Thu, 21 Jul 2022

Package Ecfun updated to version 0.3-0 with previous version 0.2-6 dated 2022-06-15

Title: Functions for 'Ecdat'
Description: Functions and vignettes to update data sets in 'Ecdat' and to create, manipulate, plot, and analyze those and similar data sets.
Author: Spencer Graves <spencer.graves@effectivedefense.org>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>

Diff between Ecfun versions 0.2-6 dated 2022-06-15 and 0.3-0 dated 2022-07-21

 DESCRIPTION                              |    8 +-
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 vignettes/UpdatingUSGDPpresidents.Rmd    |    2 
 12 files changed, 130 insertions(+), 103 deletions(-)

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Package visvow updated to version 1.3.5 with previous version 1.3.4 dated 2022-03-25

Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>

Diff between visvow versions 1.3.4 dated 2022-03-25 and 1.3.5 dated 2022-07-21

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 MD5                                |   12 +++---
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 7 files changed, 85 insertions(+), 51 deletions(-)

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New package video with initial version 0.1.0
Package: video
Title: 'Shiny' Extension of 'video.js'
Version: 0.1.0
Description: Video interactivity within 'shiny' applications using 'video.js'. Enables the status of the video to be sent from the UI to the server, and allows events such as playing and pausing the video to be triggered from the server.
License: Apache License (>= 2)
URL: https://github.com/ashbaldry/video, https://github.com/videojs/video.js
BugReports: https://github.com/ashbaldry/video/issues
Encoding: UTF-8
Depends: R (>= 2.10)
Imports: shiny, htmlwidgets, jsonlite
Suggests: rmarkdown, knitr, shinytest2, globals, testthat (>= 3.0.0)
Language: en-GB
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 17:11:08 UTC; arbal
Author: Ashley Baldry [aut, cre], Steve Heffernan [aut]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-21 17:50:02 UTC

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New package rGV with initial version 0.0.1
Package: rGV
Version: 0.0.1
Date: 2022-07-21
Title: Analysis of Continuous Glucose Monitor Data
Author: Evan Olawsky [aut, cre], Yuan Zhang [ctb], Lynn Eberly [ctb]
Maintainer: Evan Olawsky <evanolawsky@gmail.com>
Depends: R (>= 3.2.0), chron
Description: Reads in continuous glucose monitor data of many different formats, calculates a host of glycemic variability metrics, and plots glucose over time.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Imports: pastecs, zoo
NeedsCompilation: no
Packaged: 2022-07-21 15:50:48 UTC; overlord
Repository: CRAN
Date/Publication: 2022-07-21 17:40:02 UTC

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New package netcom with initial version 2.1.6
Package: netcom
Title: NETwork COMparison Inference
Version: 2.1.6
Date: 2022-7-19
Description: Infer system functioning with empirical NETwork COMparisons. These methods are part of a growing paradigm in network science that uses relative comparisons of networks to infer mechanistic classifications and predict systemic interventions. They have been developed and applied in Langendorf and Burgess (2021) <doi:10.1038/s41598-021-99251-7>, Langendorf (2020) <doi:10.1201/9781351190831-6>, and Langendorf and Goldberg (2019) <arXiv:1912.12551>.
URL: https://github.com/langendorfr/netcom
Repository: CRAN
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.1.0)
Imports: stats, dplyr, tibble, clue, expm, igraph, Matrix, pdist, pracma, vegan, magrittr, foreach, parallel, doParallel, optimx, GenSA, rlang, ggfortify, ggplot2, ggraph, reshape2
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 16:08:26 UTC; ryan
Author: Ryan Langendorf [aut, cre], Debra Goldberg [ctb], Matthew Burgess [ctb]
Maintainer: Ryan Langendorf <ryan.langendorf@colorado.edu>
Date/Publication: 2022-07-21 17:40:06 UTC

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New package howler with initial version 0.2.0
Package: howler
Title: 'Shiny' Extension of 'howler.js'
Version: 0.2.0
Description: Audio interactivity within 'shiny' applications using 'howler.js'. Enables the status of the audio player to be sent from the UI to the server, and events such as playing and pausing the audio can be triggered from the server.
License: MIT + file LICENSE
URL: https://github.com/ashbaldry/howler, https://github.com/goldfire/howler.js
BugReports: https://github.com/ashbaldry/howler/issues
Encoding: UTF-8
Imports: shiny, htmlwidgets
Suggests: rmarkdown, knitr, shinytest2, globals, testthat (>= 3.0.0)
Language: en-GB
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 17:06:04 UTC; arbal
Author: Ashley Baldry [aut, cre], James Simpson [aut]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-21 17:50:05 UTC

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Package dm updated to version 1.0.0 with previous version 0.3.0 dated 2022-07-06

Title: Relational Data Models
Description: Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut], Kirill Mueller [aut, cre] , Antoine Fabri [ctb], Darko Bergant [aut], Katharina Brunner [ctb], James Wondrasek [ctb], Indrajeet Patil [ctb] , Maelle Salmon [ctb] , energie360° AG [fnd], cynkra GmbH [fnd, cph]
Maintainer: Kirill Mueller <krlmlr+r@mailbox.org>

