Fri, 26 Nov 2021

Package tiledb updated to version 0.10.1 with previous version 0.10.0 dated 2021-11-18

Title: Universal Storage Engine for Sparse and Dense Multidimensional Arrays
Description: The universal storage engine 'TileDB' introduces a powerful on-disk format for multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations.
Author: TileDB, Inc. [aut, cph], Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>

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Package shinylogs updated to version 0.2.0 with previous version 0.1.7 dated 2019-08-21

Title: Record Everything that Happens in a 'Shiny' Application
Description: Track and record the use of applications and the user's interactions with 'Shiny' inputs. Allows to trace the inputs with which the user interacts, the outputs generated, as well as the errors displayed in the interface.
Author: Fanny Meyer [aut], Victor Perrier [aut, cre], Silex Technologies [fnd] (https://www.silex-ip.com)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package relliptical updated to version 0.9.0 with previous version 0.1.0 dated 2021-09-15

Title: The Truncated Elliptical Family of Distributions
Description: It offers random numbers generation from members of the truncated multivariate elliptical family of distribution such as the truncated versions of the Normal, Student-t, Pearson VII, Slash, Logistic, among others. Particular distributions can be provided by specifying the density generating function. It also computes the first two moments (covariance matrix as well) for some particular distributions.
Author: Katherine A. L. Valeriano [aut, cre] (<https://orcid.org/0000-0001-6388-4753>), Larissa Avila Matos [ctb] (<https://orcid.org/0000-0002-2635-0901>), Christian Galarza Morales [ctb] (<https://orcid.org/0000-0002-4818-6006>)
Maintainer: Katherine A. L. Valeriano <katandreina@gmail.com>

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Package nominatimlite updated to version 0.1.5 with previous version 0.1.4 dated 2021-10-28

Title: Interface with 'Nominatim' API Service
Description: Lite interface for getting data from 'OSM' service 'Nominatim' <https://nominatim.org/release-docs/latest/>. Extract coordinates from addresses, find places near a set of coordinates, search for amenities and return spatial objects on 'sf' format.
Author: Diego Hernangómez [aut, cre, cph] (<https://orcid.org/0000-0001-8457-4658>), Jindra Lacko [ctb, rev]
Maintainer: Diego Hernangómez <diego.hernangomezherrero@gmail.com>

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New package x3ptools with initial version 0.0.3
Package: x3ptools
Title: Tools for Working with 3D Surface Measurements
Version: 0.0.3
Date: 2021-11-23
Maintainer: Heike Hofmann <hofmann@iastate.edu>
Description: The x3p file format is specified in ISO standard 5436:2000 to describe 3d surface measurements. 'x3ptools' allows reading, writing and basic modifications to the 3D surface measurements.
Depends: R (>= 4.0)
Imports: MASS (>= 7.3), digest (>= 0.6), xml2 (>= 1.3.0), rgl (>= 0.107.14), zoo (>= 1.8-9), png (>= 0.1-7), readr (>= 2.1.0), dplyr (>= 1.0.7), pracma (>= 2.3.3), assertthat (>= 0.2.1), grDevices
Suggests: knitr, rmarkdown, testthat (>= 3.0.4), covr, here, magick (>= 2.0)
License: MIT + file LICENSE
URL: https://github.com/heike/x3ptools
BugReports: https://github.com/heike/x3ptools/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-11-26 22:07:44 UTC; hofmann
Author: Heike Hofmann [aut, cre, cph] (<https://orcid.org/0000-0001-6216-5183>), Susan Vanderplas [aut] (<https://orcid.org/0000-0002-3803-0972>), Ganesh Krishnan [aut], Eric Hare [aut] (<https://orcid.org/0000-0002-4277-3146>)
Repository: CRAN
Date/Publication: 2021-11-26 22:50:02 UTC

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Package minMSE updated to version 0.5.1 with previous version 0.3.1 dated 2020-04-23

Title: Implementation of the minMSE Treatment Assignment Method for One or Multiple Treatment Groups
Description: Performs treatment assignment for (field) experiments considering available, possibly multivariate and continuous, information (covariates, observable characteristics), that is: forms balanced treatment groups, according to the minMSE-method as proposed by Schneider and Schlather (2017) <DOI:10419/161931>.
Author: Sebastian O. Schneider, Giulia Baldini
Maintainer: Sebastian O. Schneider <sschneider@coll.mpg.de>

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Package itan updated to version 2.0.1 with previous version 2.0 dated 2021-11-26

