Mon, 25 Oct 2021

Package nimbleSCR updated to version 0.1.3 with previous version 0.1.2 dated 2021-07-01

Title: Spatial Capture-Recapture (SCR) Methods Using 'nimble'
Description: Provides utility functions, distributions, and methods for improving Markov chain Monte Carlo (MCMC) sampling efficiency for ecological Spatial Capture-Recapture (SCR) and Open Population Spatial Capture-Recapture (OPSCR) models. The methods provided implement the techniques presented in "Estimation of Large-Scale Spatial Capture-Recapture Models" (Turek, et al (2021); Eco-sphere 12(2):e03385. <doi:10.1002/ecs2.3385>).
Author: Richard Bischof [aut], Daniel Turek [aut, cre], Cyril Milleret [aut], Torbjørn Ergon [aut], Pierre Dupont [aut], Soumen Dey [aut], Wei Zhang [aut], Perry de Valpine [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>

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Package twang updated to version 2.5 with previous version 2.4 dated 2021-07-26

Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score estimating and weighting, nonresponse weighting, and diagnosis of the weights.
Author: Matthew Cefalu <Matthew_Cefalu@rand.org>, Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, and Lane Burgette
Maintainer: Matthew Cefalu <Matthew_Cefalu@rand.org>

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Package sparseMVN updated to version 0.2.2 with previous version 0.2.1.1 dated 2018-03-26

Title: Multivariate Normal Functions for Sparse Covariance and Precision Matrices
Description: Computes multivariate normal (MVN) densities, and samples from MVN distributions, when the covariance or precision matrix is sparse.
Author: Michael Braun [aut, cre, cph] (<https://orcid.org/0000-0003-4774-2119>)
Maintainer: Michael Braun <braunm@smu.edu>

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Package Matching updated to version 4.9-11 with previous version 4.9-10 dated 2021-10-09

Title: Multivariate and Propensity Score Matching with Balance Optimization
Description: Provides functions for multivariate and propensity score matching and for finding optimal balance based on a genetic search algorithm. A variety of univariate and multivariate metrics to determine if balance has been obtained are also provided. For details, see the paper by Jasjeet Sekhon (2007, <doi:10.18637/jss.v042.i07>).
Author: Jasjeet Singh Sekhon <jas.sekhon@yale.edu>
Maintainer: Jasjeet Singh Sekhon <jas.sekhon@yale.edu>

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Package drmdel updated to version 1.3.2 with previous version 1.3.1 dated 2015-01-21

Title: Dual Empirical Likelihood Inference under Density Ratio Models in the Presence of Multiple Samples
Description: Dual empirical likelihood (DEL) inference under semiparametric density ratio models (DRM) in the presence of multiple samples, including population cumulative distribution function estimation, quantile estimation and comparison, density estimation, composite hypothesis testing for DRM parameters which encompasses testing for changes in population distribution functions as a special case, etc.
Author: Song Cai
Maintainer: Song Cai <scai@math.carleton.ca>

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Package DArand updated to version 0.0.1.1 with previous version 0.0.1.0 dated 2021-09-27

Title: Differential Analysis with Random Reference Genes
Description: Differential Analysis of short RNA transcripts that can be modeled by either Poisson or Negative binomial distribution. The statistical methodology implemented in this package is based on the random selection of references genes (Desaulle et al. (2021) <arXiv:2103.09872>).
Author: Dorota Desaulle [aut, cre] (<https://orcid.org/0000-0002-3419-9447>), Yves Rozenholc [aut] (<https://orcid.org/0000-0002-3907-5101>)
Maintainer: Dorota Desaulle <dorota.desaulle@u-paris.fr>

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Package archive updated to version 1.1.2 with previous version 1.1.1 dated 2021-10-13

Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the Multi-format archive and compression library. Offers R connections and direct extraction for many archive formats including 'tar', 'ZIP', '7-zip', 'RAR', 'CAB' and compression formats including 'gzip', 'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>), Ondrej Holy [cph] (archive_write_add_filter implementation), RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>

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Package mlVAR updated to version 0.5 with previous version 0.4.4 dated 2019-10-21

Title: Multi-Level Vector Autoregression
Description: Estimates the multi-level vector autoregression model on time-series data. Three network structures are obtained: temporal networks, contemporaneous networks and between-subjects networks.
Author: Sacha Epskamp [aut, cre], Marie K. Deserno [aut], Laura F. Bringmann [aut], Myrthe Veenman [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

Diff between mlVAR versions 0.4.4 dated 2019-10-21 and 0.5 dated 2021-10-25

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Package ggbreak updated to version 0.0.7 with previous version 0.0.6 dated 2021-10-09

Title: Set Axis Break for 'ggplot2'
Description: An implementation of scale functions for setting axis breaks of a 'gg' plot.
Author: Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Shuangbin Xu [aut] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package fastai updated to version 2.1.0 with previous version 2.0.9 dated 2021-07-28

Title: Interface to 'fastai'
Description: The 'fastai' <https://docs.fast.ai/index.html> library simplifies training fast and accurate neural networks using modern best practices. It is based on research in to deep learning best practices undertaken at 'fast.ai', including 'out of the box' support for vision, text, tabular, audio, time series, and collaborative filtering models.
Author: Turgut Abdullayev [ctb, cre, cph, aut]
Maintainer: Turgut Abdullayev <turqut.a.314@gmail.com>

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Package aRtsy updated to version 0.1.4 with previous version 0.1.3 dated 2021-09-26

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 robust updated to version 0.6-0 with previous version 0.5-0.0 dated 2020-03-07

Title: Port of the S+ "Robust Library"
Description: Methods for robust statistics, a state of the art in the early 2000s, notably for robust regression and robust multivariate analysis.
Author: Jiahui Wang, Ruben Zamar <ruben@stat.ubc.ca>, Alfio Marazzi <Alfio.Marazzi@inst.hospvd.ch>, Victor Yohai <vyohai@dm.uba.ar>, Matias Salibian-Barrera <matias@stat.ubc.ca>, Ricardo Maronna <maron@mate.unlp.edu.ar>, Eric Zivot <ezivot@u.washington.edu>, David Rocke <dmrocke@ucdavis.edu>, Doug Martin, Martin Maechler <maechler@stat.math.ethz.ch>, Kjell Konis <kjell.konis@me.com>.
Maintainer: Valentin Todorov <valentin.todorov@chello.at>

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Package usethis updated to version 2.1.2 with previous version 2.1.0 dated 2021-10-16

Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.
Author: Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), Malcolm Barrett [aut] (<https://orcid.org/0000-0003-0299-5825>), RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

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Package tryCatchLog updated to version 1.3.1 with previous version 1.2.4 dated 2021-05-21

Title: Advanced 'tryCatch()' and 'try()' Functions
Description: Advanced tryCatch() and try() functions for better error handling (logging, stack trace with source code references and support for post-mortem analysis via dump files).
Author: Juergen Altfeld [aut, cre, cph], Charles Epaillard [ctb], Brandon Bertelsen [ctb], Valerian Wrobel [ctb]
Maintainer: Juergen Altfeld <jaltfeld@altfeld-im.de>

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Package Rmpfr updated to version 0.8-6 with previous version 0.8-5 dated 2021-10-06

Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Richard M. Heiberger [ctb] (formatHex(), *Bin, *Dec), John C. Nash [ctb] (hjkMpfr(), origin of unirootR()), Hans W. Borchers [ctb] (optimizeR(*, "GoldenRatio"); origin of hjkMpfr())
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package migraph updated to version 0.8.2 with previous version 0.8.1 dated 2021-10-22

Title: Multimodal and Multilevel Network Analysis
Description: A set of tools that extend common social network analysis packages for analysing multimodal and multilevel networks. It includes functions for one- and two-mode (and sometimes three-mode) centrality, centralization, clustering, and constraint, as well as for one- and two-mode network regression and block-modelling. All functions operate with matrices, edge lists, and 'igraph', 'network'/'sna', and 'tidygraph' objects. The package is released as a complement to 'Multimodal Political Networks' (2021, ISBN:9781108985000), and includes various datasets used in the book.
Author: James Hollway [cph, cre, aut, ctb] (IHEID, <https://orcid.org/0000-0002-8361-9647>)
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>

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Package kayadata updated to version 1.0.0 with previous version 0.5.1 dated 2021-03-27

Title: Kaya Identity Data for Nations and Regions
Description: Provides data for Kaya identity variables (population, gross domestic product, primary energy consumption, and energy-related CO2 emissions) for the world and for individual nations, and utility functions for looking up data, plotting trends of Kaya variables, and plotting the fuel mix for a given country or region. The Kaya identity (Yoichi Kaya and Keiichi Yokobori, "Environment, Energy, and Economy: Strategies for Sustainability" (United Nations University Press, 1998) and <https://en.wikipedia.org/wiki/Kaya_identity>) expresses a nation's or region's greenhouse gas emissions in terms of its population, per-capita Gross Domestic Product, the energy intensity of its economy, and the carbon-intensity of its energy supply.
Author: Jonathan Gilligan [cre, aut] (<https://orcid.org/0000-0003-1375-6686>)
Maintainer: Jonathan Gilligan <jonathan.gilligan@vanderbilt.edu>

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Package eirm updated to version 0.5 with previous version 0.4 dated 2021-07-04

Title: Explanatory Item Response Modeling for Dichotomous and Polytomous Items
Description: Analysis of dichotomous and polytomous response data using the explanatory item response modeling framework, as described in Bulut, Gorgun, & Yildirim-Erbasli (2021) <doi:10.3390/psych3030023>, Stanke & Bulut (2019) <doi:10.21449/ijate.515085>, and De Boeck & Wilson (2004) <doi:10.1007/978-1-4757-3990-9>. Generalized linear mixed modeling is used for estimating the effects of item-related and person-related variables on dichotomous and polytomous item responses.
Author: Okan Bulut [aut, cre] (<https://orcid.org/0000-0001-5853-1267>)
Maintainer: Okan Bulut <bulut@ualberta.ca>

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Package castor updated to version 1.7.0 with previous version 1.6.9 dated 2021-08-16

Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>

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Package individual updated to version 0.1.7 with previous version 0.1.6 dated 2021-10-14

Title: Framework for Specifying and Simulating Individual Based Models
Description: A framework which provides users a set of useful primitive elements for specifying individual based simulation models, with special attention models for infectious disease epidemiology. Users build models by specifying variables for each characteristic of individuals in the simulated population by using data structures exposed by the package. The package provides efficient methods for finding subsets of individuals based on these variables, or cohorts. Cohorts can then be targeted for variable updates or scheduled for events. Variable updates queued during a time step are executed at the end of a discrete time step, and the code places no restrictions on how individuals are allowed to interact. These data structures are designed to provide an intuitive way for users to turn their conceptual model of a system into executable code, which is fast and memory efficient.
Author: Giovanni Charles [aut, cre] (<https://orcid.org/0000-0002-7024-1200>), Sean L. Wu [aut] (<https://orcid.org/0000-0002-5781-9493>), Peter Winskill [aut] (<https://orcid.org/0000-0003-3001-4959>), Imperial College of Science, Technology and Medicine [cph]
Maintainer: Giovanni Charles <giovanni.charles@gmail.com>

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Package DSMolgenisArmadillo updated to version 1.4.0 with previous version 1.3.7 dated 2021-10-14