Diff between dm versions 0.3.0 dated 2022-07-06 and 1.0.0 dated 2022-07-21

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Package rebmix updated to version 2.14.1 with previous version 2.14.0 dated 2022-02-02

Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac, uniform or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] , Branislav Panic [ctb] , Jernej Klemenc [ctb] , Simon Oman [ctb]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>

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Package R.cache updated to version 0.16.0 with previous version 0.15.0 dated 2021-04-30

Title: Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations
Description: Memoization can be used to speed up repetitive and computational expensive function calls. The first time a function that implements memoization is called the results are stored in a cache memory. The next time the function is called with the same set of parameters, the results are momentarily retrieved from the cache avoiding repeating the calculations. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between R.cache versions 0.15.0 dated 2021-04-30 and 0.16.0 dated 2022-07-21

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Package PhaseTypeR updated to version 1.0.4 with previous version 1.0.3 dated 2022-07-14

Title: General-Purpose Phase-Type Functions
Description: General implementation of core function from phase-type theory. 'PhaseTypeR' can be used to model continuous and discrete phase-type distributions, both univariate and multivariate. The package includes functions for outputting the mean and (co)variance of phase-type distributions; their density, probability and quantile functions; functions for random draws; functions for reward-transformation; and functions for plotting the distributions as networks. For more information on these functions please refer to Bladt and Nielsen (2017, ISBN: 978-1-4939-8377-3) and Campillo Navarro (2019) <https://orbit.dtu.dk/en/publications/order-statistics-and-multivariate-discrete-phase-type-distributio>.
Author: Iker Rivas-Gonzalez [aut, cre] , Asger Hobolth [aut], Lars Noervang Andersen [aut], Colin Guetemme [aut]
Maintainer: Iker Rivas-Gonzalez <ikerrivas96@gmail.com>

Diff between PhaseTypeR versions 1.0.3 dated 2022-07-14 and 1.0.4 dated 2022-07-21

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Package Rforestry updated to version 0.9.0.116 with previous version 0.9.0.95 dated 2022-03-09

Title: Random Forests, Linear Trees, and Gradient Boosting for Inference and Interpretability
Description: Provides fast implementations of Honest Random Forests, Gradient Boosting, and Linear Random Forests, with an emphasis on inference and interpretability. Additionally contains methods for variable importance, out-of-bag prediction, regression monotonicity, and several methods for missing data imputation. Soren R. Kunzel, Theo F. Saarinen, Edward W. Liu, Jasjeet S. Sekhon (2019) <arXiv:1906.06463>.
Author: Soeren Kuenzel [aut], Theo Saarinen [aut, cre], Simon Walter [aut], Edward Liu [aut], Allen Tang [aut], Jasjeet Sekhon [aut]
Maintainer: Theo Saarinen <theo_s@berkeley.edu>

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Package heuristicsmineR updated to version 0.2.7 with previous version 0.2.6 dated 2022-07-14

Title: Discovery of Process Models with the Heuristics Miner
Description: Provides the heuristics miner algorithm for process discovery as proposed by Weijters et al. (2011) <doi:10.1109/CIDM.2011.5949453>. The algorithm builds a causal net from an event log created with the 'bupaR' package. Event logs are a set of ordered sequences of events for which 'bupaR' provides the S3 class eventlog(). The discovered causal nets can be visualised as 'htmlwidgets' and it is possible to annotate them with the occurrence frequency or processing and waiting time of process activities.
Author: Felix Mannhardt [aut, cre]
Maintainer: Felix Mannhardt <f.mannhardt@tue.nl>

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Package fossilbrush updated to version 1.0.3 with previous version 1.0.2 dated 2022-05-23

Title: Automated Cleaning of Fossil Occurrence Data
Description: Functions to automate the detection and resolution of taxonomic and stratigraphic errors in fossil occurrence datasets. Functions were developed using data from the Paleobiology Database.
Author: Joe Flannery-Sutherland [aut, cre] , Nussaïbah Raja-Schoob [aut, ctb], Ádam Kocsis [aut, ctb], Wolfgang Kiessling [aut]
Maintainer: Joe Flannery-Sutherland <jf15558@bristol.ac.uk>

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Package ptools updated to version 1.0.1 with previous version 1.0.0 dated 2022-07-16

Title: Tools for Poisson Data
Description: Functions used for analyzing count data, mostly crime counts. Includes checking difference in two Poisson counts (e-test), checking the fit for a Poisson distribution, small sample tests for counts in bins, Weighted Displacement Difference test (Wheeler and Ratcliffe, 2018) <doi:10.1186/s40163-018-0085-5>, to evaluate crime changes over time in treated/control areas. Additionally includes functions for aggregating spatial data and spatial feature engineering.
Author: Andrew Wheeler [aut, cre]
Maintainer: Andrew Wheeler <apwheele@gmail.com>

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Package messydates updated to version 0.3.1 with previous version 0.3.0 dated 2022-06-02

