2022-09-09 3.2.0
2020-09-10 3.1.2
2020-07-05 3.1.0

Permanent link
Package httk (with last version 2.2.0) was removed from CRAN

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

2022-09-08 2.2.0
2022-03-25 2.1.0
2021-05-10 2.0.4

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Package mmpca (with last version 2.0.2) was removed from CRAN

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

2022-09-08 2.0.2

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Package RVIpkg updated to version 0.3.1 with previous version 0.3.0 dated 2022-03-10

Title: Regional Vulnerability Index
Description: The Regional Vulnerability Index (RVI), a statistical measure of brain structural abnormality, quantifies an individual's similarity to the expected pattern (effect size) of deficits in schizophrenia (Kochunov P, Fan F, Ryan MC, et al. (2020) <doi:10.1002/hbm.25045>).
Author: Si Gao [aut, cre, dtc] , Peter Kochunov [aut, dtc, cph, fnd] , Kathryn Hatch [ctb, dtc] , Yizhou Ma [ctb, dtc] , Fatima Talib [ctb]
Maintainer: Si Gao <sgao@som.umaryland.edu>

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Package dynutils updated to version 1.0.10 with previous version 1.0.9 dated 2021-10-08

Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <https://dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] , Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Thu, 22 Sep 2022

Package rxode2 updated to version 2.0.8 with previous version 2.0.7 dated 2022-05-17

Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] , Melissa Hallow [aut], Wenping Wang [aut], Zufar Mulyukov [ctb], Alan Hindmarsh [ctb], Awad H. Al-Mohy [ctb], Matt Dowle [ctb], Cleve Moler [ctb], David Cooley [ctb], Drew Schmidt [ctb], Arun Srinivasan [ctb], Ernst Hair [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>

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Package GeoTcgaData updated to version 1.1.1.992 with previous version 1.1.1 dated 2022-08-12

Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>

Diff between GeoTcgaData versions 1.1.1 dated 2022-08-12 and 1.1.1.992 dated 2022-09-22

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Package bbknnR updated to version 1.0.2 with previous version 1.0.1 dated 2022-08-23

Title: Perform Batch Balanced KNN in R
Description: A fast and intuitive batch effect removal tool for single-cell data. BBKNN is originally used in the 'scanpy' python package, and now can be used with 'Seurat' seamlessly.
Author: Yuchen Li [aut, cre]
Maintainer: Yuchen Li <liyuchen_1995@outlook.com>

Diff between bbknnR versions 1.0.1 dated 2022-08-23 and 1.0.2 dated 2022-09-22

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Package IsoriX updated to version 0.9.0 with previous version 0.8.3 dated 2022-09-12

Title: Isoscape Computation and Inference of Spatial Origins using Mixed Models
Description: Building isoscapes using mixed models and inferring the geographic origin of samples based on their isotopic ratios. This package is essentially a simplified interface to several other packages which implements a new statistical framework based on mixed models. It uses 'spaMM' for fitting and predicting isoscapes, and assigning an organism's origin depending on its isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for plotting the maps produced with 'raster' using 'lattice'.
Author: Alexandre Courtiol [aut, cre] , Francois Rousset [aut] , Marie-Sophie Rohwaeder [aut], Stephanie Kramer-Schadt [aut]
Maintainer: Alexandre Courtiol <alexandre.courtiol@gmail.com>

Diff between IsoriX versions 0.8.3 dated 2022-09-12 and 0.9.0 dated 2022-09-22

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More information about IsoriX at CRAN
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