Title: Item Analysis for Multiple Choice Tests
Description: Functions for analyzing multiple choice items. These analyses include the convertion of student response into binaty data (correct/incorrect), the computation of the number of corrected responses and grade for each subject, the calculation of item difficulty and discrimination, the computation of the frecuency and point-biserial correlation for each distractor and the graphical analysis of each item.
Author: Ariel Armijo [aut, cre]
Maintainer: Ariel Armijo <arielarmijo@yahoo.es>

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Package conflicted updated to version 1.1.0 with previous version 1.0.4 dated 2019-06-21

Title: An Alternative Conflict Resolution Strategy
Description: R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package WR updated to version 1.0 with previous version 0.1.1 dated 2020-01-27

Title: Win Ratio Analysis of Composite Time-to-Event Outcomes
Description: Implements various win ratio methodologies for composite endpoints of death and non-fatal events, including the (stratified) proportional win-fractions (PW) regression models (Mao and Wang, 2020 <doi:10.1111/biom.13382>), (stratified) two-sample tests with possibly recurrent nonfatal event, and sample size calculation for standard win ratio test (Mao et al., 2021 <doi:10.1111/biom.13501>).
Author: Lu Mao and Tuo Wang
Maintainer: Lu Mao <lmao@biostat.wisc.edu>

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Package stochvol updated to version 3.2.0 with previous version 3.1.0 dated 2021-07-12

Title: Efficient Bayesian Inference for Stochastic Volatility (SV) Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Hosszejni and Kastner (2021) <doi:10.18637/jss.v100.i12> and Kastner (2016) <doi:10.18637/jss.v069.i05> and the package examples.
Author: Darjus Hosszejni [aut, cre] (<https://orcid.org/0000-0002-3803-691X>), Gregor Kastner [aut] (<https://orcid.org/0000-0002-8237-8271>)
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>

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Package itan updated to version 2.0 with previous version 1.0 dated 2017-03-28

Title: Item Analysis for Multiple Choice Tests
Description: Functions for analyzing multiple choice items. These analyses include the convertion of student response into binaty data (correct/incorrect), the computation of the number of corrected responses and grade for each subject, the calculation of item difficulty and discrimination, the computation of the frecuency and point-biserial correlation for each distractor and the graphical analysis of each item.
Author: Ariel Armijo [aut, cre]
Maintainer: Ariel Armijo <arielarmijo@yahoo.es>

Diff between itan versions 1.0 dated 2017-03-28 and 2.0 dated 2021-11-26

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Package Exact updated to version 3.1 with previous version 3.0 dated 2021-09-02

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://pcalhoun1.github.io/drat/>. The ExactData R package is approximately 25 MB.
Author: Peter Calhoun [aut, cre]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>

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Package bain updated to version 0.2.7 with previous version 0.2.6 dated 2021-09-03

Title: Bayes Factors for Informative Hypotheses
Description: Computes approximated adjusted fractional Bayes factors for equality, inequality, and about equality constrained hypotheses. For a tutorial on this method, see Hoijtink, Mulder, van Lissa, & Gu, (2019) <doi:10.31234/osf.io/v3shc>. For applications in structural equation modeling, see: Van Lissa, Gu, Mulder, Rosseel, Van Zundert, & Hoijtink, (2021) <doi:10.1080/10705511.2020.1745644>. For the statistical underpinnings, see Gu, Mulder, and Hoijtink (2018) <doi:10.1111/bmsp.12110>; Hoijtink, Gu, & Mulder, J. (2019) <doi:10.1111/bmsp.12145>; Hoijtink, Gu, Mulder, & Rosseel, (2019) <doi:10.31234/osf.io/q6h5w>.
Author: Xin Gu [aut], Herbert Hoijtink [aut], Joris Mulder [aut], Caspar J van Lissa [aut, cre], Van Zundert Camiel [ctb], Jeff Jones [ctb], Niels Waller [ctb]
Maintainer: Caspar J van Lissa <c.j.vanlissa@uu.nl>

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Package sfnetworks updated to version 0.5.3 with previous version 0.5.2 dated 2021-05-13

Title: Tidy Geospatial Networks
Description: Provides a tidy approach to spatial network analysis, in the form of classes and functions that enable a seamless interaction between the network analysis package 'tidygraph' and the spatial analysis package 'sf'.
Author: Lucas van der Meer [aut, cre] (<https://orcid.org/0000-0001-6336-8628>), Lorena Abad [aut] (<https://orcid.org/0000-0003-0554-734X>), Andrea Gilardi [aut] (<https://orcid.org/0000-0002-9424-7439>), Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>)
Maintainer: Lucas van der Meer <luukvandermeer@live.nl>