Title: 'DataSHIELD' Client for 'MOLGENIS Armadillo'
Description: 'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This package is the 'DataSHIELD' interface implementation to analyze data shared on a 'MOLGENIS Armadillo' server. 'MOLGENIS Armadillo' is a light-weight 'DataSHIELD' server using a file store and an 'RServe' server.
Author: Sido Haakma [aut, cre] (<https://orcid.org/0000-0003-1278-9144>), Tommy de Boer [aut] (<https://orcid.org/0000-0002-4492-7225>), Fleur Kelpin [aut] (<https://orcid.org/0000-0003-1527-5130>), MOLGENIS org [cph, fnd]
Maintainer: Sido Haakma <s.haakma@rug.nl>

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Package discretefit updated to version 0.1.0 with previous version 0.0.0 dated 2021-10-08

Title: Simulated Goodness-of-Fit Tests for Discrete Distributions
Description: Implements Monte Carlo simulations for goodness-of-fit (GOF) tests for discrete distributions. This includes tests based on the Chi-squared statistic, the log-likelihood-ratio (G^2) statistic, the Freeman-Tukey (Hellinger-distance) statistic, the Kolmogorov-Smirnov statistic, the Cramer-von Mises statistic as described in Choulakian, Lockhart and Stephens (1994) <doi:10.2307/3315828>, and the root-mean-square statistic, see Perkins, Tygert, and Ward (2011) <doi:10.1016/j.amc.2011.03.124>.
Author: Josh McCormick [aut, cre]
Maintainer: Josh McCormick <josh.mccormick@aya.yale.edu>

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Package BuyseTest updated to version 2.3.5 with previous version 2.3.0 dated 2021-04-23

Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better than a random observation drawn from the other group (Mann-Whitney parameter). The net benefit and win ratio statistics, i.e. the difference and ratio between the probabilities relative to the intervention and control groups, can then also be estimated. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>), non-parametric bootstrap, or permutations. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>), Julien Peron [ctb], Eva Cantagallo [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>

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Package BTSPAS updated to version 2021.11.2 with previous version 2021.11.1 dated 2021-10-11

Title: Bayesian Time-Stratified Population Analysis
Description: Provides advanced Bayesian methods to estimate abundance and run-timing from temporally-stratified Petersen mark-recapture experiments. Methods include hierarchical modelling of the capture probabilities and spline smoothing of the daily run size. Theory described in Bonner and Schwarz (2011) <doi:10.1111/j.1541-0420.2011.01599.x>.
Author: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com> and Simon J Bonner <sbonner6@uwo.ca>
Maintainer: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com>

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Package maotai updated to version 0.2.2 with previous version 0.2.1 dated 2021-09-21

Title: Tools for Matrix Algebra, Optimization and Inference
Description: Matrix is an universal and sometimes primary object/unit in applied mathematics and statistics. We provide a number of algorithms for selected problems in optimization and statistical inference. For general exposition to the topic with focus on statistical context, see the book by Banerjee and Roy (2014, ISBN:9781420095388).
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>

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Package mma updated to version 10.5-1 with previous version 10.5-0 dated 2020-12-11

Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis. The analysis method is described in Yu et al. (2014) <doi:10.4172/2155-6180.1000189> "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189; and Yu et al.(2017) <DOI:10.1016/j.sste.2017.02.001> "Exploring racial disparity in obesity: a mediation analysis considering geo-coded environmental factors", published on Spatial and Spatio-temporal Epidemiology, 21, 13-23.
Author: Qingzhao Yu and Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>

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Package metavcov updated to version 2.1.2 with previous version 2.1.1 dated 2021-10-07

Title: Computing Variances and Covariances, Visualization and Missing Data Solution for Multivariate Meta-Analysis
Description: Collection of functions to compute covariances for different effect sizes, data visualization, and single and multiple imputations for missing data. Effect sizes include correlation (r), mean difference (MD), standardized mean difference (SMD), log odds ratio (logOR), log risk ratio (logRR), and risk difference (RD).
Author: Min Lu <m.lu6@umiami.edu>
Maintainer: Min Lu <m.lu6@umiami.edu>

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Package lessR updated to version 4.0.6 with previous version 4.0.5 dated 2021-10-05

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

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Package hyper2 updated to version 2.0-1 with previous version 2.0-0 dated 2021-03-04

Title: The Hyperdirichlet Distribution, Mark 2
Description: A suite of routines for the hyperdirichlet distribution; supersedes the 'hyperdirichlet' package.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package fracture updated to version 0.2.0 with previous version 0.1.3 dated 2021-05-25

Title: Convert Decimals to Fractions
Description: Provides functions for converting decimals to a matrix of numerators and denominators or a character vector of fractions. Supports mixed or improper fractions, finding common denominators for vectors of fractions, limiting denominators to powers of ten, and limiting denominators to a maximum value. Also includes helper functions for finding the least common multiple and greatest common divisor for a vector of integers. Implemented using C++ for maximum speed.
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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Sun, 24 Oct 2021

Package paws.common updated to version 0.3.14 with previous version 0.3.13 dated 2021-10-12

Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

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Package firebase updated to version 0.2.1 with previous version 0.2.0 dated 2021-09-15

Title: Integrates 'Google Firebase' Authentication Method with 'Shiny'
Description: Authenticate users in 'Shiny' applications using 'Google Firebase' with any of the many methods provided; email and password, email link, or using a third-party provider such as 'Github', 'Twitter', or 'Google'.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>

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Package gtrendsR updated to version 1.5.0 with previous version 1.4.8 dated 2021-02-23

Title: Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information returned online by Google Trends is provided. Trends (number of hits) over the time as well as geographic representation of the results can be displayed.
Author: Philippe Massicotte [aut, cre], Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>

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Package RRPP updated to version 1.1.1 with previous version 1.1.0 dated 2021-10-09

Title: Linear Model Evaluation with Randomized Residuals in a Permutation Procedure
Description: Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. This packaged is described by Collyer & Adams (2018) <doi:10.1111/2041-210X.13029>. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre] (<https://orcid.org/0000-0003-0238-2201>), Dean Adams [aut] (<https://orcid.org/0000-0001-9172-7894>)
Maintainer: Michael Collyer <mlcollyer@gmail.com>

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Package groupdata2 updated to version 2.0.0 with previous version 1.5.0 dated 2021-07-03

Title: Creating Groups from Data
Description: Methods for dividing data into groups. Create balanced partitions and cross-validation folds. Perform time series windowing and general grouping and splitting of data. Balance existing groups with up- and downsampling or collapse them to fewer groups.
Author: Ludvig Renbo Olsen [aut, cre]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>

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Package lingtypology updated to version 1.1.7 with previous version 1.1.6 dated 2021-10-14

Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] (<https://orcid.org/0000-0003-1990-6083>), Kirill Koncha [ctb] (<https://orcid.org/0000-0003-0676-2658>), Mikhail Leonov [ctb], Anna Smirnova [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>

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Package ggside updated to version 0.1.3 with previous version 0.1.2 dated 2021-07-21

Title: Side Grammar Graphics
Description: The grammar of graphics as shown in 'ggplot2' has provided an expressive API for users to build plots. 'ggside' extends 'ggplot2' by allowing users to add graphical information about one of the main panel's axis using a familiar 'ggplot2' style API with tidy data. This package is particularly useful for visualizing metadata on a discrete axis, or summary graphics on a continuous axis such as a boxplot or a density distribution.
Author: Justin Landis [aut, cre]
Maintainer: Justin Landis <jtlandis314@gmail.com>

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Package winch updated to version 0.0.7 with previous version 0.0.6 dated 2020-11-16

Title: Portable Native and Joint Stack Traces
Description: Obtain the native stack trace and fuse it with R's stack trace for easier debugging of R packages with native code.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), R Consortium [fnd], Ian Lance Taylor [aut] (Bundled libbacktrace library), Free Software Foundation [cph] (Bundled libbacktrace library)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package GeoTcgaData updated to version 1.0.2 with previous version 1.0.1 dated 2021-08-01

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

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Package echarty updated to version 1.4.0 with previous version 0.3.1 dated 2021-07-30

Title: Minimal R/Shiny Interface to JavaScript Library 'ECharts'
Description: The goal is to deliver the full functionality of 'ECharts' with minimal overhead. 'ECharts' is based on data structures and 'echarty' users build R lists for these same data structures. One to three 'echarty' commands are usually sufficient to produce any chart.
Author: Larry Helgason [aut, cre, cph], John Coene [aut, cph]
Maintainer: Larry Helgason <larry@helgasoft.com>

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More information about echarty at CRAN
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Package SparseBiplots updated to version 4.0.1 with previous version 4.0.0 dated 2020-06-27

Title: 'HJ-Biplot' using Different Ways of Penalization Plotting with 'ggplot2'
Description: 'HJ-Biplot' is a multivariate method that allow represent multivariate data on a subspace of low dimension, in such a way that most of the variability of the information is captured in a few dimensions. This package implements three new techniques and constructs in each case the 'HJ-Biplot', adapting restrictions to reduce weights and / or produce zero weights in the dimensions, based on the regularization theories. It implements three methods of regularization: Ridge, LASSO and Elastic Net.
Author: Mitzi Isabel Cubilla-Montilla <mitzi@usal.es>, Carlos Alfredo Torres-Cubilla <carlos_t22@usal.es>, Purificacion Galindo Villardon <pgalindo@usal.es> and Ana Belen Nieto-Librero <ananieto@usal.es>
Maintainer: Mitzi Isabel Cubilla-Montilla <mitzi@usal.es>

Diff between SparseBiplots versions 4.0.0 dated 2020-06-27 and 4.0.1 dated 2021-10-24

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Sat, 23 Oct 2021

Package partitions updated to version 1.10-4 with previous version 1.10-2 dated 2021-02-23

Title: Additive Partitions of Integers
Description: Additive partitions of integers. Enumerates the partitions, unequal partitions, and restricted partitions of an integer; the three corresponding partition functions are also given. Set partitions and now compositions are included.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>), Paul Egeler [ctb] (<https://orcid.org/0000-0001-6948-9498>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between partitions versions 1.10-2 dated 2021-02-23 and 1.10-4 dated 2021-10-23

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More information about partitions at CRAN
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Package isotree updated to version 0.3.9 with previous version 0.3.0 dated 2021-08-22

Title: Isolation-Based Outlier Detection
Description: Fast and multi-threaded implementation of isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>), extended isolation forest (Hariri, Kind, Brunner (2018) <arXiv:1811.02141>), SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>), and fair-cut forest (Cortes (2019) <arXiv:1911.06646>), for isolation-based outlier detection, clustered outlier detection, distance or similarity approximation (Cortes (2019) <arXiv:1910.12362>), and imputation of missing values (Cortes (2019) <arXiv:1911.06646>), based on random or guided decision tree splitting. Provides simple heuristics for fitting the model to categorical columns and handling missing data, and offers options for varying between random and guided splits, and for using different splitting criteria.
Author: David Cortes [aut, cre, cph], Thibaut Goetghebuer-Planchon [cph] (Copyright holder of included robinmap library), David Blackman [cph] (Copyright holder of original Xoshiro code), Sebastiano Vigna [cph] (Copyright holder of original Xoshiro code)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

Diff between isotree versions 0.3.0 dated 2021-08-22 and 0.3.9 dated 2021-10-23

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More information about isotree at CRAN
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Package admisc updated to version 0.19 with previous version 0.18 dated 2021-09-01

Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'declared', 'DDIwR', 'mixed', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly flexible recoding routine.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

Diff between admisc versions 0.18 dated 2021-09-01 and 0.19 dated 2021-10-23

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More information about admisc at CRAN
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Package ExamPAData updated to version 0.5.0 with previous version 0.4.0 dated 2021-05-26

Title: Data Sets for Predictive Analytics Exam
Description: Contains all data sets for Exam PA: Predictive Analytics at <https://exampa.net/>.
Author: Guanglai Li [aut, cre], Sam Castillo [aut]
Maintainer: Guanglai Li <liguanglai@gmail.com>

Diff between ExamPAData versions 0.4.0 dated 2021-05-26 and 0.5.0 dated 2021-10-23

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Package RcppQuantuccia updated to version 0.0.5 with previous version 0.0.4 dated 2021-10-12

Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an updated variant of the header-only 'Quantuccia' project (put together initially by Peter Caspers) offering an essential subset of 'QuantLib' (and now maintained separately for the calendaring subset). See the included file 'AUTHORS' for a full list of contributors to both 'QuantLib' and 'Quantuccia'.
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppQuantuccia versions 0.0.4 dated 2021-10-12 and 0.0.5 dated 2021-10-23

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Package malaytextr updated to version 0.1.2 with previous version 0.1.1 dated 2021-08-17

Title: Text Mining for Bahasa Malaysia
Description: It is designed to work with text written in Bahasa Malaysia. We provide functions and data sets that will make working with Bahasa Malaysia text much easier. For word stemming in particular, we will look up the Malay words in a dictionary and then proceed to remove "extra suffix" as explained in Khan, Rehman Ullah, Fitri Suraya Mohamad, Muh Inam UlHaq, Shahren Ahmad Zadi Adruce, Philip Nuli Anding, Sajjad Nawaz Khan, and Abdulrazak Yahya Saleh Al-Hababi (2017) <https://ijrest.net/vol-4-issue-12.html> . This package includes a dictionary of Malay words that may be used to perform word stemming.
Author: Zahier Nasrudin [aut, cre] (<https://orcid.org/0000-0002-7060-776X>)
Maintainer: Zahier Nasrudin <zahiernasrudin@gmail.com>

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More information about malaytextr at CRAN
Permanent link

Package easylabel updated to version 0.2.2 with previous version 0.1.0 dated 2021-10-05

Title: Interactive Scatter Plot and Volcano Plot Labels
Description: Interactive labelling of scatter plots, volcano plots and Manhattan plots using a 'shiny' and 'plotly' interface. Users can hover over points to see where specific points are located and click points on/off to easily label them. Labels can be dragged around the plot to place them optimally. Plots can be exported directly to PDF for publication.
Author: Myles Lewis [aut, cre] (<https://orcid.org/0000-0001-9365-5345>), Katriona Goldmann [aut] (<https://orcid.org/0000-0002-9073-6323>), Cankut Cubuk [ctb] (<https://orcid.org/0000-0003-4646-0849>)
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>

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Package HDShOP updated to version 0.1.2 with previous version 0.1.1 dated 2021-09-02

Title: High-Dimensional Shrinkage Optimal Portfolios
Description: Constructs shrinkage estimators of high-dimensional mean-variance portfolios and performs high-dimensional tests on optimality of a given portfolio. The techniques developed in Bodnar et al. (2018) <doi:10.1016/j.ejor.2017.09.028>, Bodnar et al. (2019) <doi:10.1109/TSP.2019.2929964>, Bodnar et al. (2020) <doi:10.1109/TSP.2020.3037369> are central to the package. They provide simple and feasible estimators and tests for optimal portfolio weights, which are applicable for 'large p and large n' situations where p is the portfolio dimension (number of stocks) and n is the sample size. The package also includes tools for constructing portfolios based on shrinkage estimators of the mean vector and covariance matrix as well as a new Bayesian estimator for the Markowitz efficient frontier recently developed by Bauder et al. (2021) <doi:10.1080/14697688.2020.1748214>.
Author: Taras Bodnar [aut] (<https://orcid.org/0000-0001-7855-8221>), Solomiia Dmytriv [aut] (<https://orcid.org/0000-0003-1855-3044>), Yarema Okhrin [aut] (<https://orcid.org/0000-0003-4704-5233>), Dmitry Otryakhin [aut, cre] (<https://orcid.org/0000-0002-4700-7221>), Nestor Parolya [aut] (<https://orcid.org/0000-0003-2147-2288>)
Maintainer: Dmitry Otryakhin <d.otryakhin.acad@protonmail.ch>

Diff between HDShOP versions 0.1.1 dated 2021-09-02 and 0.1.2 dated 2021-10-23

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Package PSCBS updated to version 0.66.0 with previous version 0.65.0 dated 2019-05-05

Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut], Venkatraman E. Seshan [aut], Adam B. Olshen [aut], Paul T. Spellman [aut], Richard A. Olshen [aut], Frank E Harrell Jr [ctb] (Weighted quantile estimator adopted from Hmisc::wtd.quantile())
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package AzureRMR updated to version 2.4.3 with previous version 2.4.2 dated 2021-06-03

Title: Interface to 'Azure Resource Manager'
Description: A lightweight but powerful R interface to the 'Azure Resource Manager' REST API. The package exposes a comprehensive class framework and related tools for creating, updating and deleting 'Azure' resource groups, resources and templates. While 'AzureRMR' can be used to manage any 'Azure' service, it can also be extended by other packages to provide extra functionality for specific services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>

Diff between AzureRMR versions 2.4.2 dated 2021-06-03 and 2.4.3 dated 2021-10-23

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Package samc updated to version 2.0.0 with previous version 1.4.1 dated 2021-09-02

Title: Spatial Absorbing Markov Chains
Description: Implements functions for working with absorbing Markov chains. The implementation is based on the framework described in "Toward a unified framework for connectivity that disentangles movement and mortality in space and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>, which applies them to spatial ecology. This framework incorporates both resistance and absorption with spatial absorbing Markov chains (SAMC) to provide several short-term and long-term predictions for metrics related to connectivity in landscapes. Despite the ecological context of the framework, this package can be used in any application of absorbing Markov chains.
Author: Andrew Marx [aut, cre, cph] (<https://orcid.org/0000-0002-7456-1631>), Robert Fletcher [ctb] (<https://orcid.org/0000-0003-1717-5707>), Miguel Acevedo [ctb] (<https://orcid.org/0000-0002-8289-1497>), Jorge Sefair [ctb] (<https://orcid.org/0000-0002-5887-8938>), Chao Wang [ctb] (<https://orcid.org/0000-0003-2706-5122>)
Maintainer: Andrew Marx <andrewjmarx@ufl.edu>

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Package deldir updated to version 1.0-6 with previous version 1.0-5 dated 2021-10-09

Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation. Calculates the centroidal Voronoi (Dirichlet) tessellation using Lloyd's algorithm.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

Diff between deldir versions 1.0-5 dated 2021-10-09 and 1.0-6 dated 2021-10-23

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Package boot.heterogeneity updated to version 1.1.5 with previous version 1.1.2 dated 2021-01-07

Title: A Bootstrap-Based Heterogeneity Test for Meta-Analysis
Description: Implements a bootstrap-based heterogeneity test for standardized mean differences (d), Fisher-transformed Pearson's correlations (r), and natural-logarithm-transformed odds ratio (or) in meta-analysis studies. Depending on the presence of moderators, this Monte Carlo based test can be implemented in the random- or mixed-effects model. This package uses rma() function from the R package 'metafor' to obtain parameter estimates and likelihoods, so installation of R package 'metafor' is required. This approach refers to the studies of Anscombe (1956) <doi:10.2307/2332926>, Haldane (1940) <doi:10.2307/2332614>, Hedges (1981) <doi:10.3102/10769986006002107>, Hedges & Olkin (1985, ISBN:978-0123363800), Silagy, Lancaster, Stead, Mant, & Fowler (2004) <doi:10.1002/14651858.CD000146.pub2>, Viechtbauer (2010) <doi:10.18637/jss.v036.i03>, and Zuckerman (1994, ISBN:978-0521432009).
Author: Ge Jiang [aut, cre], Han Du [aut], Zijun Ke [ctb]
Maintainer: Ge Jiang <gejiang2@illinois.edu>

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Fri, 22 Oct 2021

Package ramchoice updated to version 2.0 with previous version 1.1 dated 2019-07-11

Title: Revealed Preference and Attention Analysis in Random Limited Attention Models
Description: It is widely documented in psychology, economics and other disciplines that socio-economic agent may not pay full attention to all available alternatives, rendering standard revealed preference theory invalid. This package implements the estimation and inference procedures of Cattaneo, Ma, Masatlioglu and Suleymanov (2020) <arXiv:1712.03448> and Cattaneo, Cheung, Ma, and Masatlioglu (2021) <arXiv:2110.10650>, which utilizes standard choice data to partially identify and estimate a decision maker's preference and attention. For inference, several simulation-based critical values are provided.
Author: Matias D. Cattaneo, Paul Cheung, Xinwei Ma, Yusufcan Masatlioglu, Elchin Suleymanov
Maintainer: Xinwei Ma <x1ma@ucsd.edu>

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Package metasens updated to version 1.0-0 with previous version 0.6-0 dated 2021-01-15

Title: Statistical Methods for Sensitivity Analysis in Meta-Analysis
Description: The following methods are implemented to evaluate how sensitive the results of a meta-analysis are to potential bias in meta-analysis and to support Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 5 'Small-Study Effects in Meta-Analysis': - Copas selection model described in Copas & Shi (2001) <DOI:10.1177/096228020101000402>; - limit meta-analysis by Rücker et al. (2011) <DOI:10.1093/biostatistics/kxq046>; - upper bound for outcome reporting bias by Copas & Jackson (2004) <DOI:10.1111/j.0006-341X.2004.00161.x>; - imputation methods for missing binary data by Gamble & Hollis (2005) <DOI:10.1016/j.jclinepi.2004.09.013> and Higgins et al. (2008) <DOI:10.1177/1740774508091600>; - LFK index test and Doi plot by Furuya-Kanamori et al. (2018) <DOI:10.1097/XEB.0000000000000141>.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>), James R. Carpenter [aut] (<https://orcid.org/0000-0003-3890-6206>), Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

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Package SPOT updated to version 2.5.12 with previous version 2.5.8 dated 2021-08-04

Title: Sequential Parameter Optimization Toolbox
Description: A set of tools for model-based optimization and tuning of algorithms (hyperparameter tuning). It includes surrogate models, optimizers, and design of experiment approaches. The main interface is spot, which uses sequentially updated surrogate models for the purpose of efficient optimization. The main goal is to ease the burden of objective function evaluations, when a single evaluation requires a significant amount of resources.
Author: Thomas Bartz-Beielstein [aut, cre] (<https://orcid.org/0000-0002-5938-5158>), Martin Zaefferer [aut] (<https://orcid.org/0000-0003-2372-2092>), Frederik Rehbach [aut] (<https://orcid.org/0000-0003-0922-8629>), Margarita Rebolledo [ctb], Joerg Stork [ctb] (0000-0002-7471-3498), Christian Lasarczyk [ctb]
Maintainer: Thomas Bartz-Beielstein <tbb@bartzundbartz.de>

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Package Runuran updated to version 0.35 with previous version 0.34 dated 2021-08-11

