Fri, 04 Sep 2020

Package seqmon updated to version 2.4 with previous version 2.3 dated 2019-03-05

Title: Group Sequential Design Class for Clinical Trials
Description: S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.
Author: David A Schoenfeld and Hui Zheng
Maintainer: Hui Zheng <hzheng1@mgh.harvard.edu>

Diff between seqmon versions 2.3 dated 2019-03-05 and 2.4 dated 2020-09-04

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Package modelsummary updated to version 0.6.1 with previous version 0.6.0 dated 2020-09-02

Title: Summary Tables and Plots for Statistical Models and Data: Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several statistical models side-by-side. Draw coefficient plots, multi-level cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and correlation matrices. This package supports dozens of statistical models, and it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint, Excel, RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or 'knitr' dynamic documents.
Author: Vincent Arel-Bundock [aut, cre] (<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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Package GMMAT updated to version 1.3.0 with previous version 1.2.0 dated 2020-05-15

Title: Generalized Linear Mixed Model Association Tests
Description: Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) <DOI:10.1016/j.ajhg.2016.02.012>. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) <DOI:10.1016/j.ajhg.2018.12.012>, including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.
Author: Han Chen, Matthew P. Conomos, Duy T. Pham
Maintainer: Han Chen <Han.Chen.2@uth.tmc.edu>

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Package ExactMultinom updated to version 0.1.2 with previous version 0.1.1 dated 2020-09-04

Title: Multinomial Goodness-of-Fit Tests
Description: Computes exact p-values for multinomial goodness-of-fit tests based on multiple test statistics, namely, Pearson's chi-square, the log-likelihood ratio and the probability mass statistic. Implements the algorithm detailed in Resin (2020) <arXiv:2008.12682>. Estimates based on the classical asymptotic chi-square approximation or Monte-Carlo simulation can also be computed.
Author: Johannes Resin
Maintainer: Johannes Resin <johannes.resin@h-its.org>

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Package divest updated to version 0.9.0 with previous version 0.8.2 dated 2020-01-09

Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to sort DICOM-format medical image files, and convert them to NIfTI-1 format.
Author: Jon Clayden [aut, cre] (<https://orcid.org/0000-0002-6608-0619>), Chris Rorden [aut], Martin J Fiedler [cph], Cong Xu [cph], Pascal Gloor [cph]
Maintainer: Jon Clayden <code@clayden.org>

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Package ciTools updated to version 0.6.0 with previous version 0.5.2 dated 2020-06-12

Title: Confidence or Prediction Intervals, Quantiles, and Probabilities for Statistical Models
Description: Functions to append confidence intervals, prediction intervals, and other quantities of interest to data frames. All appended quantities are for the response variable, after conditioning on the model and covariates. This package has a data frame first syntax that allows for easy piping. Currently supported models include (log-) linear, (log-) linear mixed, generalized linear models, generalized linear mixed models, and accelerated failure time models.
Author: John Haman [cre, aut], Matthew Avery [aut], Institute for Defense Analyses [cph]
Maintainer: John Haman <jhaman@ida.org>

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Package stplanr updated to version 0.7.2 with previous version 0.7.1 dated 2020-08-28

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/>; calculation of route segment attributes such as bearing and aggregate flow; and 'travel watershed' analysis. See Lovelace and Ellison (2018) <doi:10.32614/RJ-2018-053> and vignettes for details.
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] (Author of overline), Nick Bearman [ctb] (Co-author of gclip), Nikolai Berkoff [ctb] (Co-author of line2route), 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>

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Package fauxnaif updated to version 0.6.1 with previous version 0.6.0 dated 2020-08-03

Title: Convert Values to NA
Description: Provides a replacement for dplyr::na_if(). Allows you to specify multiple values to be replaced with NA using a single function.
Author: Alexander Rossell Hayes [aut, cre, cph] (<https://orcid.org/0000-0001-9412-0457>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>

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Package psych updated to version 2.0.8 with previous version 2.0.7 dated 2020-07-26