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Package ncdf4 updated to version 1.18 with previous version 1.17.1 dated 2021-11-06

Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
Description: Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files (either version 4 or "classic" version 3) can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdf package, which only worked with netcdf version 3 files. For various reasons the names of the functions have had to be changed from the names in the ncdf package. The old ncdf package is still available at the URL given below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4 packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 files.
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: David Pierce <dpierce@ucsd.edu>

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Package strucchangeRcpp updated to version 1.5-3-1.0.4 with previous version 1.5-3-1.0.3 dated 2021-05-26

Title: Testing, Monitoring, and Dating Structural Changes: C++ Version
Description: A fast implementation with additional experimental features for testing, monitoring and dating structural changes in (linear) regression models. 'strucchangeRcpp' features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g. cumulative/moving sum, recursive/moving estimates) and F statistics, respectively. These methods are described in Zeileis et al. (2002) <doi:10.18637/jss.v007.i02>. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals, and their magnitude as well as the model fit can be evaluated using a variety of statistical measures.
Author: Dainius Masiliunas [aut, cre] (<https://orcid.org/0000-0001-5654-1277>), Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>), Marius Appel [aut], Friedrich Leisch [aut], Kurt Hornik [aut], Christian Kleiber [aut], Andrei Mirt [ctb] (<https://orcid.org/0000-0003-3654-2090>), Bruce Hansen [ctb], Edgar C. Merkle [ctb]
Maintainer: Dainius Masiliunas <pastas4@gmail.com>

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Package stplanr updated to version 0.8.6 with previous version 0.8.5 dated 2021-11-01

Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. Enables common transport planning tasks including: downloading and cleaning transport datasets; creating geographic "desire lines" from origin-destination (OD) data; route assignment, locally and via interfaces to routing services such as <https://cyclestreets.net/> and calculation of route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>. This package Suggests the 'pct' package which at the time of writing is unavailable on CRAN. You can install it from the repository 'itsleeds/pct' on GitHub.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Richard Ellison [aut], Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>), Barry Rowlingson [ctb], Nick Bearman [ctb], Nikolai Berkoff [ctb], Scott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10), Mark Padgham [ctb], Andrea Gilardi [ctb] (<https://orcid.org/0000-0002-9424-7439>)
Maintainer: Robin Lovelace <rob00x@gmail.com>

Diff between stplanr versions 0.8.5 dated 2021-11-01 and 0.8.6 dated 2021-11-26

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Package spatstat.core updated to version 2.3-2 with previous version 2.3-1 dated 2021-11-02

Title: Core Functionality of the 'spatstat' Family
Description: Functionality for data analysis and modelling of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported. Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley [aut, cre], Rolf Turner [aut], Ege Rubak [aut], Kasper Klitgaard Berthelsen [ctb], Achmad Choiruddin [ctb], Jean-Francois Coeurjolly [ctb], Ottmar Cronie [ctb], Tilman Davies [ctb], Chiara Fend [ctb], Julian Gilbey [ctb], Yongtao Guan [ctb], Ute Hahn [ctb], Kassel Hingee [ctb], Abdollah Jalilian [ctb], Marie-Colette van Lieshout [ctb], Greg McSwiggan [ctb], Tuomas Rajala [ctb], Suman Rakshit [ctb], Dominic Schuhmacher [ctb], Rasmus Plenge Waagepetersen [ctb], Hangsheng Wang [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package sn updated to version 2.0.1 with previous version 2.0.0 dated 2021-03-28

Title: The Skew-Normal and Related Distributions Such as the Skew-t and the SUN
Description: Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t and the SUN families. For the skew-normal and the skew-t distributions, statistical methods are provided for data fitting and model diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini [aut, cre] (<https://orcid.org/0000-0002-7583-1269>)
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

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Package sjPlot updated to version 2.8.10 with previous version 2.8.9 dated 2021-07-10

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>), Carsten Schwemmer [ctb], Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>), Amir Djalovski [ctb], Johannes Titz [ctb] (<https://orcid.org/0000-0002-1102-5719>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package shrinkTVP updated to version 2.0.4 with previous version 2.0.3 dated 2021-10-21