Title: R Interface to the 'UNU.RAN' Random Variate Generators
Description: Interface to the 'UNU.RAN' library for Universal Non-Uniform RANdom variate generators. Thus it allows to build non-uniform random number generators from quite arbitrary distributions. In particular, it provides an algorithm for fast numerical inversion for distribution with given density function. In addition, the package contains densities, distribution functions and quantiles from a couple of distributions.
Author: Josef Leydold [aut, cre], Wolfgang H"ormann [aut]
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>

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Package stevemisc updated to version 1.3.0 with previous version 1.2.0 dated 2021-07-27

Title: Steve's Miscellaneous Functions
Description: These are miscellaneous functions that I find useful for my research and teaching. The contents include themes for plots, functions for simulating quantities of interest from regression models, functions for simulating various forms of fake data for instructional/research purposes, and many more. All told, the functions provided here are broadly useful for data organization, data presentation, data recoding, and data simulation.
Author: Steve Miller [aut, cre], Ben Bolker [ctb], Dave Armstrong [ctb], John Fox [ctb], Winston Chang [ctb], Brian Ripley [ctb], Bill Venables [ctb], Pascal van Kooten [ctb], Gerko Vink [ctb], Paul Williamson [ctb], Andreas Beger [ctb] (<https://orcid.org/0000-0003-1883-3169>)
Maintainer: Steve Miller <steven.v.miller@gmail.com>

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Package ARTofR updated to version 0.3.3 with previous version 0.2.3 dated 2021-10-05

Title: Who Ever Care About the [Art of R] Scripts?
Description: For instructions, check <https://github.com/Hzhang-ouce/ARTofR>. This is a wrapper of 'bannerCommenter', for generating neat comments!
Author: Huanyuan Zhang [aut, cre] (<https://orcid.org/0000-0003-4801-8771>)
Maintainer: Huanyuan Zhang <hyzhang1996@gmail.com>

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Package text2map updated to version 0.1.1 with previous version 0.1.0 dated 2021-08-24

Title: R Tools for Text Matrices, Embeddings, and Networks
Description: This is a collection of functions optimized for working with for working with various kinds of text matrices. Focusing on the text matrix as the primary object – which is represented either as a base R dense matrix or a 'Matrix' package sparse matrix – allows for a consistent and intuitive interface that stays close to the underlying mathematical foundation of computational text analysis. In particular, the package includes functions for working with word embeddings, text networks, and document-term matrices. Methods developed in Stoltz and Taylor (2019) <doi:10.1007/s42001-019-00048-6>, Taylor and Stoltz (2020) <doi:10.1007/s42001-020-00075-8>, Taylor and Stoltz (2020) <doi:10.15195/v7.a23>, and Stoltz and Taylor (2021) <doi:10.1016/j.poetic.2021.101567>.
Author: Dustin Stoltz [aut, cre] (<https://orcid.org/0000-0002-4774-0765>), Marshall Taylor [aut] (<https://orcid.org/0000-0002-7440-0723>)
Maintainer: Dustin Stoltz <dss219@lehigh.edu>

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Package SPARTAAS updated to version 1.1.0 with previous version 1.0.0 dated 2021-02-22

Title: Statistical Methods for Archaeology
Description: Statistical pattern recognition and dating using archaeological artefacts assemblages. Package of statistical tools for archaeology. hclustcompro(perioclust): Bellanger Lise, Coulon Arthur, Husi Philippe (2020, ISBN:978-3-030-60103-4). mapclust: Bellanger Lise, Coulon Arthur, Husi Philippe (2021) <doi:10.1016/j.jas.2021.105431>. seriograph: Desachy Bruno (2004) <doi:10.3406/pica.2004.2396>.
Author: Lise Bellanger [aut], Philippe Husi [aut], Arthur Coulon [aut, cre], Bruno Desachy [ctb], Benjamin Martineau [ctb]
Maintainer: Arthur Coulon <arthur-coulon@outlook.fr>

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Package profoc updated to version 0.8.5 with previous version 0.8.4 dated 2021-09-15

Title: Probabilistic Forecast Combination Using CRPS Learning
Description: Combine probabilistic forecasts using CRPS learning algorithms proposed in Berrisch, Ziel (2021) <arXiv:2102.00968>. The package implements multiple online learning algorithms like Bernstein online aggregation; see Wintenberger (2014) <arXiv:1404.1356>. Quantile regression is also implemented for comparison purposes. Model parameters can be tuned automatically with respect to the loss of the forecast combination. Methods like predict(), update(), plot() and print() are available for convenience. This package utilizes the optim C++ library for numeric optimization <https://github.com/kthohr/optim>.
Author: Jonathan Berrisch [cre] (<https://orcid.org/0000-0002-4944-9074>), Florian Ziel [aut] (<https://orcid.org/0000-0002-2974-2660>)
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>

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Package ATAforecasting updated to version 0.0.55 with previous version 0.0.54 dated 2021-10-20

Title: Automatic Time Series Analysis and Forecasting Using the Ata Method
Description: The Ata method (Yapar et al. (2019) <doi:10.15672/hujms.461032>), an alternative to exponential smoothing (described in Yapar (2016) <doi:10.15672/HJMS.201614320580>, Yapar et al. (2017) <doi:10.15672/HJMS.2017.493>), is a new univariate time series forecasting method which provides innovative solutions to issues faced during the initialization and optimization stages of existing forecasting methods. Forecasting performance of the Ata method is superior to existing methods both in terms of easy implementation and accurate forecasting. It can be applied to non-seasonal or seasonal time series which can be decomposed into four components (remainder, level, trend and seasonal). This methodology performed well on the M3 and M4-competition data. This package was written based on Ali Sabri Taylan’s PhD dissertation.
Author: Ali Sabri Taylan [aut, cre, cph] (<https://orcid.org/0000-0001-9514-934X>), Hanife Taylan Selamlar [aut, cph] (<https://orcid.org/0000-0002-4091-884X>), Guckan Yapar [aut, ths, cph] (<https://orcid.org/0000-0002-0971-6676>)
Maintainer: Ali Sabri Taylan <alisabritaylan@gmail.com>

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Package varTestnlme updated to version 1.1.1 with previous version 1.1.0 dated 2021-10-11

Title: Variance Components Testing for Linear and Nonlinear Mixed Effects Models
Description: An implementation of the Likelihood ratio Test (LRT) for testing that, in a (non)linear mixed effects model, the variances of a subset of the random effects are equal to zero. There is no restriction on the subset of variances that can be tested: for example, it is possible to test that all the variances are equal to zero. Note that the implemented test is asymptotic. This package should be used on model fits from packages 'nlme', 'lmer', and 'saemix'. Charlotte Baey, Paul-Henry Cournède and Estelle Kuhn (2019) <doi:10.1016/j.csda.2019.01.014>.
Author: Charlotte Baey [aut, cre] (<https://orcid.org/0000-0002-1413-1058>), Estelle Kuhn [aut]
Maintainer: Charlotte Baey <charlotte.baey@univ-lille.fr>

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Package permuco updated to version 1.1.1 with previous version 1.1.0 dated 2019-12-19

Title: Permutation Tests for Regression, (Repeated Measures) ANOVA/ANCOVA and Comparison of Signals
Description: Functions to compute p-values based on permutation tests. Regression, ANOVA and ANCOVA, omnibus F-tests, marginal unilateral and bilateral t-tests are available. Several methods to handle nuisance variables are implemented (Kherad-Pajouh, S., & Renaud, O. (2010) <doi:10.1016/j.csda.2010.02.015> ; Kherad-Pajouh, S., & Renaud, O. (2014) <doi:10.1007/s00362-014-0617-3> ; Winkler, A. M., Ridgway, G. R., Webster, M. A., Smith, S. M., & Nichols, T. E. (2014) <doi:10.1016/j.neuroimage.2014.01.060>). An extension for the comparison of signals issued from experimental conditions (e.g. EEG/ERP signals) is provided. Several corrections for multiple testing are possible, including the cluster-mass statistic (Maris, E., & Oostenveld, R. (2007) <doi:10.1016/j.jneumeth.2007.03.024>) and the threshold-free cluster enhancement (Smith, S. M., & Nichols, T. E. (2009) <doi:10.1016/j.neuroimage.2008.03.061>).
Author: Jaromil Frossard [aut, cre], Olivier Renaud [aut]
Maintainer: Jaromil Frossard <jaromil.frossard@unige.ch>

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Package pedmut updated to version 0.3.0 with previous version 0.2.0 dated 2020-07-30

Title: Mutation Models for Pedigree Likelihood Computations
Description: A collection of functions for modelling mutations in pedigrees with marker data, as used e.g. in likelihood computations with microsatellite data. Implemented models include proportional and stepwise models, as well as random models for experimental work, and custom models allowing the user to apply any valid mutation matrix. Allele lumping is done following the lumpability criteria of Kemeny and Snell (1976), ISBN:0387901922.
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 corto updated to version 1.1.10 with previous version 1.1.9 dated 2021-09-29

Title: Inference of Gene Regulatory Networks
Description: We present 'corto' (Correlation Tool), a simple package to infer gene regulatory networks and visualize master regulators from gene expression data using DPI (Data Processing Inequality) and bootstrapping to recover edges. An initial step is performed to calculate all significant edges between a list of source nodes (centroids) and target genes. Then all triplets containing two centroids and one target are tested in a DPI step which removes edges. A bootstrapping process then calculates the robustness of the network, eventually re-adding edges previously removed by DPI. The algorithm has been optimized to run outside a computing cluster, using a fast correlation implementation. The package finally provides functions to calculate network enrichment analysis from RNA-Seq and ATAC-Seq signatures as described in the article by Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
Author: Federico M. Giorgi [aut, cre], Daniele Mercatelli [ctb], Gonzalo Lopez-Garcia [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>

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Package tsibble updated to version 1.1.0 with previous version 1.0.1 dated 2021-04-12

Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') for temporal data in an data- and model-oriented format. The 'tsibble' provides tools to easily manipulate and analyse temporal data, such as filling in time gaps and aggregating over calendar periods.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>), Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>), Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>), Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>), Tyler Smith [ctb], Wil Davis [ctb]
Maintainer: Earo Wang <earo.wang@gmail.com>

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Package stevedore updated to version 0.9.4 with previous version 0.9.3 dated 2020-01-12

Title: Docker Client
Description: Work with containers over the Docker API. Rather than using system calls to interact with a docker client, using the API directly means that we can receive richer information from docker. The interface in the package is automatically generated using the 'OpenAPI' (a.k.a., 'swagger') specification, and all return values are checked in order to make them type stable.
Author: Rich FitzJohn [aut, cre]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

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Package openair updated to version 2.8-5 with previous version 2.8-4 dated 2021-09-15

Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically hourly time series and both monitoring data and dispersion model output can be analysed. Many functions can also be applied to other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre], Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>

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Package migraph updated to version 0.8.1 with previous version 0.7.1 dated 2021-09-25

Title: Multimodal and Multilevel Network Analysis
Description: A set of tools that extend common social network analysis packages for analysing multimodal and multilevel networks. It includes functions for one- and two-mode (and sometimes three-mode) centrality, centralization, clustering, and constraint, as well as for one- and two-mode network regression and block-modelling. All functions operate with matrices, edge lists, and 'igraph', 'network'/'sna', and 'tidygraph' objects. The package is released as a complement to 'Multimodal Political Networks' (2021, ISBN:9781108985000), and includes various datasets used in the book.
Author: James Hollway [cph, cre, aut, ctb] (IHEID, <https://orcid.org/0000-0002-8361-9647>)
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>