Title: Procedures for Psychological, Psychometric, and Personality Research
Description: A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>

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Package vader updated to version 0.2.0 with previous version 0.1.1 dated 2020-06-09

Title: Valence Aware Dictionary and sEntiment Reasoner (VADER)
Description: A lexicon and rule-based sentiment analysis tool that is specifically attuned to sentiments expressed in social media, and works well on texts from other domains. Hutto & Gilbert (2014) <https://www.aaai.org/ocs/index.php/ICWSM/ICWSM14/paper/view/8109/8122>.
Author: Katherine Roehrick [aut, cre]
Maintainer: Katherine Roehrick <kr.gitcode@gmail.com>

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Package diversitree updated to version 0.9-14 with previous version 0.9-13 dated 2020-01-16

Title: Comparative 'Phylogenetic' Analyses of Diversification
Description: Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.
Author: Richard G. FitzJohn [aut, cre], Emma Goldberg [aut], Karen Magnuson-Ford [aut], Roger Sidje [aut]
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>

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Package pubchunks updated to version 0.3.0 with previous version 0.2.2 dated 2020-06-28

Title: Fetch Sections of XML Scholarly Articles
Description: Get chunks of XML scholarly articles without having to know how to work with XML. Custom mappers for each publisher and for each article section pull out the information you want. Works with outputs from package 'fulltext', 'xml2' package documents, and file paths to XML documents.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <sckott@protonmail.com>

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Package tsgui updated to version 0.2.1 with previous version 0.0.3 dated 2017-09-18

Title: A Gui for Simulating Time Series
Description: This gui shows realisations of times series, currently ARMA and GARCH processes. It might be helpful for teaching and studying.
Author: Martin Schlather [aut, cre],
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between tsgui versions 0.0.3 dated 2017-09-18 and 0.2.1 dated 2020-09-04

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Package pairwiseComparisons updated to version 2.0.0 with previous version 1.1.2 dated 2020-06-23

Title: Multiple Pairwise Comparison Tests
Description: Multiple pairwise comparison tests on tidy data for one-way analysis of variance for both between-subjects and within-subjects designs. Currently, it supports only the most common types of statistical analyses and tests: parametric (Welch's and Student's t-test), nonparametric (Durbin-Conover and Dunn test), robust (Yuen’s trimmed means test), and Bayes Factor (Student's t-test).
Author: Indrajeet Patil [cre, aut, cph] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package visvow updated to version 1.1.0 with previous version 1.0.0 dated 2020-08-26

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>

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Package SPAtest updated to version 3.1.2 with previous version 3.0.2 dated 2020-01-10

Title: Score Test and Meta-Analysis Based on Saddlepoint Approximation
Description: Performs score test using saddlepoint approximation to estimate the null distribution. Also prepares summary statistics for meta-analysis and performs meta-analysis to combine multiple association results. For the latest version, please check <https://github.com/leeshawn/SPAtest>.
Author: Rounak Dey, Seunggeun Lee
Maintainer: Rounak Dey <deyrnk@umich.edu>

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Package zen4R updated to version 0.4-2 with previous version 0.4-1 dated 2020-09-03

Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by 'Zenodo' and upload of files.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>), Julien Barde [ctb] (<https://orcid.org/0000-0002-3519-6141>), Stephen Eglen [ctb] (<https://orcid.org/0000-0001-8607-8025>), Hans Van Calster [ctb] (<https://orcid.org/0000-0001-8595-8426>), Floris Vanderhaeghe [ctb] (<https://orcid.org/0000-0002-6378-6229>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

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Package stochvolTMB updated to version 0.1.2 with previous version 0.1.0 dated 2020-09-02

Title: Likelihood Estimation of Stochastic Volatility Models
Description: Parameter estimation for stochastic volatility models using maximum likelihood. The latent log-volatility is integrated out of the likelihood using the Laplace approximation. The models are fitted via 'TMB' (Template Model Builder) (Kristensen, Nielsen, Berg, Skaug, and Bell (2016) <doi:10.18637/jss.v070.i05>).
Author: Jens Christian Wahl <jens.c.wahl@gmail.com>
Maintainer: Jens Christian Wahl <jens.c.wahl@gmail.com>