Title: Efficient Bayesian Inference for Time-Varying Parameter Models with Shrinkage
Description: Efficient Markov chain Monte Carlo (MCMC) algorithms for fully Bayesian estimation of time-varying parameter models with shrinkage priors. Details on the algorithms used are provided in Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006> and Cadonna et al. (2020) <doi:10.3390/econometrics8020020>. For details on the package, please see Knaus et al. (2021) <doi:10.18637/jss.v100.i13>.
Author: Peter Knaus [aut, cre] (<https://orcid.org/0000-0001-6498-7084>), Angela Bitto-Nemling [aut], Annalisa Cadonna [aut] (<https://orcid.org/0000-0003-0360-7628>), Sylvia Frühwirth-Schnatter [aut] (<https://orcid.org/0000-0003-0516-5552>), Daniel Winkler [ctb], Kemal Dingic [ctb]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>

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Package ribd updated to version 1.3.1 with previous version 1.3.0 dated 2021-05-28

Title: Pedigree-based Relatedness Coefficients
Description: Recursive algorithms for computing various relatedness coefficients, including pairwise kinship, kappa and identity coefficients. Both autosomal and X-linked coefficients are computed. Founders are allowed to be inbred, enabling construction of any given kappa coefficients (Vigeland (2020) <doi:10.1007/s00285-020-01505-x>). In addition to the standard pairwise coefficients, 'ribd' also computes a range of lesser-known coefficients, including generalised kinship coefficients (Karigl (1981) <doi:10.1111/j.1469-1809.1981.tb00341.x>; Weeks and Lange (1988) <https:www.ncbi.nlm.nih.gov/pmc/articles/PMC1715269>), two-locus coefficients (Thompson (1988) <doi:10.1093/imammb/5.4.261>) and multi-person coefficients. This package is part of the 'ped suite', a collection of packages for pedigree analysis in R. Several methods of 'ribd' are featured in the online app 'QuickPed' available at <https://magnusdv.shinyapps.io/quickped>.
Author: Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>

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Package rex updated to version 1.2.1 with previous version 1.2.0 dated 2020-04-21

Title: Friendly Regular Expressions
Description: A friendly interface for the construction of regular expressions.
Author: Kevin Ushey [aut, cre], Jim Hester [aut], Robert Krzyzanowski [aut]
Maintainer: Kevin Ushey <kevinushey@gmail.com>

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Package RAthena updated to version 2.4.0 with previous version 2.3.0 dated 2021-10-26

Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this 'Python' 'Boto3' Software Development Kit ('SDK') <https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package nodbi updated to version 0.5.1 with previous version 0.5.0 dated 2021-11-21

Title: 'NoSQL' Database Connector
Description: Simplified document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1'.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Rich FitzJohn [aut], Jeroen Ooms [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>

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Package noctua updated to version 2.4.0 with previous version 2.3.0 dated 2021-10-26

Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' <https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package memoise updated to version 2.0.1 with previous version 2.0.0 dated 2021-01-26

Title: 'Memoisation' of Functions
Description: Cache the results of a function so that when you call it again with the same arguments it returns the previously computed value.
Author: Hadley Wickham [aut], Jim Hester [aut], Winston Chang [aut, cre], Kirill Müller [aut], Daniel Cook [aut], Mark Edmondson [ctb]
Maintainer: Winston Chang <winston@rstudio.com>

Diff between memoise versions 2.0.0 dated 2021-01-26 and 2.0.1 dated 2021-11-26

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Package Luminescence updated to version 0.9.16 with previous version 0.9.15 dated 2021-09-02

Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] (<https://orcid.org/0000-0002-0734-2199>), Christoph Burow [aut, trl, dtc] (<https://orcid.org/0000-0002-5023-4046>), Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>), Margret C. Fuchs [aut] (<https://orcid.org/0000-0001-7210-1132>), Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>), Manfred Fischer [aut, trl], Johannes Friedrich [aut] (<https://orcid.org/0000-0002-0805-9547>), Norbert Mercier [aut] (<https://orcid.org/0000-0002-6375-9108>), Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>), Claire Christophe [ctb], Antoine Zink [ctb] (<https://orcid.org/0000-0001-7146-1101>), Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>), Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>), Anne Philippe [aut] (<https://orcid.org/0000-0002-5331-5087>), Guillaume Guerin [ctb] (<https://orcid.org/0000-0001-6298-5579>), Svenja Riedesel [aut] (<https://orcid.org/0000-0003-2936-8776>), Martin Autzen [aut] (<https://orcid.org/0000-0001-6249-426X>), Pierre Guibert [ctb] (<https://orcid.org/0000-0001-8969-8684>), Dirk Mittelstrass [aut] (<https://orcid.org/0000-0002-9567-8791>), Harrison J. Gray [aut] (<https://orcid.org/0000-0002-4555-7473>), Jean-Michel Galharret [aut] (<https://orcid.org/0000-0003-2219-8727>), Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@aber.ac.uk>