Title: A Flexible Class for Messy Dates
Description: Contains a set of tools for constructing and coercing into and from the "mdate" class. This date class implements ISO 8601-2:2019(E) and allows regular dates to be annotated to express unspecified date components, approximate or uncertain date components, date ranges, and sets of dates. This is useful for describing and analysing temporal information, whether historical or recent, where date precision may vary.
Author: James Hollway [cre, aut, ctb] , Henrique Sposito [ctb] , Jael Tan [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>

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Package datardis updated to version 0.0.3 with previous version 0.0.2 dated 2021-11-15

Title: Data from the Doctor Who Series
Description: Explore data related to the Doctor Who TV series.
Author: Jonathan Kitt [aut, cre]
Maintainer: Jonathan Kitt <jonathan.kitt@protonmail.com>

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Package spant updated to version 2.1.0 with previous version 2.0.0 dated 2022-06-22

Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] , Yong Wang [ctb], John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

Diff between spant versions 2.0.0 dated 2022-06-22 and 2.1.0 dated 2022-07-21

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Package Rgff updated to version 0.1.3 with previous version 0.1.2 dated 2022-06-27

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 0.1.2 dated 2022-06-27 and 0.1.3 dated 2022-07-21

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Package mlr3 updated to version 0.13.4 with previous version 0.13.3 dated 2022-03-01

Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the building blocks of machine learning. Provides 'R6' objects for tasks, learners, resamplings, and measures. The package is geared towards scalability and larger datasets by supporting parallelization and out-of-memory data-backends like databases. While 'mlr3' focuses on the core computational operations, add-on packages provide additional functionality.
Author: Michel Lang [cre, aut] , Bernd Bischl [aut] , Jakob Richter [aut] , Patrick Schratz [aut] , Giuseppe Casalicchio [ctb] , Stefan Coors [ctb] , Quay Au [ctb] , Martin Binder [aut], Marc Becker [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3 versions 0.13.3 dated 2022-03-01 and 0.13.4 dated 2022-07-21

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More information about mlr3 at CRAN
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Package stars updated to version 0.5-6 with previous version 0.5-5 dated 2021-12-18

Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] , Michael Sumner [ctb] , Etienne Racine [ctb], Adriano Fantini [ctb], David Blodgett [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between stars versions 0.5-5 dated 2021-12-18 and 0.5-6 dated 2022-07-21

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New package robustmeta with initial version 1.1-1
Package: robustmeta
Title: Robust Inference for Meta-Analysis with Influential Outlying Studies
Version: 1.1-1
Date: 2022-07-09
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Description: Robust inference methods for fixed-effect and random-effects models of meta-analysis are implementable. The robust methods are developed using the density power divergence that is a robust estimating criterion developed in machine learning theory, and can effectively circumvent biases and misleading results caused by influential outliers. The density power divergence is originally introduced by Basu et al. (1998) <doi:10.1093/biomet/85.3.549>, and the meta-analysis methods are developed by Noma et al. (2022) <forthcoming>.
Depends: R (>= 3.5.0)
Imports: stats, metafor
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-21 09:34:00 UTC; Hisashi
Author: Hisashi Noma [aut, cre], Shonosuke Sugasawa [aut], Toshi A. Furukawa [aut]
Repository: CRAN
Date/Publication: 2022-07-21 12:50:02 UTC

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New package rgrass with initial version 0.3-2
Package: rgrass
Version: 0.3-2
Date: 2022-07-21
Title: Interface Between 'GRASS' Geographical Information System and 'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Depends: R (>= 3.3.0), XML
Imports: stats, utils, methods
Suggests: terra, sp (>= 0.9), knitr, rmarkdown, sf, stars, raster
VignetteBuilder: knitr
SystemRequirements: GRASS (>= 7)
License: GPL (>= 2)
URL: https://rsbivand.github.io/rgrass/, https://grass.osgeo.org/, https://github.com/rsbivand/rgrass, https://lists.osgeo.org/mailman/listinfo/grass-stats
BugReports: https://github.com/rsbivand/rgrass/issues/
NeedsCompilation: no
Packaged: 2022-07-21 09:19:06 UTC; rsb
Author: Roger Bivand [cre, aut] , Rainer Krug [ctb] , Markus Neteler [ctb] , Sebastian Jeworutzki [ctb] , Floris Vanderhaeghe [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Repository: CRAN
Date/Publication: 2022-07-21 12:50:05 UTC

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New package normalizeH with initial version 1.0.0
Package: normalizeH
Version: 1.0.0
Date: 2022-07-20
Title: Normalize Hadamard Matrix
Author: Baidya Nath Mandal [aut, cre]
Maintainer: Baidya Nath Mandal <mandal.stat@gmail.com>
Depends: R (>= 4.2.0)
Suggests: HadamardR
Description: Normalize a given Hadamard matrix. A Hadamard matrix is said to be normalized when its first row and first column entries are all 1, see Hedayat, A. and Wallis, W. D. (1978) "Hadamard matrices and their applications. The Annals of Statistics, 1184-1238." <doi:10.1214/aos/1176344370>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-07-20 05:27:10 UTC; b
Repository: CRAN
Date/Publication: 2022-07-21 12:30:02 UTC