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Package jsonvalidate updated to version 1.3.1 with previous version 1.1.0 dated 2019-06-25

Title: Validate 'JSON' Schema
Description: Uses the node library 'is-my-json-valid' or 'ajv' to validate 'JSON' against a 'JSON' schema. Drafts 04, 06 and 07 of 'JSON' schema are supported.
Author: Rich FitzJohn [aut, cre], Rob Ashton [aut], Alicia Schep [ctb], Ian Lyttle [ctb], Kara Woo [ctb], Mathias Buus [cph], Evgeny Poberezkin [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

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Package spant updated to version 1.15.0 with previous version 1.14.0 dated 2021-07-23

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] (<https://orcid.org/0000-0002-2089-3956>), Yong Wang [ctb], John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

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 spant-1.15.0/spant/man/acquire.Rd                        |   46 +--
 spant-1.15.0/spant/man/add_noise.Rd                      |   46 +--
 spant-1.15.0/spant/man/align.Rd                          |    2 
 spant-1.15.0/spant/man/append_coils.Rd                   |   38 +-
 spant-1.15.0/spant/man/append_dyns.Rd                    |   38 +-
 spant-1.15.0/spant/man/apply_axes.Rd                     |   60 ++--
 spant-1.15.0/spant/man/apply_mrs.Rd                      |   44 +--
 spant-1.15.0/spant/man/auto_phase.Rd                     |   50 +--
 spant-1.15.0/spant/man/bbase.Rd                          |   46 +--
 spant-1.15.0/spant/man/bc_constant.Rd                    |   40 +-
 spant-1.15.0/spant/man/calc_ed_from_lambda.Rd            |   42 +-
 spant-1.15.0/spant/man/calc_peak_info_vec.Rd             |   40 +-
 spant-1.15.0/spant/man/calc_spec_diff.Rd                 |   42 +-
 spant-1.15.0/spant/man/calc_spec_snr.Rd                  |   88 +++---
 spant-1.15.0/spant/man/crop_td_pts.Rd                    |   42 +-
 spant-1.15.0/spant/man/ecc.Rd                            |   52 +--
 spant-1.15.0/spant/man/elliptical_mask.Rd                |   58 ++--
 spant-1.15.0/spant/man/est_noise_sd.Rd                   |   46 +--
 spant-1.15.0/spant/man/fit_amps.Rd                       |   58 ++--
 spant-1.15.0/spant/man/fp_phase_correct.Rd               |   44 +--
 spant-1.15.0/spant/man/ft_dyn.Rd                         |   38 +-
 spant-1.15.0/spant/man/gausswin_2d.Rd                    |   62 ++--
 spant-1.15.0/spant/man/get_1h_brain_basis_paras.Rd       |   48 +--
 spant-1.15.0/spant/man/get_1h_brain_basis_paras_v1.Rd    |   48 +--
 spant-1.15.0/spant/man/get_1h_brain_basis_paras_v2.Rd    |   48 +--
 spant-1.15.0/spant/man/get_2d_psf.Rd                     |   46 +--
 spant-1.15.0/spant/man/get_head_dyns.Rd                  |only
 spant-1.15.0/spant/man/get_mrsi2d_seg.Rd                 |   48 +--
 spant-1.15.0/spant/man/get_mrsi_voi.Rd                   |   46 +--
 spant-1.15.0/spant/man/get_mrsi_voxel.Rd                 |   50 +--
 spant-1.15.0/spant/man/get_mrsi_voxel_xy_psf.Rd          |   50 +--
 spant-1.15.0/spant/man/get_seg_ind.Rd                    |   42 +-
 spant-1.15.0/spant/man/get_tail_dyns.Rd                  |only
 spant-1.15.0/spant/man/get_voi_seg.Rd                    |   38 +-
 spant-1.15.0/spant/man/get_voi_seg_psf.Rd                |   38 +-
 spant-1.15.0/spant/man/get_voxel.Rd                      |   54 +--
 spant-1.15.0/spant/man/grid_shift_xy.Rd                  |   42 +-
 spant-1.15.0/spant/man/lb.Rd                             |   54 +--
 spant-1.15.0/spant/man/mean_mrs_list.Rd                  |   34 +-
 spant-1.15.0/spant/man/mrs_data2basis.Rd                 |   42 +-
 spant-1.15.0/spant/man/mrs_data2vec.Rd                   |   54 +--
 spant-1.15.0/spant/man/nifti_flip_lr.Rd                  |   42 +-
 spant-1.15.0/spant/man/peak_info.Rd                      |   72 ++---
 spant-1.15.0/spant/man/plot_bc.Rd                        |   36 +-
 spant-1.15.0/spant/man/plot_slice_map.Rd                 |   94 +++---
 spant-1.15.0/spant/man/re_weighting.Rd                   |   42 +-
 spant-1.15.0/spant/man/read_basis.Rd                     |    4 
 spant-1.15.0/spant/man/read_basis_ac.Rd                  |only
 spant-1.15.0/spant/man/read_lcm_coord.Rd                 |   36 +-
 spant-1.15.0/spant/man/read_mrs_tqn.Rd                   |   64 ++--
 spant-1.15.0/spant/man/read_tqn_result.Rd                |   48 +--
 spant-1.15.0/spant/man/rectangular_mask.Rd               |   58 ++--
 spant-1.15.0/spant/man/rep_mrs.Rd                        |   54 +--
 spant-1.15.0/spant/man/resample_img.Rd                   |   42 +-
 spant-1.15.0/spant/man/scale_mrs_amp.Rd                  |   40 +-
 spant-1.15.0/spant/man/scale_spec.Rd                     |   72 ++---
 spant-1.15.0/spant/man/seq_cpmg_ideal.Rd                 |   50 +--
 spant-1.15.0/spant/man/seq_mega_press_ideal.Rd           |   84 ++---
 spant-1.15.0/spant/man/seq_press_ideal.Rd                |   50 +--
 spant-1.15.0/spant/man/seq_pulse_acquire.Rd              |   42 +-
 spant-1.15.0/spant/man/seq_pulse_acquire_31p.Rd          |   42 +-
 spant-1.15.0/spant/man/seq_slaser_ideal.Rd               |   54 +--
 spant-1.15.0/spant/man/seq_spin_echo_ideal.Rd            |   46 +--
 spant-1.15.0/spant/man/seq_spin_echo_ideal_31p.Rd        |   46 +--
 spant-1.15.0/spant/man/seq_steam_ideal.Rd                |   50 +--
 spant-1.15.0/spant/man/set_lw.Rd                         |   42 +-
 spant-1.15.0/spant/man/set_mask_xy_mat.Rd                |   44 +--
 spant-1.15.0/spant/man/shift_basis.Rd                    |   40 +-
 spant-1.15.0/spant/man/sim_basis.Rd                      |   64 ++--
 spant-1.15.0/spant/man/sim_basis_1h_brain.Rd             |   70 ++--
 spant-1.15.0/spant/man/sim_basis_1h_brain_press.Rd       |   70 ++--
 spant-1.15.0/spant/man/sim_basis_tqn.Rd                  |   66 ++--
 spant-1.15.0/spant/man/sim_brain_1h.Rd                   |   82 ++---
 spant-1.15.0/spant/man/sim_mol.Rd                        |   80 ++---
 spant-1.15.0/spant/man/sim_zero.Rd                       |   50 +--
 spant-1.15.0/spant/man/spec_op.Rd                        |   64 ++--
 spant-1.15.0/spant/man/spin_sys.Rd                       |   42 +-
 spant-1.15.0/spant/man/spm_pve2categorical.Rd            |   38 +-
 spant-1.15.0/spant/man/sub_mean_dyns.Rd                  |   34 +-
 spant-1.15.0/spant/man/sum_mrs.Rd                        |   44 +--
 spant-1.15.0/spant/man/td_conv_filt.Rd                   |   42 +-
 spant-1.15.0/spant/man/varpro_3_para_opts.Rd             |  100 +++----
 spant-1.15.0/spant/man/varpro_basic_opts.Rd              |only
 spant-1.15.0/spant/man/varpro_opts.Rd                    |   96 +++---
 spant-1.15.0/spant/man/write_basis_tqn.Rd                |   46 +--
 spant-1.15.0/spant/man/zf.Rd                             |   52 +--
 spant-1.15.0/spant/tests/testthat/abfit_res_coarse.rds   |binary
 spant-1.15.0/spant/tests/testthat/abfit_res_default.rds  |binary
 spant-1.15.0/spant/tests/testthat/abfit_res_fine.rds     |binary
 spant-1.15.0/spant/tests/testthat/abfit_res_no_optim.rds |binary
 spant-1.15.0/spant/tests/testthat/abfit_sim_mrs_data.rds |binary
 spant-1.15.0/spant/tests/testthat/abfit_sim_res.rds      |binary
 spant-1.15.0/spant/tests/testthat/test_qm_sim.R          |   12 
 111 files changed, 2479 insertions(+), 2316 deletions(-)

More information about spant at CRAN
Permanent link

Package SDAResources updated to version 0.1.1 with previous version 0.1.0 dated 2021-05-17

Title: Datasets and Functions for 'Sampling: Design and Analysis, 3rd Edition'
Description: Includes all the datasets of 'Sampling: Design and Analysis' (3rd edition by Sharon Lohr) in R format and additional functions for analyzing and graphing probability samples.
Author: Yan Lu [aut, cre], Sharon Lohr [aut]
Maintainer: Yan Lu <yanlu@unm.edu>

Diff between SDAResources versions 0.1.0 dated 2021-05-17 and 0.1.1 dated 2021-10-22