Diff between Luminescence versions 0.9.15 dated 2021-09-02 and 0.9.16 dated 2021-11-26

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Permanent link

Package IntCal updated to version 0.3.0 with previous version 0.2.3 dated 2021-10-06

Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided here in a single data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98) and postbomb curves. Also provided are functions to copy the curves into memory, and to plot the curves and their underlying data, as well as functions to calibrate radiocarbon dates.
Author: Maarten Blaauw [aut, cre] (<https://orcid.org/0000-0002-5680-1515>)
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>

Diff between IntCal versions 0.2.3 dated 2021-10-06 and 0.3.0 dated 2021-11-26

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Package HardyWeinberg updated to version 1.7.4 with previous version 1.7.3 dated 2021-11-17

Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) <doi:10.1126/science.28.706.49> for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi: 10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots. The functionality of the package is explained in detail in a related JSS paper <doi:10.18637/jss.v064.i03>.
Author: Jan Graffelman [aut, cre], Christopher Chang [ctb], Xavi Puig [ctb], Jan Wigginton [ctb], Leonardo Ortoleva [ctb], William R. Engels [ctb]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>

Diff between HardyWeinberg versions 1.7.3 dated 2021-11-17 and 1.7.4 dated 2021-11-26

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More information about HardyWeinberg at CRAN
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Package gslnls updated to version 1.1.0 with previous version 1.0.2 dated 2021-10-13

Title: GSL Nonlinear Least-Squares Fitting
Description: An R interface to nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquadt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>

Diff between gslnls versions 1.0.2 dated 2021-10-13 and 1.1.0 dated 2021-11-26

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More information about gslnls at CRAN
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Package COINr updated to version 0.6.0 with previous version 0.5.5 dated 2021-09-16

Title: Composite Indicator Construction and Analysis
Description: A comprehensive high-level package for composite indicator construction and analysis. It is a "development environment" for composite indicators and scoreboards, which includes utilities for construction (indicator selection, denomination, imputation, data treatment, normalisation, weighting and aggregation) and analysis (multivariate analysis, correlation plotting, short cuts for principal component analysis, global sensitivity analysis, and more). A composite indicator is completely encapsulated inside a single hierarchical list called a "COIN". This allows a fast and efficient work flow, as well as making quick copies, testing methodological variations and making comparisons. It also includes many plotting options, both statistical (scatter plots, distribution plots) as well as for presenting results (maps, bar charts, radar charts, and more). Finally, three Shiny apps are available which enable fast data exploration, results presentation, and checking the effects of altering weights. Full documentation is found in the online book at <https://bluefoxr.github.io/COINrDoc/>, as well as the vignette.
Author: William Becker [aut, cre, cph] (<https://orcid.org/0000-0002-6467-4472>)
Maintainer: William Becker <william.becker@bluefoxdata.eu>

Diff between COINr versions 0.5.5 dated 2021-09-16 and 0.6.0 dated 2021-11-26

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Package BVAR updated to version 1.0.2 with previous version 1.0.1 dated 2020-09-27

Title: Hierarchical Bayesian Vector Autoregression
Description: Estimation of hierarchical Bayesian vector autoregressive models following Kuschnig & Vashold (2021) <doi:10.18637/jss.v100.i14>. Implements hierarchical prior selection for conjugate priors in the fashion of Giannone, Lenza & Primiceri (2015) <doi:10.1162/REST_a_00483>. Functions to compute and identify impulse responses, calculate forecasts, forecast error variance decompositions and scenarios are available. Several methods to print, plot and summarise results facilitate analysis.
Author: Nikolas Kuschnig [aut, cre] (<https://orcid.org/0000-0002-6642-2543>), Lukas Vashold [aut] (<https://orcid.org/0000-0002-3562-3414>), Michael McCracken [dtc], Serena Ng [dtc]
Maintainer: Nikolas Kuschnig <nikolas.kuschnig@wu.ac.at>