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Package siplab updated to version 1.5 with previous version 1.4 dated 2019-04-01

Title: Spatial Individual-Plant Modelling
Description: A platform for computing competition indices and experimenting with spatially explicit individual-based vegetation models.
Author: Oscar Garcia <https://orcid.org/0000-0002-8995-1341>
Maintainer: Oscar Garcia <garcia@dasometrics.net>

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Package RTL updated to version 0.1.4 with previous version 0.1.3 dated 2020-06-07

Title: Risk Tool Library
Description: Collection of functions and metadata to complement core packages in Finance and Commodities, including futures expiry tables and <https://www.morningstar.com/products/commodities-and-energy/> API functions. See <https://github.com/risktoollib/RTL>.
Author: Philippe Cote [aut, cre], Nima Safaian [aut]
Maintainer: Philippe Cote <pcote@ualberta.ca>

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Package rkeops updated to version 1.4.1.1 with previous version 1.4.1 dated 2020-05-25

Title: Kernel Operations on the GPU, with Autodiff, without Memory Overflows
Description: The 'KeOps' library lets you compute generic reductions of very large arrays whose entries are given by a mathematical formula. It combines a tiled reduction scheme with an automatic differentiation engine, and can be used through 'R', 'Matlab', 'NumPy' or 'PyTorch' backends. It is perfectly suited to the computation of Kernel dot products and the associated gradients, even when the full kernel matrix does not fit into the GPU memory.
Author: Benjamin Charlier [aut] (<http://imag.umontpellier.fr/~charlier/>), Jean Feydy [aut] (<https://www.math.ens.fr/~feydy/>), Joan A. Glaunès [aut] (<https://www.mi.parisdescartes.fr/~glaunes/>), Ghislain Durif [aut, cre] (<https://gdurif.perso.math.cnrs.fr/>), François-David Collin [ctb] (Development-related consulting and support), Daniel Frey [ctb] (Author of the included C++ library 'sequences')
Maintainer: Ghislain Durif <gd.dev@libertymail.net>

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Package insee updated to version 0.9.0 with previous version 0.8.0 dated 2020-08-02

Title: Tools to Easily Download Data from INSEE BDM Database
Description: Using embedded sdmx queries, get the data of more than 150 000 insee series from bdm database. Have a look at the detailed sdmx web service page with the following link : <https://www.insee.fr/en/information/2868055>.
Author: Hadrien Leclerc [aut, cre], INSEE [cph]
Maintainer: Hadrien Leclerc <hadrien.leclerc@insee.fr>

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Package fbst updated to version 1.2 with previous version 1.0 dated 2020-06-04

Title: The Full Bayesian Significance Test and the e-Value
Description: Provides access to a range of functions for computing and visualising the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available. For details on the computation and theory of the FBST see <arXiv:2005.13181>.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>

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Package synoptReg updated to version 1.0.2 with previous version 1.0.1 dated 2020-03-23

Title: Synoptic Climate Classification and Spatial Regionalization of Environmental Data
Description: Set of functions to compute different types of synoptic classification methods and for analysing their effect on environmental variables. More information about the methods used in Lemus-Canovas et al. 2019 <DOI:10.1016/j.atmosres.2019.01.018> and Martin-Vide et al. 2008 <DOI:10.5194/asr-2-99-2008>.
Author: Marc Lemus-Canovas [aut, cre] (<https://orcid.org/0000-0002-0925-3827>), Dominic Roye) [aut] (<https://orcid.org/0000-0002-5516-6396>)
Maintainer: Marc Lemus-Canovas <mlemus@ub.edu>

Diff between synoptReg versions 1.0.1 dated 2020-03-23 and 1.0.2 dated 2020-09-04

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Package dispRity updated to version 1.4.2 with previous version 1.4.1 dated 2020-06-03