 DESCRIPTION               |   11 +
 MD5                       |  270 ++++++++++++++++++++++++++++++++++++++--------
 NAMESPACE                 |    6 +
 R/Functions.R             |   94 +++++++++++++---
 R/agpop.R                 |   44 +++----
 R/agpps.R                 |   87 +++++++++-----
 R/agsrs.R                 |   17 +-
 R/agstrat.R               |   47 ++++----
 R/algebra.R               |   15 +-
 R/anthrop.R               |only
 R/anthsrs.R               |   16 +-
 R/anthuneq.R              |only
 R/artifratio.R            |only
 R/asafellow.R             |only
 R/auditresult.R           |only
 R/auditselect.R           |only
 R/azcounties.R            |only
 R/baseball.R              |only
 R/books.R                 |only
 R/census1920.R            |only
 R/census2010.R            |only
 R/cherry.R                |only
 R/classes.R               |   13 +-
 R/classpps.R              |   18 +--
 R/classppsjp.R            |only
 R/college.R               |  131 ++++++++++++----------
 R/collegerg.R             |  176 ++++++++++++++++++++++++++++-
 R/collshr.R               |only
 R/coots.R                 |   28 +++-
 R/counties.R              |only
 R/crimes.R                |only
 R/deadtrees.R             |   13 +-
 R/divorce.R               |only
 R/gini.R                  |only
 R/golfsrs.R               |only
 R/gpa.R                   |   15 +-
 R/healthjournals.R        |only
 R/htcdf.R                 |only
 R/htpop.R                 |only
 R/htsrs.R                 |   20 ++-
 R/htstrat.R               |   10 +
 R/hunting.R               |only
 R/impute.R                |   31 +++--
 R/integerwt.R             |only
 R/intellonline.R          |only
 R/intelltel.R             |only
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 R/ipums.R                 |only
 R/journal.R               |only
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 R/nhanes.R                |  119 +++++++++++---------
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 R/schools.R               |   39 +++---
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 man/agpop.Rd              |   36 +++---
 man/agpps.Rd              |   82 +++++++++----
 man/agsrs.Rd              |    8 -
 man/agstrat.Rd            |   44 ++++---
 man/algebra.Rd            |   14 +-
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 man/classes.Rd            |   12 +-
 man/classpps.Rd           |   16 +-
 man/classppsjp.Rd         |only
 man/college.Rd            |  130 ++++++++++++----------
 man/collegerg.Rd          |  175 ++++++++++++++++++++++++++++-
 man/collshr.Rd            |only
 man/coots.Rd              |   25 +++-
 man/counties.Rd           |only
 man/crimes.Rd             |only
 man/deadtrees.Rd          |   10 +
 man/divorce.Rd            |only
 man/emppmf.Rd             |only
 man/gini.Rd               |only
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 man/gpa.Rd                |   13 +-
 man/healthjournals.Rd     |only
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 man/htpop.Rd              |only
 man/htsrs.Rd              |   18 ++-
 man/htstrat.Rd            |    8 -
 man/hunting.Rd            |only
 man/impute.Rd             |   29 +++-
 man/integerwt.Rd          |only
 man/intellonline.Rd       |only
 man/intelltel.Rd          |only
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 man/intervals_ex40.Rd     |   31 +++--
 man/ipums.Rd              |only
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 man/mysteries.Rd          |only
 man/nhanes.Rd             |  103 ++++++++++-------
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 man/rnt.Rd                |only
 man/sample70.Rd           |only
 man/santacruz.Rd          |   17 ++
 man/schools.Rd            |   37 +++---
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 man/shorebirds.Rd         |only
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 man/syc.Rd                |  166 ++++++++++++++++++++++------
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 man/winter.Rd             |only
 man/wtshare.Rd            |only
 227 files changed, 1724 insertions(+), 669 deletions(-)

More information about SDAResources at CRAN
Permanent link

Package QF updated to version 0.0.6 with previous version 0.0.4 dated 2021-02-18

Title: Density, Cumulative and Quantile Functions of Quadratic Forms
Description: The computation of quadratic form (QF) distributions is often not trivial and it requires numerical routines. The package contains functions aimed at evaluating the exact distribution of quadratic forms (QFs) and ratios of QFs. In particular, we propose to evaluate density, quantile and distribution functions of positive definite QFs and ratio of independent positive QFs by means of an algorithm based on the numerical inversion of Mellin transforms.
Author: Aldo Gardini [aut, cre], Fedele Greco [aut], Carlo Trivisano [aut]
Maintainer: Aldo Gardini <aldo.gardini2@unibo.it>

Diff between QF versions 0.0.4 dated 2021-02-18 and 0.0.6 dated 2021-10-22

 QF-0.0.4/QF/cleanup                     |only
 QF-0.0.4/QF/configure                   |only
 QF-0.0.4/QF/configure.ac                |only
 QF-0.0.4/QF/src/Makevars.in             |only
 QF-0.0.6/QF/DESCRIPTION                 |    9 ++++-----
 QF-0.0.6/QF/MD5                         |   25 ++++++++++++-------------
 QF-0.0.6/QF/R/Distributions_depratio.R  |    7 +++++--
 QF-0.0.6/QF/R/MellinQF.R                |    4 ++++
 QF-0.0.6/QF/R/MellinQF_ratio.R          |    6 ++++++
 QF-0.0.6/QF/man/pQF_depratio.Rd         |    2 +-
 QF-0.0.6/QF/src/Makevars                |only
 QF-0.0.6/QF/src/Makevars.ucrt           |only
 QF-0.0.6/QF/src/Makevars.win            |   17 +++++++++--------
 QF-0.0.6/QF/src/RcppExports.cpp         |    5 +++++
 QF-0.0.6/QF/src/get_mellin_QF.cpp       |    6 +++++-
 QF-0.0.6/QF/src/get_mellin_QF_ratio.cpp |    2 +-
 QF-0.0.6/QF/tools                       |only
 17 files changed, 52 insertions(+), 31 deletions(-)

More information about QF at CRAN
Permanent link

Package mlr3proba updated to version 0.4.2 with previous version 0.4.1 dated 2021-09-07

Title: Probabilistic Supervised Learning for 'mlr3'
Description: Provides extensions for probabilistic supervised learning for 'mlr3'. This includes extending the regression task to probabilistic and interval regression, adding a survival task, and other specialized models, predictions, and measures.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>), Franz Kiraly [aut], Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>), Nurul Ain Toha [ctb], Andreas Bender [ctb] (<https://orcid.org/0000-0001-5628-8611>)
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>

Diff between mlr3proba versions 0.4.1 dated 2021-09-07 and 0.4.2 dated 2021-10-22

 DESCRIPTION                                              |   16 
 MD5                                                      |  164 ++++-----
 NEWS.md                                                  |    4 
 R/LearnerDensHistogram.R                                 |    2 
 R/LearnerDensKDE.R                                       |    6 
 R/LearnerSurv.R                                          |    4 
 R/LearnerSurvCoxPH.R                                     |    6 
 R/LearnerSurvKaplan.R                                    |    2 
 R/MeasureSurv.R                                          |    2 
 R/MeasureSurvAUC.R                                       |    2 
 R/MeasureSurvCalibrationAlpha.R                          |    4 
 R/MeasureSurvCindex.R                                    |   26 -
 R/MeasureSurvDCalibration.R                              |    6 
 R/MeasureSurvGraf.R                                      |    6 
 R/MeasureSurvIntLogloss.R                                |    6 
 R/MeasureSurvIntegrated.R                                |    4 
 R/MeasureSurvLogloss.R                                   |    2 
 R/MeasureSurvSchmid.R                                    |    6 
 R/PipeOpCrankCompositor.R                                |   10 
 R/PipeOpDistrCompositor.R                                |   16 
 R/PipeOpPredRegrSurv.R                                   |   50 +-
 R/PipeOpPredSurvRegr.R                                   |   25 -
 R/PipeOpPredTransformer.R                                |   13 
 R/PipeOpProbregrCompositor.R                             |   54 +--
 R/PipeOpSurvAvg.R                                        |   35 +-
 R/PipeOpTaskRegrSurv.R                                   |   37 +-
 R/PipeOpTaskSurvRegr.R                                   |  156 ++++-----
 R/PipeOpTaskTransformer.R                                |   15 
 R/PipeOpTransformer.R                                    |    7 
 R/PredictionDataSurv.R                                   |   11 
 R/PredictionDens.R                                       |    2 
 R/PredictionSurv.R                                       |    8 
 R/TaskDens_X.R                                           |    4 
 R/TaskGeneratorSimdens.R                                 |    2 
 R/TaskGeneratorSimsurv.R                                 |    8 
 R/TaskSurv.R                                             |    1 
 R/TaskSurv_X.R                                           |    8 
 R/bibentries.R                                           |  110 +++---
 R/cindex.R                                               |    6 
 R/helpers.R                                              |    2 
 R/histogram.R                                            |    4 
 R/integrated_scores.R                                    |   18 -
 R/pecs.R                                                 |   80 ++--
 R/pipelines.R                                            |  255 +++++++--------
 R/surv_measures.R                                        |    4 
 R/surv_return.R                                          |    6 
 R/zzz.R                                                  |   16 
 README.md                                                |    1 
 build/partial.rdb                                        |binary
 man/MeasureSurvIntegrated.Rd                             |    2 
 man/TaskSurv.Rd                                          |    1 
 man/mlr3proba-package.Rd                                 |    8 
 man/mlr_graphs_crankcompositor.Rd                        |   20 -
 man/mlr_graphs_distrcompositor.Rd                        |   24 -
 man/mlr_graphs_probregrcompositor.Rd                     |   40 +-
 man/mlr_graphs_survaverager.Rd                           |   22 -
 man/mlr_graphs_survbagging.Rd                            |   22 -
 man/mlr_graphs_survtoregr.Rd                             |   66 +--
 man/mlr_measures_dens.logloss.Rd                         |    2 
 man/mlr_measures_surv.intlogloss.Rd                      |    2 
 man/mlr_measures_surv.logloss.Rd                         |    7 
 man/mlr_pipeops_compose_distr.Rd                         |   14 
 man/mlr_pipeops_compose_probregr.Rd                      |   34 +-
 man/mlr_pipeops_survavg.Rd                               |   14 
 man/mlr_pipeops_trafopred_regrsurv.Rd                    |   34 +-
 man/mlr_pipeops_trafopred_survregr.Rd                    |   18 -
 man/mlr_pipeops_trafotask_regrsurv.Rd                    |   28 -
 man/mlr_pipeops_trafotask_survregr.Rd                    |   94 ++---
 man/mlr_task_generators_simsurv.Rd                       |    6 
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Package ggVennDiagram updated to version 1.2.0 with previous version 1.1.4 dated 2021-07-07

Title: A 'ggplot2' Implement of Venn Diagram
Description: Easy-to-use functions to generate 2-7 sets Venn plot in publication quality. 'ggVennDiagram' plot Venn using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections of them, then separately plot Venn in three components: set edges, set labels, and regions. From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar.
Author: Chun-Hui Gao [aut, cre] (<https://orcid.org/0000-0002-1445-7939>), Guangchuang Yu [ctb] (<https://orcid.org/0000-0002-6485-8781>), Adrian Dusa [ctb]
Maintainer: Chun-Hui Gao <gaospecial@gmail.com>

Diff between ggVennDiagram versions 1.1.4 dated 2021-07-07 and 1.2.0 dated 2021-10-22

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Package geoBayes updated to version 0.7.0 with previous version 0.6.3 dated 2019-12-02

Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes Methods
Description: Functions to fit geostatistical data. The data can be continuous, binary or count data and the models implemented are flexible. Conjugate priors are assumed on some parameters while inference on the other parameters can be done through a full Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>

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Package RcmdrPlugin.UCA updated to version 4.5-1 with previous version 4.4-3 dated 2021-04-02

Title: UCA Rcmdr Plug-in
Description: Some extensions to Rcmdr (R Commander), randomness test, variance test for one normal sample and predictions using active model, made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>

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Package multid updated to version 0.2.0 with previous version 0.1.0 dated 2021-09-20

Title: Multivariate Difference Between Two Groups
Description: Estimation of multivariate differences between two groups (e.g., multivariate sex differences) with regularized regression methods and predictive approach. See Lönnqvist & Ilmarinen (2021) <doi:10.1007/s11109-021-09681-2> and Ilmarinen et al. (2021) <doi:10.31234/osf.io/j59bs>.
Author: Ville-Juhani Ilmarinen [aut, cre] (<https://orcid.org/0000-0001-9493-379X>)
Maintainer: Ville-Juhani Ilmarinen <vj.ilmarinen@gmail.com>

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Package geos updated to version 0.1.2 with previous version 0.1.1 dated 2021-05-18