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Package BFpack updated to version 1.0.0 with previous version 0.3.2 dated 2021-02-02

Title: Flexible Bayes Factor Testing of Scientific Expectations
Description: Implementation of various default Bayes factors for testing statistical hypotheses. The package is intended for applied quantitative researchers in the social and behavioral sciences, medical research, and related fields. The Bayes factor tests can be executed for statistical models such as univariate and multivariate normal linear models, generalized linear models, special cases of linear mixed models, survival models, relational event models. Parameters that can be tested are location parameters (e.g., group means, regression coefficients), variances (e.g., group variances), and measures of association (e.g,. bivariate correlations), among others. The statistical underpinnings are described in Mulder, Hoijtink, and Xin (2019) <arXiv:1904.00679>, Mulder and Gelissen (2019) <arXiv:1807.05819>, Mulder (2016) <DOI:10.1016/j.jmp.2014.09.004>, Mulder and Fox (2019) <DOI:10.1214/18-BA1115>, Mulder and Fox (2013) <DOI:10.1007/s11222-011-9295-3>, Boeing-Messing, van Assen, Hofman, Hoijtink, and Mulder (2017) <DOI:10.1037/met0000116>, Hoijtink, Mulder, van Lissa, and Gu, (2018) <DOI:10.31234/osf.io/v3shc>, Gu, Mulder, and Hoijtink, (2018) <DOI:10.1111/bmsp.12110>, Hoijtink, Gu, and Mulder, (2018) <DOI:10.1111/bmsp.12145>, and Hoijtink, Gu, Mulder, and Rosseel, (2018) <DOI:10.1037/met0000187>. When using the packages, please refer to Mulder et al. (2021) <DOI:10.18637/jss.v100.i18>.
Author: Joris Mulder [aut, cre], Caspar van Lissa [aut, ctb], Donald R. Williams [aut, ctb], Xin Gu [aut], Anton Olsson-Collentine [aut, ctb], Florian Boeing-Messing [aut, ctb], Jean-Paul Fox [aut, ctb], Janosch Menke [ctb], Robbie van Aert [ctb], Barry Brown [ctb], James Lovato [ctb], Kathy Russell [ctb], Lapack 3.8 [ctb], Jack Dongarra [ctb], Jim Bunch [ctb], Cleve Moler [ctb], Gilbert Stewart [ctb], John Burkandt [ctb], Ashwith Rego [ctb], Alexander Godunov [ctb], Alan Miller [ctb], Jean-Pierre Moreau [ctb], The R Core Team [cph]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>

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Package bayesPop updated to version 9.0-0 with previous version 8.1-3 dated 2020-05-05

Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate and life expectancy (Raftery et al., 2012 <doi:10.1073/pnas.1211452109>).
Author: Hana Sevcikova, Adrian Raftery, Thomas Buettner
Maintainer: Hana Sevcikova <hanas@uw.edu>

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Package survivoR updated to version 0.9.6 with previous version 0.9.5 dated 2021-11-20

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]
Maintainer: Daniel Oehm <danieloehm@gmail.com>

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Package pubmed.mineR updated to version 1.0.19 with previous version 1.0.18 dated 2021-07-26

Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>

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Package gpindex updated to version 0.3.9 with previous version 0.3.6 dated 2021-10-02

Title: Generalized Price and Quantity Indexes
Description: A small package for calculating lots of different price indexes, and by extension quantity indexes. Provides tools to build and work with any type of bilateral generalized-mean index (of which most price indexes are), along with a few important indexes that don't belong to the generalized-mean family (e.g., superlative quadratic-mean indexes, GEKS). Implements and extends many of the methods in Balk (2008, ISBN:978-1-107-40496-0), von der Lippe (2001, ISBN:3-8246-0638-0), and the CPI manual (2020, ISBN:978-1-51354-298-0) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <stevemartin041@gmail.com>

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Package googlePubsubR updated to version 0.0.2 with previous version 0.0.1 dated 2021-11-12

Title: R Interface for Google 'Cloud Pub/Sub' REST API
Description: Provides an easy to use interface to the 'Google Pub/Sub' REST API <https://cloud.google.com/pubsub/docs/reference/rest>.
Author: Andrea Dodet [aut, cre]
Maintainer: Andrea Dodet <andodet@gmail.com>

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Package aRtsy updated to version 0.1.5 with previous version 0.1.4 dated 2021-10-25