Title: Measuring Disparity
Description: A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics (Guillerme (2018) <doi:10.1111/2041-210X.13022>). The package also provides functions for looking at disparity in a serial way (e.g. disparity through time - Guillerme and Cooper (2018) <doi:10.1111/pala.12364>) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph], Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>

Diff between dispRity versions 1.4.1 dated 2020-06-03 and 1.4.2 dated 2020-09-04

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Package uroot updated to version 2.1-2 with previous version 2.0-11 dated 2019-08-19

Title: Unit Root Tests for Seasonal Time Series
Description: Seasonal unit roots and seasonal stability tests. P-values based on response surface regressions are available for both tests. P-values based on bootstrap are available for seasonal unit root tests.
Author: Javier López-de-Lacalle [aut], Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

Diff between uroot versions 2.0-11 dated 2019-08-19 and 2.1-2 dated 2020-09-04

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Package synthpop updated to version 1.6-0 with previous version 1.5-1 dated 2019-03-20

Title: Generating Synthetic Versions of Sensitive Microdata for Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>.
Author: Beata Nowok [aut, cre], Gillian M Raab [aut], Chris Dibben [ctb], Joshua Snoke [ctb], Caspar van Lissa [ctb]
Maintainer: Beata Nowok <beata.nowok@gmail.com>

Diff between synthpop versions 1.5-1 dated 2019-03-20 and 1.6-0 dated 2020-09-04

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New package pagemap with initial version 0.1.0
Package: pagemap
Type: Package
Title: Create Mini Map for Web Pages
Version: 0.1.0
Date: 2020-08-29
Authors@R: c( person(given = "Wei", family = "Su", role = c("aut", "cre"), email = "swsoyee@gmail.com"), person(given = "Lars", family = "Jung", role = c("aut", "cph"), comment = "pagemap library in htmlwidgets/lib, https://github.com/lrsjng/pagemap"))
Maintainer: Wei Su <swsoyee@gmail.com>
Description: Quickly and easily add a mini map to your 'rmarkdown' html documents.
Imports: htmlwidgets
Suggests: knitr, shiny, rmarkdown, devtools
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-08-31 11:47:38 UTC; wsu
Author: Wei Su [aut, cre], Lars Jung [aut, cph] (pagemap library in htmlwidgets/lib, https://github.com/lrsjng/pagemap)
Repository: CRAN
Date/Publication: 2020-09-04 08:22:07 UTC

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New package ExactMultinom with initial version 0.1.1
Package: ExactMultinom
Type: Package
Title: Multinomial Goodness-of-Fit Tests
Version: 0.1.1
Author: Johannes Resin
Maintainer: Johannes Resin <johannes.resin@h-its.org>
Description: Computes exact p-values for multinomial goodness-of-fit tests based on multiple test statistics, namely, Pearson's chi-square, the log-likelihood ratio and the probability mass statistic. Implements the algorithm detailed in Resin (2020) <arXiv:2008.12682>. Estimates based on the classical asymptotic chi-square approximation or Monte-Carlo simulation can also be computed.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.4), stats
LinkingTo: Rcpp
Encoding: UTF-8
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-08-31 11:31:11 UTC; resinjs
Repository: CRAN
Date/Publication: 2020-09-04 08:12:13 UTC

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Package WVPlots updated to version 1.2.8 with previous version 1.2.7 dated 2020-08-24

Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'. Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions, conditioned scatter plot with marginal densities, box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between WVPlots versions 1.2.7 dated 2020-08-24 and 1.2.8 dated 2020-09-04

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 NAMESPACE                      |    1 
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Package sdetorus updated to version 0.1.7 with previous version 0.1.6 dated 2020-08-31