Title: Open Source Geometry Engine ('GEOS') R API
Description: Provides an R API to the Open Source Geometry Engine ('GEOS') library (<https://trac.osgeo.org/geos/>) and a vector format with which to efficiently store 'GEOS' geometries. High-performance functions to extract information from, calculate relationships between, and transform geometries are provided. Finally, facilities to import and export geometry vectors to other spatial formats are provided.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>), Edzer Pebesma [aut] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>

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Package cancensus updated to version 0.4.7 with previous version 0.4.6 dated 2021-10-21

Title: Access, Retrieve, and Work with Canadian Census Data and Geography
Description: Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer), Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for correspondence), Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>

Diff between cancensus versions 0.4.6 dated 2021-10-21 and 0.4.7 dated 2021-10-22

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Package C443 updated to version 3.2.2 with previous version 3.2.1 dated 2021-06-27

Title: See a Forest for the Trees
Description: Get insight into a forest of classification trees, by calculating similarities between the trees, and subsequently clustering them. Each cluster is represented by it's most central cluster member. The package implements the methodology described in Sies & Van Mechelen (2020) <doi:10.1007/s00357-019-09350-4>.
Author: Aniek Sies [aut, cre], Iven Van Mechelen [ths]
Maintainer: Aniek Sies <aniek.sies@kuleuven.be>

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Package bayesmove updated to version 0.2.1 with previous version 0.2.0 dated 2021-04-26

Title: Non-Parametric Bayesian Analyses of Animal Movement
Description: Methods for assessing animal movement from telemetry and biologging data using non-parametric Bayesian methods. This includes features for pre- processing and analysis of data, as well as the visualization of results from the models. This framework does not rely on standard parametric density functions, which provides flexibility during model fitting. Further details regarding part of this framework can be found in Cullen et al. (2021) <doi:10.1101/2020.11.05.369702>.
Author: Joshua Cullen [aut, cre, cph] (<https://orcid.org/0000-0002-6935-9340>), Denis Valle [aut, cph]
Maintainer: Joshua Cullen <joshcullen10@gmail.com>

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Package AlphaPart updated to version 0.8.4 with previous version 0.8.3 dated 2021-09-28

Title: Partition/Decomposition of Breeding Values by Paths of Information
Description: A software that implements a method for partitioning genetic trends to quantify the sources of genetic gain in breeding programmes. The partitioning method is described in Garcia-Cortes et al. (2008) <doi:10.1017/S175173110800205X>. The package includes the main function AlphaPart for partitioning breeding values and auxiliary functions for manipulating data and summarizing, visualizing, and saving results.
Author: Gregor Gorjanc [aut, cre] (<https://orcid.org/0000-0001-8008-2787>), Jana Obsteter [aut] (<https://orcid.org/0000-0003-1511-3916>), Thiago de Paula Oliveira [aut] (<https://orcid.org/0000-0002-4555-2584>)
Maintainer: Gregor Gorjanc <highlander.research.lab@gmail.com>

Diff between AlphaPart versions 0.8.3 dated 2021-09-28 and 0.8.4 dated 2021-10-22

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Package RcppEnsmallen updated to version 0.2.18.0.1 with previous version 0.2.17.0.1 dated 2021-07-06

Title: Header-Only C++ Mathematical Optimization Library for 'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library (by the 'MLPACK' team) that provides a simple set of abstractions for writing an objective function to optimize. Provided within are various standard and cutting-edge optimizers that include full-batch gradient descent techniques, small-batch techniques, gradient-free optimizers, and constrained optimization. The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library and pairs the appropriate header files from 'armadillo' through the 'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor 'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under 3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2, 'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under similar terms. Note that 'Ensmallen' requires a compiler that supports 'C++11' and 'Armadillo' 9.800 or later.
Author: James Joseph Balamuta [aut, cre, cph] (<https://orcid.org/0000-0003-2826-8458>), Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package quantregGrowth updated to version 1.3-1 with previous version 1.3-0 dated 2021-06-11

Title: Growth Charts via Smooth Regression Quantiles with Automatic Smoothness Estimation and Additive Terms
Description: Fits non-crossing regression quantiles as a function of linear covariates and multiple smooth terms, including varying coefficients, via B-splines with L1-norm difference penalties. The smoothing parameters are estimated as part of the model fitting, see Muggeo and others (2021) <doi:10.1177/1471082X20929802>. Monotonicity and concavity constraints on the fitted curves are allowed, see Muggeo and others (2013) <doi:10.1007/s10651-012-0232-1> and also <doi:10.13140/RG.2.2.12924.85122> for some code examples.
Author: Vito M. R. Muggeo [aut, cre] (<https://orcid.org/0000-0002-3386-4054>)
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>

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Package SamplerCompare updated to version 1.3.2 with previous version 1.3.1 dated 2021-09-28

Title: A Framework for Comparing the Performance of MCMC Samplers
Description: A framework for running sets of MCMC samplers on sets of distributions with a variety of tuning parameters, along with plotting functions to visualize the results of those simulations.
Author: Madeleine Thompson, except dchud.f and dchdd.f, which were written by G. W. Stewart.
Maintainer: Madeleine Thompson <madeleineth@gmail.com>

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Package rvcheck updated to version 0.2.1 with previous version 0.2.0 dated 2021-09-14

Title: R/Package Version Check
Description: Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
Author: Guangchuang Yu [aut, cre], Chun-hui Gao [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package RPostgreSQL updated to version 0.7-3 with previous version 0.7-2 dated 2021-10-06

Title: R Interface to the 'PostgreSQL' Database System
Description: Database interface and 'PostgreSQL' driver for 'R'. This package provides a Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' database systems. In order to build and install this package from source, 'PostgreSQL' itself must be present your system to provide 'PostgreSQL' functionality via its libraries and header files. These files are provided as 'postgresql-devel' package under some Linux distributions. On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Author: Joe Conway, Dirk Eddelbuettel, Tomoaki Nishiyama, Sameer Kumar Prayaga (during 2008), Neil Tiffin
Maintainer: Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>

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Package mrbin updated to version 1.6.1 with previous version 1.6.0 dated 2021-08-23

Title: Magnetic Resonance Binning, Integration and Normalization
Description: Nuclear Magnetic Resonance is widely used in Life Science research. The package (<doi:10.1021/acs.jproteome.0c00684>) converts 1D or 2D data into a matrix of values suitable for further data analysis and performs basic processing steps in a reproducible way. Negative values, a common issue in such data, are replaced by positive values. All used parameters are stored in a readable text file and can be restored from that file to enable exact reproduction of the data at a later time.
Author: Matthias Klein [aut, cre] (<https://orcid.org/0000-0001-7455-5381>)
Maintainer: Matthias Klein <klein.663@osu.edu>

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Package mark updated to version 0.4.0 with previous version 0.3.0 dated 2021-09-18

Title: Miscellaneous, Analytic R Kernels
Description: Miscellaneous functions and wrappers for development in other packages created, maintained by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre] (0000-0001-9788-3628)
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>

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Thu, 21 Oct 2021

Package grates updated to version 0.3.0 with previous version 0.2.0 dated 2021-05-28

Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating grouped date classes. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

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Package biocompute updated to version 1.1.0 with previous version 1.0.6 dated 2021-09-29

Title: Create and Manipulate BioCompute Objects
Description: Tools to create, validate, and export BioCompute Objects described in King et al. (2019) <doi:10.17605/osf.io/h59uh>. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard. A checksum validator and a JSON schema validator are provided. This package also supports exporting BioCompute Objects as JSON, PDF, HTML, or 'Word' documents, and exporting to cloud-based platforms.
Author: Jeffrey Grover [aut, cre] (<https://orcid.org/0000-0001-6246-1767>), Soner Koc [aut] (<https://orcid.org/0000-0002-0772-6600>), Nan Xiao [aut] (<https://orcid.org/0000-0002-0250-5673>), Dennis Dean [aut] (<https://orcid.org/0000-0002-7621-9717>), Seven Bridges Genomics [cph, fnd]
Maintainer: Jeffrey Grover <jeffrey.grover@sevenbridges.com>

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Package argparse updated to version 2.1.2 with previous version 2.1.1 dated 2021-09-08

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>

Diff between argparse versions 2.1.1 dated 2021-09-08 and 2.1.2 dated 2021-10-21

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Package relations updated to version 0.6-10 with previous version 0.6-9 dated 2019-10-26

Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.
Author: David Meyer [aut], Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package rasciidoc updated to version 3.1.4 with previous version 3.1.3 dated 2021-08-22

Title: Create Reports Using R and 'asciidoc'
Description: Inspired by Karl Broman`s reader on using 'knitr' with 'asciidoc' (<https://kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is merely a wrapper to 'knitr' and 'asciidoc'.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

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Package appler updated to version 0.1.2 with previous version 0.1.1 dated 2021-05-24

Title: 'Apple App Store' and 'iTunes' Data Extraction
Description: Using 'Apple App Store' <https://www.apple.com/app-store/> web scraping and 'iTunes' API <https://affiliate.itunes.apple.com/resources/documentation/itunes-store-web-service-search-api/> to extract content information, app ratings and reviews.
Author: Ashley Baldry [aut, cre]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>

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Package RALSA updated to version 1.0.2 with previous version 1.0.1 dated 2021-05-28

Title: R Analyzer for Large-Scale Assessments
Description: Prepare and analyze data from large-scale assessments and surveys with complex sampling and assessment design (see 'Rutkowski', 2010 <doi:10.3102/0013189X10363170>). Such studies are, for example, international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical interface is available for the non-technical user.The package includes functions to covert the original data from 'SPSS' into 'R' data sets keeping the user-defined missing values, merge data from different respondents and/or countries, generate variable dictionaries, modify data, produce descriptive statistics (percentages, means, percentiles, benchmarks) and multivariate statistics (correlations, linear regression, binary logistic regression). The number of supported studies and analysis types will increase in future. For a general presentation of the package, see 'Mirazchiyski', 2021a (<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of the package, see 'Mirazchiyski', 2021b (<doi:10.3390/psych3020018>).
Author: Plamen V. Mirazchiyski [aut, cre], INERI [aut]
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>

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Package OAIHarvester updated to version 0.3-3 with previous version 0.3-2 dated 2021-05-03

Title: Harvest Metadata Using OAI-PMH Version 2.0
Description: Harvest metadata using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) version 2.0 (for more information, see <https://www.openarchives.org/OAI/openarchivesprotocol.html>).
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package DCSmooth updated to version 1.1.2 with previous version 1.0.2 dated 2021-08-25

Title: Nonparametric Regression and Bandwidth Selection for Spatial Models
Description: Nonparametric smoothing techniques for data on a lattice and functional time series. Smoothing is done via kernel regression or local polynomial regression, a bandwidth selection procedure based on an iterative plug-in algorithm is implemented. This package allows for modeling a dependency structure of the error terms of the nonparametric regression model. Methods used in this paper are described in Feng/Schaefer (2021) <https://ideas.repec.org/p/pdn/ciepap/144.html>, Schaefer/Feng (2021) <https://ideas.repec.org/p/pdn/ciepap/143.html>.
Author: Bastian Schaefer [aut, cre], Sebastian Letmathe [ctb], Yuanhua Feng [ths]
Maintainer: Bastian Schaefer <bastian.schaefer@uni-paderborn.de>

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Package APCI updated to version 1.0.3 with previous version 1.0.2 dated 2021-10-01