Title: Generative Art with 'ggplot2'
Description: Provides algorithms for creating artworks in the 'ggplot2' language that incorporate some form of randomness.
Author: Koen Derks [aut, cre]
Maintainer: Koen Derks <koen-derks@hotmail.com>

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Package whomds updated to version 1.0.1 with previous version 1.0.0 dated 2021-11-23

Title: Calculate Results from WHO Model Disability Survey Data
Description: The Model Disability Survey (MDS) <https://www.who.int/disabilities/data/en/> is a World Health Organization (WHO) general population survey instrument to assess the distribution of disability within a country or region, grounded in the International Classification of Functioning, Disability and Health <https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health>. This package provides fit-for-purpose functions for calculating and presenting the results from this survey, as used by the WHO. The package primarily provides functions for implementing Rasch Analysis (see Andrich (2011) <doi:10.1586/erp.11.59>) to calculate a metric scale for disability.
Author: Lindsay Lee [aut, cre], Carolina Fellinghauer [ctb], World Health Organization [cph]
Maintainer: Lindsay Lee <lindsayevanslee@gmail.com>

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Package qrNLMM updated to version 3.2 with previous version 3.1 dated 2021-09-26

Title: Quantile Regression for Nonlinear Mixed-Effects Models
Description: Quantile regression (QR) for Nonlinear Mixed-Effects Models via the asymmetric Laplace distribution (ALD). It uses the Stochastic Approximation of the EM (SAEM) algorithm for deriving exact maximum likelihood estimates and full inference results for the fixed-effects and variance components. It also provides prediction and graphical summaries for assessing the algorithm convergence and fitting results.
Author: Christian E. Galarza <chedgala@espol.edu.ec> and Victor H. Lachos <hlachos@uconn.edu>
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>

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Package GWpcor updated to version 0.1.7 with previous version 0.1.6 dated 2021-01-10

Title: Geographically Weighted Partial Correlation Coefficient
Description: Implements a geographically weighted partial correlation which is an extension from gwss() function in the 'GWmodel' package (Percival and Tsutsumida (2017) <doi:10.1553/giscience2017_01_s36>).
Author: Narumasa Tsutsumida [aut, cre] (<https://orcid.org/0000-0002-6333-0301>), Joseph Percival [aut]
Maintainer: Narumasa Tsutsumida <rsnaru.jp@gmail.com>

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Package canvasXpress updated to version 1.37.0 with previous version 1.35.0 dated 2021-06-25

Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <https://www.canvasxpress.org> for more information.
Author: Isaac Neuhaus [aut], Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>

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Package bssm updated to version 2.0.0 with previous version 1.1.7-1 dated 2021-09-21

Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space Models
Description: Efficient methods for Bayesian inference of state space models via particle Markov chain Monte Carlo (MCMC) and MCMC based on parallel importance sampling type weighted estimators (Vihola, Helske, and Franks, 2020, <doi:10.1111/sjos.12492>). Gaussian, Poisson, binomial, negative binomial, and Gamma observation densities and basic stochastic volatility models with linear-Gaussian state dynamics, as well as general non-linear Gaussian models and discretised diffusion models are supported.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>), Matti Vihola [aut] (<https://orcid.org/0000-0002-8041-7222>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package argparse updated to version 2.1.3 with previous version 2.1.2 dated 2021-10-21

Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to be used with Rscript to write "#!" shebang scripts that gracefully accept positional and optional arguments and automatically generate usage.
Author: Trevor L Davis [aut, cre], Allen Day [ctb] (Some documentation and examples ported from the getopt package.), Python Software Foundation [ctb] (Some documentation from the optparse Python module.), Paul Newell [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>

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Package neuronorm updated to version 1.0.1 with previous version 1.0.0 dated 2021-07-20

Title: Preprocessing of Structural MRI for Multiple Neurodegenerative Diseases
Description: Preprocessing pipeline for normalizing and cleaning T1-weighted, T2-weighted and FLAIR MRI images coming from different sources, diseases, patients, scanners and sites.
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-Philippe Fortin [cph], Elizabeth M. Sweeney [cph], John Muschelli [cph], Ciprian M. Crainiceanu [cph], Russell T. Shinohara [cph], Yongyue Zhang [cph], J. Michae Brady [cph], Stephen Smith [cph]
Maintainer: David Payares <davidpayaresg@gmail.com>

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Package GDELTtools updated to version 1.5 with previous version 1.2 dated 2014-02-27