Title: Statistical Tools for Toroidal Diffusions
Description: Implementation of statistical methods for the estimation of toroidal diffusions. Several diffusive models are provided, most of them belonging to the Langevin family of diffusions on the torus. Specifically, the wrapped normal and von Mises processes are included, which can be seen as toroidal analogues of the Ornstein-Uhlenbeck diffusion. A collection of methods for approximate maximum likelihood estimation, organized in four blocks, is given: (i) based on the exact transition probability density, obtained as the numerical solution to the Fokker-Plank equation; (ii) based on wrapped pseudo-likelihoods; (iii) based on specific analytic approximations by wrapped processes; (iv) based on maximum likelihood of the stationary densities. The package allows the reproducibility of the results in García-Portugués et al. (2019) <doi:10.1007/s11222-017-9790-2>.
Author: Eduardo García-Portugués [aut, cre] (<https://orcid.org/0000-0002-9224-4111>)
Maintainer: Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>

Diff between sdetorus versions 0.1.6 dated 2020-08-31 and 0.1.7 dated 2020-09-04

 DESCRIPTION           |   10 +++++-----
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 NEWS.md               |    4 ++++
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 4 files changed, 13 insertions(+), 9 deletions(-)

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New package RUVIIIC with initial version 1.0.16
Package: RUVIIIC
Type: Package
Title: RUV-III-C
Version: 1.0.16
Date: 2020-08-31
Author: Rohan Shah [aut, cre], Sean Peters [ctb], Qing Zhong [ctb], Children's Medical Research Institute [cph]
Maintainer: Rohan Shah <rshah@cmri.org.au>
Description: Variations of Remove Unwanted Variation-III (RUV-III) known as RUV-III-C (RUV-III Complete). RUV-III performs normalisation using negative control variables and replication. RUV-III-C extends this method to cases where the data contains missing values, by applying RUV-III to complete subsets of the data. Originally designed for SWATH-MS proteomics datasets. Poulos et al. (2020) <doi:10.1038/s41467-020-17641-3>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyLoad: yes
LazyData: yes
SystemRequirements: C++11
LinkingTo: Rcpp, RcppEigen, RSpectra, RcppProgress
Suggests: ruv, testthat
Depends: R (>= 3.5), RSpectra, progress
Collate: 'RcppExports.R' 'RUVIII_C.R' 'RUVIII_C_Varying.R' 'data.R' 'roxygen.R'
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-08-31 09:04:35 UTC; rshah
Repository: CRAN
Date/Publication: 2020-09-04 07:52:08 UTC

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New package RLumModel with initial version 0.2.7
Package: RLumModel
Type: Package
Title: Solving Ordinary Differential Equations to Understand Luminescence
Version: 0.2.7
Date: 2020-09-01
Author: Johannes Friedrich [aut, trl, cre] (<https://orcid.org/0000-0002-0805-9547>), Sebastian Kreutzer [aut, ths] (<https://orcid.org/0000-0002-0734-2199>), Christoph Schmidt [aut, ths] (<https://orcid.org/0000-0002-2309-3209>)
Authors@R: c( person("Johannes", "Friedrich", role = c("aut","trl","cre"), comment = c(ORCID = "0000-0002-0805-9547"), email = "johannes.friedrich@posteo.de"), person("Sebastian", "Kreutzer", role = c("aut", "ths"), comment = c(ORCID = "0000-0002-0734-2199")), person("Christoph", "Schmidt", role = c("aut", "ths"), comment = c(ORCID = "0000-0002-2309-3209")) )
Maintainer: Johannes Friedrich <johannes.friedrich@posteo.de>
Description: A collection of functions to simulate luminescence signals in quartz and Al2O3 based on published models.
Contact: Package Developer Team <developer@model.r-luminescence.de>
License: GPL-3
Depends: R (>= 3.5.0), utils, Luminescence (>= 0.9.0)
Imports: deSolve (>= 1.21), methods, Rcpp (>= 1.0.1)
Suggests: testthat (>= 2.1.1), R.rsp (>= 0.44.0)
URL: https://CRAN.R-project.org/package=RLumModel
Collate: RLumModel-package.R RcppExports.R calc_signal.R calc_concentrations.R create_DRT.sequence.R create_SAR.sequence.R extract_pars.R model_LuminescenceSignals.R read_SEQ2R.R set_pars.R simulate_CW_OSL.R simulate_heating.R simulate_illumination.R simulate_irradiation.R simulate_LM_OSL.R simulate_pause.R simulate_RF.R simulate_RF_and_heating.R simulate_TL.R translate_sequence.R
RoxygenNote: 7.1.1
Encoding: UTF-8
LazyData: true
VignetteBuilder: R.rsp
LinkingTo: Rcpp (>= 1.0.1), RcppArmadillo (>= 0.9.400.2.0)
NeedsCompilation: yes
Packaged: 2020-09-01 18:03:28 UTC; johannes
Repository: CRAN
Date/Publication: 2020-09-04 07:02:27 UTC