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New package htmcglm with initial version 0.0.1
Package: htmcglm
Title: Hypothesis Testing for McGLMs
Version: 0.0.1
Author: Lineu Alberto Cavazani de Freitas [aut, cre], Wagner Hugo Bonat [ctb], Walmes Marques Zeviani [ctb]
Maintainer: Lineu Alberto Cavazani de Freitas <lineuacf@gmail.com>
Description: Performs hypothesis testing for multivariate covariance generalized linear models (McGLMs). McGLM is a general framework for non-normal multivariate data analysis, designed to handle multivariate response variables, along with a wide range of temporal and spatial correlation structures defined in terms of a covariance link function combined with a matrix linear predictor involving known matrices. The models take non-normality into account in the conventional way by means of a variance function, and the mean structure is modelled by means of a link function and a linear predictor. The models are fitted using an efficient Newton scoring algorithm based on quasi-likelihood and Pearson estimating functions, using only second-moment assumptions. This provides a unified approach to a wide variety of different types of response variables and covariance structures, including multivariate extensions of repeated measures, time series, longitudinal, spatial and spatio-temporal structures. The package offers a user-friendly interface for fitting McGLMs similar to the glm() R function.
License: MIT + file LICENSE
URL: https://github.com/lineu96/htmcglm
Encoding: UTF-8
Imports: stats, doBy, Matrix, mcglm, sjmisc, stringr
NeedsCompilation: no
Packaged: 2022-07-20 20:13:15 UTC; lacf14
Repository: CRAN
Date/Publication: 2022-07-21 12:10:06 UTC

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New package ensModelVis with initial version 0.1.0
Package: ensModelVis
Title: Visualisations for Model Ensembles
Version: 0.1.0
Description: Displays for model fits of multiple models and their ensembles. For classification models, the plots are heatmaps, for regression, scatterplots.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, forcats, ggplot2, magrittr, rlang, tidyr
URL: https://github.com/domijan/ensModelVis
BugReports: https://github.com/domijan/ensModelVis/issues
Suggests: discrim, glmnet, kernlab, knitr, MASS, nnet, ranger, rmarkdown, stacks, stringr, tidymodels
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 06:36:40 UTC; katarina
Author: Katarina Domijan [aut, cre]
Maintainer: Katarina Domijan <domijank@tcd.ie>
Repository: CRAN
Date/Publication: 2022-07-21 12:40:02 UTC

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New package connectapi with initial version 0.1.1.1
Package: connectapi
Title: Utilities for Interacting with the 'RStudio Connect' Server API
Version: 0.1.1.1
Description: Provides a helpful 'R6' class and methods for interacting with the 'RStudio Connect' Server API along with some meaningful utility functions for regular tasks. API documentation varies by 'RStudio Connect' installation and version, but the latest documentation is also hosted publicly at <https://docs.rstudio.com/connect/api/>.
License: MIT + file LICENSE
URL: https://github.com/rstudio/connectapi
Imports: config, dplyr, fs, glue, httr, lifecycle, magrittr, progress, purrr, R6, rlang (>= 0.4.2), tibble, uuid, vctrs (>= 0.3.0), yaml, bit64, jsonlite
Suggests: crayon, flexdashboard, ggplot2, gridExtra, htmltools, knitr, lubridate, processx, rmarkdown, rprojroot, spelling, testthat, rsconnect, webshot2, covr, mockery, devtools
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2022-07-20 20:50:15 UTC; r124525
Author: Sean Lopp [aut], Cole Arendt [aut, cre], RStudio PBC [cph, fnd]
Maintainer: Cole Arendt <cole@rstudio.com>
Repository: CRAN
Date/Publication: 2022-07-21 12:20:02 UTC

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New package amapro with initial version 0.1.0
Package: amapro
Title: Thin Wrapper for Mapping Library 'AMap' by 'AutoNavi'
Date: 2022-07-20
Version: 0.1.0
Author: Larry Helgason [aut, cre, cph]
Maintainer: Larry Helgason <larry@helgasoft.com>
Description: Build and control interactive 2D and 3D maps with 'R/Shiny'. Lean set of powerful commands wrapping native calls to 'AMap' <https://lbs.amap.com/api/jsapi-v2/summary/>. Deliver rich mapping functionality with minimal overhead.
URL: https://github.com/helgasoft/amapro/
BugReports: https://github.com/helgasoft/amapro/issues/
Depends: R (>= 4.1.0)
Imports: htmlwidgets, shiny (>= 1.7.0), tcltk (>= 4.2.0)
Suggests: knitr, rmarkdown
License: Apache License (>= 2)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 03:31:33 UTC; gugu
Repository: CRAN
Date/Publication: 2022-07-21 12:30:04 UTC

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Package AdaptFitOS updated to version 0.69 with previous version 0.68 dated 2022-02-25