Title: Download, Slice, and Normalize GDELT V1 Data
Description: The GDELT V1 Event data set is over 37 GB now and growing 250 MB a month. The number of source articles has increased over time and unevenly across countries. This package makes it easy to download a subset of that data, then normalize that data to facilitate valid time series analysis.
Author: Stephen R. Haptonstahl, Thomas Scherer, Timo Thoms, and Patrick Wheatley
Maintainer: Stephen R. Haptonstahl <srh@haptonstahl.org>

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Package eseis updated to version 0.6.0 with previous version 0.5.0 dated 2019-12-17

Title: Environmental Seismology Toolbox
Description: Environmental seismology is a scientific field that studies the seismic signals, emitted by Earth surface processes. This package provides all relevant functions to read/write seismic data files, prepare, analyse and visualise seismic data, and generate reports of the processing history.
Author: Michael Dietze [cre, aut, trl], Christoph Burow [ctb], Sophie Lagarde [ctb, trl]
Maintainer: Michael Dietze <mdietze@gfz-potsdam.de>

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 eseis-0.6.0/eseis/man/aux_stationinfofile.Rd                          |    2 
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 73 files changed, 927 insertions(+), 323 deletions(-)

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Package clustrd updated to version 1.3.9 with previous version 1.3.8 dated 2021-11-18

Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data (Markos, Iodice D'Enza and van de Velden 2019; <DOI:10.18637/jss.v091.i10>). For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>

Diff between clustrd versions 1.3.8 dated 2021-11-18 and 1.3.9 dated 2021-11-26

 DESCRIPTION         |    8 ++++----
 MD5                 |   24 ++++++++++++------------
 R/boot_clusmca.R    |    4 ++--
 R/boot_cluspca.R    |    6 +++---
 R/boot_cluspcamix.R |   11 ++++++-----
 R/clu_means.R       |    7 +++----
 R/cluspca.R         |   16 ++++++++--------
 R/cluspcamix.R      |   31 ++++++++++++++++++++-----------
 R/global_bootclus.R |    6 +++---
 R/local_bootclus.R  |   22 ++++++++++++----------
 R/plot.clusmca.R    |    1 -
 R/plot.cluspcamix.R |   16 ++++++++--------
 man/mybond.Rd       |    2 +-
 13 files changed, 82 insertions(+), 72 deletions(-)

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Package automultinomial (with last version 2.0.0) was removed from CRAN

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

2018-10-31 2.0.0
2016-10-05 1.0.0

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Package retrocombinator (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:

2021-11-11 1.0.0

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Package genekitr (with last version 0.2.1) was removed from CRAN

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

2021-09-11 0.2.1

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Package resemble (with last version 2.0.0) was removed from CRAN

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

2020-11-09 2.0.0

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Package eSIR (with last version 0.4.1) was removed from CRAN

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

2021-11-11 0.4.1

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New package hospitals with initial version 0.1.0
Package: hospitals
Title: Portuguese 'NHS' Hospitals
Version: 0.1.0
Description: A data set of the Portuguese 'NHS' hospitals.
License: CC0
URL: https://github.com/nhs-pt/hospitals
BugReports: https://github.com/nhs-pt/hospitals/issues
Encoding: UTF-8
LazyData: true
Imports: magrittr, stringr, tibble
Depends: R (>= 2.10)
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-11-25 12:00:01 UTC; rmagno
Author: Ramiro Magno [aut, cre] (<https://orcid.org/0000-0001-5226-3441>), CINTESIS [cph, fnd]
Maintainer: Ramiro Magno <ramiro.magno@gmail.com>
Repository: CRAN
Date/Publication: 2021-11-26 08:20:02 UTC

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New package bsreg with initial version 0.0.1
Package: bsreg
Title: Bayesian Spatial Regression Models
Version: 0.0.1
Date: 2021-11-24
Author: Nikolas Kuschnig [aut, cre] (<https://orcid.org/0000-0002-6642-2543>)
Maintainer: Nikolas Kuschnig <nikolas.kuschnig@wu.ac.at>
Description: Fit Bayesian models with a focus on spillover effects. Implements linear specifications (with or without shrinkage), allows for spatial lags of the dependent, explanatories, and error term, parameterised connectivity, and stochastic volatility.
Depends: R (>= 3.5.0)
Imports: R6, Matrix, stats, graphics, utils, grDevices
Suggests: stochvol
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-11-25 09:21:09 UTC; nikolas
Repository: CRAN
Date/Publication: 2021-11-26 08:20:07 UTC

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