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Package ridge updated to version 2.7 with previous version 2.6 dated 2020-09-02

Title: Ridge Regression with Automatic Selection of the Penalty Parameter
Description: Linear and logistic ridge regression functions. Additionally includes special functions for genome-wide single-nucleotide polymorphism (SNP) data.
Author: Steffen Moritz [aut, cre] (<https://orcid.org/0000-0002-0085-1804>), Erika Cule [aut], Dan Frankowski [aut]
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>

Diff between ridge versions 2.6 dated 2020-09-02 and 2.7 dated 2020-09-04

 DESCRIPTION     |    8 ++++----
 MD5             |   14 +++++++-------
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New package hyperoverlap with initial version 1.0
Package: hyperoverlap
Title: Overlap Detection in n-Dimensional Space
Version: 1.0
Description: Uses support vector machines to identify a perfectly separating hyperplane (linear or curvilinear) between two entities in high-dimensional space. If this plane exists, the entities do not overlap. Applications include overlap detection in morphological, resource or environmental dimensions. More details can be found in: Brown et al. (2020) <doi:10.1111/2041-210X.13363> .
Authors@R: c(person("Matilda", "Brown", email = "matilda.brown@utas.edu.au", role = c("aut", "cre"), comment= c( ORCID = "0000-0003-2536-8365")), person("Greg", "Jordan", role="aut"))
Depends: R (>= 3.4.0)
Imports: e1071, matlib, ggplot2, rgl, misc3d, methods, stats, MASS, graphics
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, plotrix, rlang
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-08-31 07:52:33 UTC; matilda
Author: Matilda Brown [aut, cre] (<https://orcid.org/0000-0003-2536-8365>), Greg Jordan [aut]
Maintainer: Matilda Brown <matilda.brown@utas.edu.au>
Repository: CRAN
Date/Publication: 2020-09-04 07:42:08 UTC

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Package DALEX updated to version 2.0 with previous version 1.3.1.1 dated 2020-08-01

Title: moDel Agnostic Language for Exploration and eXplanation
Description: Unverified black box model is the path to the failure. Opaqueness leads to distrust. Distrust leads to ignoration. Ignoration leads to rejection. DALEX package xrays any model and helps to explore and explain its behaviour. Machine Learning (ML) models are widely used and have various applications in classification or regression. Models created with boosting, bagging, stacking or similar techniques are often used due to their high performance. But such black-box models usually lack of direct interpretability. DALEX package contains various methods that help to understand the link between input variables and model output. Implemented methods help to explore model on the level of a single instance as well as a level of the whole dataset. All model explainers are model agnostic and can be compared across different models. DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration. Find more details in (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>), Szymon Maksymiuk [aut] (<https://orcid.org/0000-0002-3120-1601>), Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

Diff between DALEX versions 1.3.1.1 dated 2020-08-01 and 2.0 dated 2020-09-04

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 DALEX-2.0/DALEX/R/predict.R                                      |    2 
 DALEX-2.0/DALEX/R/predict_diagnostics.R                          |    2 
 DALEX-2.0/DALEX/R/predict_parts.R                                |    2 
 DALEX-2.0/DALEX/R/predict_profile.R                              |    2 
 DALEX-2.0/DALEX/R/print_explainer.R                              |    2 
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 DALEX-2.0/DALEX/man/model_info.Rd                                |    4 
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Package RVAideMemoire updated to version 0.9-78 with previous version 0.9-77 dated 2020-06-15

Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime Herv<e9>
Maintainer: Maxime Herv<e9> <maxime.herve@univ-rennes1.fr>

Diff between RVAideMemoire versions 0.9-77 dated 2020-06-15 and 0.9-78 dated 2020-09-04

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Package explore updated to version 0.6.1 with previous version 0.5.5 dated 2020-04-06

Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code or use an easy to remember set of tidy functions for exploratory data analysis. Introduces three main verbs. explore() to graphically explore a variable or table, describe() to describe a variable or table and report() to create an automated report.
Author: Roland Krasser
Maintainer: Roland Krasser <roland.krasser@gmail.com>

Diff between explore versions 0.5.5 dated 2020-04-06 and 0.6.1 dated 2020-09-04

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Package tram updated to version 0.5-1 with previous version 0.5-0 dated 2020-08-31

Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models implemented in package 'mlt'. Available models include Cox models, some parametric survival models (Weibull, etc.), models for ordered categorical variables, normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression (Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to transformation models for clustered data is provided (Hothorn, 2019, <arxiv:1910.09219>). Multivariate conditional transformation models (<arxiv:1906.03151>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>), Luisa Barbanti [aut], Brian Ripley [ctb], Bill Venables [ctb], Douglas M. Bates [ctb], Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package rsm updated to version 2.10.2 with previous version 2.10 dated 2018-09-02

Title: Response-Surface Analysis
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis. A good reference on these methods is Chapter 10 of Wu, C-F J and Hamada, M (2009) "Experiments: Planning, Analysis, and Parameter Design Optimization" ISBN 978-0-471-69946-0.
Author: Russell Lenth [aut, cre]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>

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Package nanotime updated to version 0.3.2 with previous version 0.3.1 dated 2020-08-10

Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type. Three additional classes offer interval, period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package MFPCA updated to version 1.3-6 with previous version 1.3-5 dated 2020-04-25

Title: Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis for data observed on different dimensional domains. The estimation algorithm relies on univariate basis expansions for each element of the multivariate functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>. Multivariate and univariate functional data objects are represented by S4 classes for this type of data implemented in the package 'funData'. For more details on the general concepts of both packages and a case study, see Happ-Kurz (2020) <doi:10.18637/jss.v093.i05>.
Author: Clara Happ-Kurz [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Maintainer: Clara Happ-Kurz <clara.happ@stat.uni-muenchen.de>

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Package maxLik updated to version 1.4-4 with previous version 1.4-0 dated 2020-07-31

Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation, non-linear optimization, and related tools. It includes a unified way to call different optimizers, and classes and methods to handle the results from the Maximum Likelihood viewpoint. It also includes a number of convenience tools for testing and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>, Arne Henningsen <arne.henningsen@gmail.com>, with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>

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Package mapdeck updated to version 0.3.4 with previous version 0.3.3 dated 2020-05-14

Title: Interactive Maps Using 'Mapbox GL JS' and 'Deck.gl'
Description: Provides a mechanism to plot an interactive map using 'Mapbox GL' (<https://docs.mapbox.com/mapbox-gl-js/api/>), a javascript library for interactive maps, and 'Deck.gl' (<https://deck.gl/>), a javascript library which uses 'WebGL' for visualising large data sets.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>

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Package logistf updated to version 1.23.1 with previous version 1.23 dated 2018-07-19

Title: Firth's Bias-Reduced Logistic Regression
Description: Fit a logistic regression model using Firth's bias reduction method, equivalent to penalization of the log-likelihood by the Jeffreys prior. Confidence intervals for regression coefficients can be computed by penalized profile likelihood. Firth's method was proposed as ideal solution to the problem of separation in logistic regression. If needed, the bias reduction can be turned off such that ordinary maximum likelihood logistic regression is obtained.
Author: Georg Heinze [aut, cre], Meinhard Ploner [aut], Daniela Dunkler [ctb], Harry Southworth [ctb]
Maintainer: ORPHANED

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