Title: Adaptive Semiparametric Additive Regression with Simultaneous Confidence Bands and Specification Tests
Description: Fits semiparametric additive regression models with spatially adaptive penalized splines and computes simultaneous confidence bands and associated specification (lack-of-fit) tests. Simultaneous confidence bands cover the entire curve with a prescribed level of confidence and allow us to assess the estimation uncertainty for the whole curve. In contrast to pointwise confidence bands, they permit statements about the statistical significance of certain features (e.g. bumps) in the underlying curve.The method allows for handling of spatially heterogeneous functions and their derivatives as well as heteroscedasticity in the data. See Wiesenfarth et al. (2012) <doi:10.1080/01621459.2012.682809>.
Author: Manuel Wiesenfarth [aut, cre], Tatyana Krivobokova [aut], Matt Wand [ctb] , Catherine Loader [cph, ctb] , Jiayang Sun [cph, ctb] , Lucent Technologies [cph]
Maintainer: Manuel Wiesenfarth <m.wiesenfarth@dkfz.de>

Diff between AdaptFitOS versions 0.68 dated 2022-02-25 and 0.69 dated 2022-07-21

 DESCRIPTION       |    8 ++++----
 MD5               |    8 ++++----
 build/partial.rdb |binary
 src/local.h       |    2 +-
 src/smisc.c       |    6 +++---
 5 files changed, 12 insertions(+), 12 deletions(-)

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Package parallelly updated to version 1.32.1 with previous version 1.32.0 dated 2022-06-07

Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between parallelly versions 1.32.0 dated 2022-06-07 and 1.32.1 dated 2022-07-21

 DESCRIPTION               |    8 ++++----
 MD5                       |   14 +++++++-------
 NEWS.md                   |   10 ++++++++++
 R/makeClusterPSOCK.R      |    1 +
 R/options.R               |   20 ++++++++++----------
 man/availableCores.Rd     |    6 +++---
 man/parallelly.options.Rd |   20 ++++++++++----------
 tests/makeClusterPSOCK.R  |    3 +++
 8 files changed, 48 insertions(+), 34 deletions(-)

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New package nextGenShinyApps with initial version 1.5
Package: nextGenShinyApps
Title: Advanced Tools for Building the Next Generation of 'Shiny' Applications and Dashboards
Version: 1.5
Author: Obinna Obianom
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Description: Responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts and style sheets are based on 'jQuery' <https://jquery.com/> and 'Bootstrap' <https://getbootstrap.com/>.
License: MIT + file LICENSE
URL: https://github.com/oobianom/nextGenShinyApps
BugReports: https://github.com/oobianom/nextGenShinyApps
Depends: R (>= 3.4)
Imports: utils, shiny, htmltools
Suggests: rmarkdown, knitr, qpdf
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-US
LazyData: false
NeedsCompilation: no
Packaged: 2022-07-20 17:15:30 UTC; in198
Repository: CRAN
Date/Publication: 2022-07-21 12:00:02 UTC

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Package mirai updated to version 0.5.2 with previous version 0.5.0 dated 2022-06-21

Title: Minimalist Async Evaluation Framework for R
Description: Extremely simple and lightweight method for concurrent / parallel code execution, built on 'nanonext' and 'NNG' (Nanomsg Next Gen) technology.
Author: Charlie Gao [aut, cre] , Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>

Diff between mirai versions 0.5.0 dated 2022-06-21 and 0.5.2 dated 2022-07-21

 DESCRIPTION       |   10 +++++-----
 MD5               |   10 +++++-----
 NAMESPACE         |    3 ++-
 NEWS.md           |    4 ++++
 R/mirai-package.R |    5 ++---
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 6 files changed, 23 insertions(+), 19 deletions(-)

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Package fdaMocca updated to version 0.1-1 with previous version 0.1-0 dated 2021-10-21

Title: Model-Based Clustering for Functional Data with Covariates
Description: Routines for model-based functional cluster analysis for functional data with optional covariates. The idea is to cluster functional subjects (often called functional objects) into homogenous groups by using spline smoothers (for functional data) together with scalar covariates. The spline coefficients and the covariates are modelled as a multivariate Gaussian mixture model, where the number of mixtures corresponds to the number of clusters. The parameters of the model are estimated by maximizing the observed mixture likelihood via an EM algorithm (Arnqvist and Sjöstedt de Luna, 2019) <arXiv:1904.10265>. The clustering method is used to analyze annual lake sediment from lake Kassjön (Northern Sweden) which cover more than 6400 years and can be seen as historical records of weather and climate.
Author: Natalya Pya Arnqvist[aut, cre], Per Arnqvist [aut, cre], Sara Sjoestedt de Luna [aut]
Maintainer: Natalya Pya Arnqvist <nat.pya@gmail.com>

Diff between fdaMocca versions 0.1-0 dated 2021-10-21 and 0.1-1 dated 2022-07-21

 ChangeLog            |only
 DESCRIPTION          |    8 ++++----
 MD5                  |    9 +++++----
 R/fitmocca.r         |   10 +++++-----
 man/mocca.Rd         |    2 +-
 man/summary.mocca.Rd |    2 +-
 6 files changed, 16 insertions(+), 15 deletions(-)

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New package EnrichIntersect with initial version 0.1
Package: EnrichIntersect
Title: Enrichment Analysis and Intersecting Sankey Diagram
Version: 0.1
Date: 2022-07-20
Description: A flexible tool for enrichment analysis based on user-defined sets is provided. 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.
License: MIT + file LICENSE
Depends: R (>= 4.0)
Encoding: UTF-8
Imports: ggplot2, dplyr, networkD3, jsonlite, htmlwidgets, webshot2, grDevices, methods
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-20 18:24:36 UTC; zhiz
Author: Zhi Zhao [aut, cre], Manuela Zucknick [aut], Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Repository: CRAN
Date/Publication: 2022-07-21 12:00:15 UTC

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New package autohrf with initial version 1.0.3
Package: autohrf
Title: Automated Generation of Data-Informed GLM Models in Task-Based fMRI Data Analysis
Version: 1.0.3
Maintainer: Jure Demsar <jure.demsar@fri.uni-lj.si>
Description: Analysis of task-related functional magnetic resonance imaging (fMRI) activity at the level of individual participants is commonly based on general linear modelling (GLM) that allows us to estimate to what extent the blood oxygenation level dependent (BOLD) signal can be explained by task response predictors specified in the GLM model. The predictors are constructed by convolving the hypothesised timecourse of neural activity with an assumed hemodynamic response function (HRF). To get valid and precise estimates of task response, it is important to construct a model of neural activity that best matches actual neuronal activity. The construction of models is most often driven by predefined assumptions on the components of brain activity and their duration based on the task design and specific aims of the study. However, our assumptions about the onset and duration of component processes might be wrong and can also differ across brain regions. This can result in inappropriate or suboptimal models, bad fitting of the model to the actual data and invalid estimations of brain activity. Here we present an approach in which theoretically driven models of task response are used to define constraints based on which the final model is derived computationally using the actual data. Specifically, we developed 'autohrf' — a package for the 'R' programming language that allows for data-driven estimation of HRF models. The package uses genetic algorithms to efficiently search for models that fit the underlying data well. The package uses automated parameter search to find the onset and duration of task predictors which result in the highest fitness of the resulting GLM based on the fMRI signal under predefined restrictions. We evaluate the usefulness of the 'autohrf' package on publicly available datasets of task-related fMRI activity. Our results suggest that by using 'autohrf' users can find better task related brain activity models in a quick and efficient manner.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: cowplot (>= 1.1.1), doParallel (>= 1.0.17), dplyr (>= 1.0.8), foreach (>= 1.5.2), ggplot2 (>= 3.3.5), gtools (>= 3.9.2), lubridate (>= 1.8.0), magrittr (>= 2.0.2), RColorBrewer (>= 1.1)
Suggests: knitr (>= 1.38), testthat (>= 3.1.3)
VignetteBuilder: knitr
URL: https://github.com/demsarjure/autohrf
BugReports: https://github.com/demsarjure/autohrf/issues
NeedsCompilation: no
Packaged: 2022-07-20 17:50:56 UTC; jure
Author: Jure Demsar [cre, aut], Nina Purg [aut], Grega Repovs [aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-07-21 12:00:11 UTC

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Package RclusTool (with last version 0.91.3) was removed from CRAN

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

2020-02-04 0.91.3
2020-01-09 0.91.2
2019-12-12 0.91.1
2019-11-06 0.91

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Package rrapply updated to version 1.2.5 with previous version 1.2.4 dated 2022-03-07

Title: Revisiting Base Rapply
Description: The minimal 'rrapply'-package contains a single function rrapply(), providing an extended implementation of 'R'-base rapply() by allowing to recursively apply a function to elements of a nested list based on a general condition function and including the possibility to prune or aggregate nested list elements from the result. In addition, special arguments can be supplied to access the name, location, parents and siblings in the nested list of the element under evaluation. The rrapply() function builds upon rapply()'s native 'C' implementation and requires no other package dependencies.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>

Diff between rrapply versions 1.2.4 dated 2022-03-07 and 1.2.5 dated 2022-07-21

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 rrapply-1.2.5/rrapply/src/flatten.c                       |   64 ++-
 rrapply-1.2.5/rrapply/src/init.c                          |    4 
 rrapply-1.2.5/rrapply/src/list.c                          |   64 ++-
 rrapply-1.2.5/rrapply/src/rrapply.c                       |  235 +++++++++----
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Package overlapping updated to version 1.8 with previous version 1.7 dated 2021-12-06

Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>

Diff between overlapping versions 1.7 dated 2021-12-06 and 1.8 dated 2022-07-21

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 overlapping-1.8/overlapping/build/partial.rdb |binary
 6 files changed, 22 insertions(+), 18 deletions(-)

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Package FamEvent (with last version 2.1) was removed from CRAN

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

2021-03-17 2.1
2019-03-21 2.0
2017-03-26 1.3
2016-09-30 1.2
2016-03-09 1.1
2016-02-09 1.0

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Package factset.protobuf.stach.v2 (with last version 1.0.3) was removed from CRAN

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2022-02-02 1.0.3

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Package cffdrs (with last version 1.8.18) was removed from CRAN

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2020-06-03 1.8.18

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Package gesca (with last version 1.0.4) was removed from CRAN

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2017-09-28 1.0.4
2016-07-25 1.0.3
2016-05-04 1.0.2
2016-03-04 1.0.1
2016-03-02 1.0

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Package VARsignR (with last version 0.1.3) was removed from CRAN

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2015-12-21 0.1.3

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2016-08-24 0.1.2
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Package rtweet updated to version 1.0.2 with previous version 0.7.0 dated 2020-01-08

Title: Collecting Twitter Data
Description: An implementation of calls designed to collect and organize Twitter data via Twitter's REST and stream Application Program Interfaces (API), which can be found at the following URL: <https://developer.twitter.com/en/docs>.
Author: Michael W. Kearney [aut] , Lluis Revilla Sancho [aut, cre] , Hadley Wickham [aut] , Andrew Heiss [rev] , Francois Briatte [rev], Jonathan Sidi [ctb]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>

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Package R.filesets updated to version 2.15.0 with previous version 2.14.0 dated 2020-12-08

Title: Easy Handling of and Access to Files Organized in Structured Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between R.filesets versions 2.14.0 dated 2020-12-08 and 2.15.0 dated 2022-07-21

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Package monobin updated to version 0.2.4 with previous version 0.2.3 dated 2022-04-18

Title: Monotonic Binning for Credit Rating Models
Description: Performs monotonic binning of numeric risk factor in credit rating models (PD, LGD, EAD) development. All functions handle both binary and continuous target variable. Functions that use isotonic regression in the first stage of binning process have an additional feature for correction of minimum percentage of observations and minimum target rate per bin. Additionally, monotonic trend can be identified based on raw data or, if known in advance, forced by functions' argument. Missing values and other possible special values are treated separately from so-called complete cases.
Author: Andrija Djurovic [aut, cre]
Maintainer: Andrija Djurovic <djandrija@gmail.com>

Diff between monobin versions 0.2.3 dated 2022-04-18 and 0.2.4 dated 2022-07-21

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New package MetaSKAT with initial version 0.82
Package: MetaSKAT
Title: Meta Analysis for SNP-Set (Sequence) Kernel Association Test
Version: 0.82
Date: 2022-07-21
Author: Seunggeun Lee [aut, cre]
Maintainer: Seunggeun (Shawn) Lee <lee7801@snu.ac.kr>
Description: Functions for Meta-analysis Burden Test, Sequence Kernel Association Test (SKAT) and Optimal SKAT (SKAT-O) by Lee et al. (2013) <doi:10.1016/j.ajhg.2013.05.010>. These methods use summary-level score statistics to carry out gene-based meta-analysis for rare variants.
License: GPL (>= 2)
SystemRequirements: Little Endian
Depends: R (>= 2.13.0)
Imports: SKAT (>= 2.0.1)
NeedsCompilation: yes
Packaged: 2022-07-21 07:06:00 UTC; LEE7801
Repository: CRAN
Date/Publication: 2022-07-21 09:20:02 UTC

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Package fiberLD updated to version 0.1-7 with previous version 0.1-6 dated 2019-02-18

Title: Fiber Length Determination
Description: Routines for estimating tree fiber (tracheid) length distributions in the standing tree based on increment core samples. Two types of data can be used with the package, increment core data measured by means of an optical fiber analyzer (OFA), e.g. such as the Kajaani Fiber Lab, or measured by microscopy. Increment core data analyzed by OFAs consist of the cell lengths of both cut and uncut fibres (tracheids) and fines (such as ray parenchyma cells) without being able to identify which cells are cut or if they are fines or fibres. The microscopy measured data consist of the observed lengths of the uncut fibres in the increment core. A censored version of a mixture of the fine and fiber length distributions is proposed to fit the OFA data, under distributional assumptions (Svensson et al., 2006) <doi:10.1111/j.1467-9469.2006.00501.x>. The package offers two choices for the assumptions of the underlying density functions of the true fiber (fine) lenghts of those fibers (fines) that at least partially appear in the increment core, being the generalized gamma and the log normal densities.
Author: Natalya Pya Arnqvist[aut, cre], Sara Sjoestedt de Luna [aut], Konrad Abramowicz [aut]
Maintainer: Natalya Pya Arnqvist <nat.pya@gmail.com>

Diff between fiberLD versions 0.1-6 dated 2019-02-18 and 0.1-7 dated 2022-07-21

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 DESCRIPTION      |   16 ++-
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New package did2s with initial version 0.7.0
Package: did2s
Title: Two-Stage Difference-in-Differences Following Gardner (2021)
Version: 0.7.0
Description: Estimates Two-way Fixed Effects difference-in-differences/event-study models using the approach proposed by Gardner (2021). To avoid the problems caused by OLS estimation of the Two-way Fixed Effects model, this function first estimates the fixed effects and covariates using untreated observations and then in a second stage, estimates the treatment effects.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), fixest (>= 0.10.1)
Imports: data.table, ggplot2, glue, stats, stringr, rlang, cli, Matrix, Rcpp, did, broom, methods, staggered, didimputation, boot
URL: http://kylebutts.com/did2s/
Suggests: rmarkdown, knitr, haven, testthat (>= 3.0.0)
VignetteBuilder: knitr
LinkingTo: RcppArmadillo, Rcpp
NeedsCompilation: yes
Packaged: 2022-07-20 22:53:14 UTC; kylebutts
Author: Kyle Butts [aut, cre] , John Gardner [aut] , Grant McDermott [ctb] , Laurent Berge [ctb]
Maintainer: Kyle Butts <kyle.butts@colorado.edu>
Repository: CRAN
Date/Publication: 2022-07-21 09:40:02 UTC

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Package rcarbon updated to version 1.4.4 with previous version 1.4.3 dated 2022-02-17

Title: Calibration and Analysis of Radiocarbon Dates
Description: Enables the calibration and analysis of radiocarbon dates, often but not exclusively for the purposes of archaeological research. It includes functions not only for basic calibration, uncalibration, and plotting of one or more dates, but also a statistical framework for building demographic and related longitudinal inferences from aggregate radiocarbon date lists, including: Monte-Carlo simulation test (Timpson et al 2014 <doi:10.1016/j.jas.2014.08.011>), random mark permutation test (Crema et al 2016 <doi:10.1371/journal.pone.0154809>) and spatial permutation tests (Crema, Bevan, and Shennan 2017 <doi:10.1016/j.jas.2017.09.007>).
Author: Andrew Bevan [aut] , Enrico Crema [aut, cre] , R. Kyle Bocinsky [ctb], Martin Hinz [ctb], Philip Riris [ctb], Fabio Silva [ctb]
Maintainer: Enrico Crema <enrico.crema@gmail.com>

Diff between rcarbon versions 1.4.3 dated 2022-02-17 and 1.4.4 dated 2022-07-21

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Package multiColl updated to version 2.0 with previous version 1.0 dated 2019-07-18

Title: Collinearity Detection in a Multiple Linear Regression Model
Description: The detection of worrying approximate collinearity in a multiple linear regression model is a problem addressed in all existing statistical packages. However, we have detected deficits regarding to the incorrect treatment of qualitative independent variables and the role of the intercept of the model. The objective of this package is to correct these deficits. In this package will be available detection and treatment techniques traditionally used as the recently developed.
Author: R. Salmeron, C. Garcia and J. Garcia
Maintainer: R. Salmeron <romansg@ugr.es>

Diff between multiColl versions 1.0 dated 2019-07-18 and 2.0 dated 2022-07-21

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Package fImport updated to version 4021.86 with previous version 3042.85 dated 2017-11-20

Title: Rmetrics - Importing Economic and Financial Data
Description: Provides a collection of utility functions to download and manage data sets from the Internet or from other sources.
Author: Diethelm Wuertz [aut] , Tobias Setz [aut], Yohan Chalabi [aut], Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

Diff between fImport versions 3042.85 dated 2017-11-20 and 4021.86 dated 2022-07-21

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Package briKmeans updated to version 1.0 with previous version 0.1 dated 2021-02-15

Title: Package for Brik, Fabrik and Fdebrik Algorithms to Initialise Kmeans
Description: Implementation of the BRIk, FABRIk and FDEBRIk algorithms to initialise k-means. These methods are intended for the clustering of multivariate and functional data, respectively. They make use of the Modified Band Depth and bootstrap to identify appropriate initial seeds for k-means, which are proven to be better options than many techniques in the literature. Torrente and Romo (2021) <doi:10.1007/s00357-020-09372-3> It makes use of the functions kma and kma.similarity, from the archived package fdakma, by Alice Parodi et al.
Author: Javier Albert Smet <javas@kth.se> and Aurora Torrente <etorrent@est-econ.uc3m.es>. Alice Parodi, Mirco Patriarca, Laura Sangalli, Piercesare Secchi, Simone Vantini and Valeria Vitelli, as contributors.
Maintainer: Aurora Torrente <etorrent@est-econ.uc3m.es>

Diff between briKmeans versions 0.1 dated 2021-02-15 and 1.0 dated 2022-07-21

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Package baseflow (with last version 0.13.2) was removed from CRAN

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

2021-03-18 0.13.2
2021-03-05 0.13.0
2021-01-15 0.12.3
2021-01-05 0.12.2
2020-12-11 0.12.1
2020-03-16 0.12.0

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Package tbart (with last version 1.0) was removed from CRAN

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

2015-02-13 1.0
2014-08-16 0.9.1
2013-06-19 0.9

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Package changepoint.mv (with last version 1.0.2) was removed from CRAN

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

2020-08-07 1.0.2

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Package cito (with last version 1.0.0) was removed from CRAN

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

2022-07-20 1.0.0

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