Title: A New Age-Period-Cohort Model for Describing and Investigating Inter-Cohort Differences and Life Course Dynamics
Description: It implemented Age-Period-Interaction Model (APC-I Model) proposed in the paper of Liying Luo and James S. Hodges in 2019. A new age-period-cohort model for describing and investigating inter-cohort differences and life course dynamics.
Author: Jiahui Xu [aut, cre], Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>

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Package sodium updated to version 1.2.0 with previous version 1.1 dated 2017-03-31

Title: A Modern and Easy-to-Use Crypto Library
Description: Bindings to 'libsodium': a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a state-of-the-art Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package shrinkTVP updated to version 2.0.3 with previous version 2.0.2 dated 2021-05-13

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>.
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 windex updated to version 2.0.3 with previous version 2.0.2 dated 2021-04-14

Title: Analysing Convergent Evolution using the Wheatsheaf Index
Description: Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other random but perhaps useful functions.
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle <kevin.arbuckle@swansea.ac.uk>

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Package RSC updated to version 2.0.1 with previous version 2.0 dated 2021-10-17

Title: Robust and Sparse Correlation Matrix
Description: Performs robust and sparse correlation matrix estimation. Robustness is achieved based on a simple robust pairwise correlation estimator, while sparsity is obtained based on thresholding. The optimal thresholding is tuned via cross-validation. See Serra, Coretto, Fratello and Tagliaferri (2018) <doi:10.1093/bioinformatics/btx642>.
Author: Luca Coraggio [cre, aut], Pietro Coretto [aut], Angela Serra [aut], Roberto Tagliaferri [ctb]
Maintainer: Luca Coraggio <luca.coraggio@unina.it>

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Package epicontacts updated to version 1.1.2 with previous version 1.1.0 dated 2017-11-21

Title: Handling, Visualisation and Analysis of Epidemiological Contacts
Description: A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.
Author: Finlay Campbell [aut, cre], Thibaut Jombart [aut], Nistara Randhawa [aut], Bertrand Sudre [aut], VP Nagraj [aut], Thomas Crellen [aut], Zhian N. Kamvar [aut]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>

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Package bRacatus updated to version 1.0.5 with previous version 1.0.4 dated 2021-05-28

Title: A Method to Estimate the Accuracy and Biogeographical Status of Georeferenced Biological Data
Description: Automated assessment of accuracy and geographical status of georeferenced biological data. The methods rely on reference regions, namely checklists and range maps. Includes functions to obtain data from the Global Biodiversity Information Facility <https://www.gbif.org/> and from the Global Inventory of Floras and Traits <https://gift.uni-goettingen.de/home>. Alternatively, the user can input their own data. Furthermore, provides easy visualisation of the data and the results through the plotting functions. Especially suited for large datasets. The reference for the methodology is: Arlé et al. (under review).
Author: Eduardo Arlé [aut, cre], Alexander Zizka [aut], Patrick Weigelt [ctb], Sam Levin [ctb], Carsten Meyer [ths]
Maintainer: Eduardo Arlé <eduardo.arle@idiv.de>

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Package apexcharter updated to version 0.3.0 with previous version 0.2.0 dated 2021-05-11

Title: Create Interactive Chart with the JavaScript 'ApexCharts' Library
Description: Provides an 'htmlwidgets' interface to 'apexcharts.js'. 'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API. 'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], Juned Chhipa [cph] (apexcharts.js library), Mike Bostock [cph] (d3.format library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package RandomFieldsUtils updated to version 0.5.6 with previous version 0.5.5 dated 2021-10-05

Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb], Brian D. Ripley [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

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Package IOHanalyzer updated to version 0.1.6.1 with previous version 0.1.5.2 dated 2021-05-31

Title: Data Analysis Part of 'IOHprofiler'
Description: The data analysis module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides statistical analysis methods for the benchmark data generated by optimization heuristics, which can be visualized through a web-based interface. The benchmark data is usually generated by the experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.
Author: Hao Wang [cre, aut], Diederick Vermetten [aut], Carola Doerr [aut], Thomas Bäck [aut]
Maintainer: Hao Wang <h.wang@liacs.leidenuniv.nl>

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Package monobin updated to version 0.2.0 with previous version 0.1.1 dated 2021-08-02

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>

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Package nominatimlite updated to version 0.1.3 with previous version 0.1.2 dated 2021-10-07

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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Package sociome updated to version 2.1.0 with previous version 2.0.0 dated 2021-02-24

Title: Operationalizing Social Determinants of Health Data for Researchers
Description: Accesses raw data via API and calculates social determinants of health measures for user-specified locations in the US, returning them in tidyverse- and sf-compatible data frames.
Author: Nik Krieger [aut, cre], Jarrod Dalton [aut], Cindy Wang [aut], Adam Perzynski [aut], National Institutes of Health/National Institute on Aging [fnd] (The development of this software package was supported by a research grant from the National Institutes of Health/National Institute on Aging, (Principal Investigators: Jarrod E. Dalton, PhD and Adam T. Perzynski, PhD; Grant Number: 5R01AG055480-02). All of its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.)
Maintainer: Nik Krieger <nk@case.edu>

Diff between sociome versions 2.0.0 dated 2021-02-24 and 2.1.0 dated 2021-10-21

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Package RedditExtractoR updated to version 3.0.5 with previous version 3.0.3 dated 2021-09-03

Title: Reddit Data Extraction Toolkit
Description: A collection of tools for extracting structured data from <https://www.reddit.com/>.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>

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Package tLagPropOdds updated to version 1.2 with previous version 1.1 dated 2021-10-20

Title: Proportional Odds Model with Censored, Time-Lagged Categorical Outcome
Description: Implements a semiparametric estimator for the odds ratio model with censored, time-lagged, ordered categorical outcome in a randomized clinical trial that incorporates baseline and time-dependent information. Tsiatis, A. A. and Davidian, M. (2021) <arXiv:2106.15559>.
Author: Marie Davidian [aut], A. A. Tsiatis [aut], Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>

Diff between tLagPropOdds versions 1.1 dated 2021-10-20 and 1.2 dated 2021-10-21

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Package rflexscan updated to version 1.0.0 with previous version 0.4.0 dated 2021-01-19

Title: The Flexible Spatial Scan Statistic
Description: Functions for the detection of spatial clusters using the flexible spatial scan statistic developed by Tango and Takahashi (2005) <doi:10.1186/1476-072X-4-11>. This package implements a wrapper for the C routine used in the FleXScan 3.1.2 <https://sites.google.com/site/flexscansoftware/home> developed by Takahashi, Yokoyama, and Tango. For details, see Otani et al. (2021) <doi:10.18637/jss.v099.i13>.
Author: Takahiro Otani, Kunihiko Takahashi
Maintainer: Takahiro Otani <otani@med.nagoya-cu.ac.jp>

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Package cancensus updated to version 0.4.6 with previous version 0.4.5 dated 2021-10-20

Title: Access, Retrieve, and Work with Canadian Census Data and Geography
Description: Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer), Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for correspondence), Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>

Diff between cancensus versions 0.4.5 dated 2021-10-20 and 0.4.6 dated 2021-10-21

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Package tabxplor updated to version 1.0.2 with previous version 1.0.1 dated 2021-09-14

Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data exploration, by creating them, manipulating them, and adding color helpers to highlight important informations. All functions are "tidy", pipe-friendly, and render data frames which can be easily manipulated. Tables can be exported to Excel and in html with formats and colors.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>

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Package textTinyR updated to version 1.1.6 with previous version 1.1.5 dated 2021-10-13

Title: Text Processing for Small or Big Data Files
Description: It offers functions for splitting, parsing, tokenizing and creating a vocabulary for big text data files. Moreover, it includes functions for building a document-term matrix and extracting information from those (term-associations, most frequent terms). It also embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. Lastly, it includes functions for Word Vector Representations (i.e. 'GloVe', 'fasttext') and incorporates functions for the calculation of (pairwise) text document dissimilarities. The source code is based on 'C++11' and exported in R through the 'Rcpp', 'RcppArmadillo' and 'BH' packages.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

Diff between textTinyR versions 1.1.5 dated 2021-10-13 and 1.1.6 dated 2021-10-21

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Package VancouvR updated to version 0.1.7 with previous version 0.1.6 dated 2021-07-09

Title: Access the 'City of Vancouver' Open Data API
Description: Wrapper around the 'City of Vancouver' Open Data API <https://opendata.vancouver.ca/api/v2/console> to simplify and standardize access to 'City of Vancouver' open data. Functionality to list the data catalogue and access data and geographic records.
Author: Jens von Bergmann
Maintainer: Jens von Bergmann <jens@mountainmath.ca>

Diff between VancouvR versions 0.1.6 dated 2021-07-09 and 0.1.7 dated 2021-10-21

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Package HDBRR updated to version 1.1.2 with previous version 1.1.1 dated 2021-09-22

Title: High Dimensional Bayesian Ridge Regression without MCMC
Description: The svd(singular value decomposition) or qr decomposition was using for the implementation, this avoid the recursion optimizing the time in the compute.
Author: Sergio Perez-Elizalde Developer [aut], Blanca Monroy-Castillo Developer [aut, cre], Paulino Perez-Rodriguez User [ctb], Jose Crossa User [ctb]
Maintainer: Blanca Monroy-Castillo Developer <blancamonroy.96@gmail.com>

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Package fasstr updated to version 0.3.3 with previous version 0.3.2 dated 2020-11-07

Title: Analyze, Summarize, and Visualize Daily Streamflow Data
Description: The Flow Analysis Summary Statistics Tool for R, 'fasstr', provides various functions to tidy and screen daily stream discharge data, calculate and visualize various summary statistics and metrics, and compute annual trending and volume frequency analyses. It features useful function arguments for filtering of and handling dates, customizing data and metrics, and the ability to pull daily data directly from the Water Survey of Canada hydrometric database (<https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>).
Author: Jon Goetz [aut, cre] (<https://orcid.org/0000-0002-4993-1119>), Carl James Schwarz [aut], Robin Pike [ctb], Province of British Columbia [cph]
Maintainer: Jon Goetz <jon.goetz@gov.bc.ca>

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Wed, 20 Oct 2021

Package igoR updated to version 0.1.3 with previous version 0.1.2 dated 2021-08-04

Title: Intergovernmental Organizations Database
Description: Tools to extract information from the Intergovernmental Organizations ('IGO') Database , version 3, provided by the Correlates of War Project <https://correlatesofwar.org/>. See also Pevehouse, J. C. et al. (2020), <doi:10.1177/0022343319881175>. Version 3 includes information from 1815 to 2014.
Author: Diego Hernangómez [aut, cre, cph] (<https://orcid.org/0000-0001-8457-4658>)
Maintainer: Diego Hernangómez <diego.hernangomezherrero@gmail.com>

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Package meta updated to version 5.0-1 with previous version 5.0-0 dated 2021-10-11

Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from 'RevMan 5'; - prediction interval, Hartung-Knapp method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression; - generalised linear mixed models; - produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

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Permanent link

Package vietnameseConverter updated to version 0.4.0 with previous version 0.3.1 dated 2021-09-27

Title: Convert Vietnamese Encodings
Description: Conversion of characters from unsupported Vietnamese character encodings to Unicode characters. These Vietnamese encodings (TCVN3, VISCII, VPS) are not natively supported in R and lead to printing of wrong characters and garbled text (mojibake). This package fixes that problem and provides readable output with the correct Unicode characters (with or without diacritics).
Author: Juergen Niedballa [aut, cre] (<https://orcid.org/0000-0002-9187-2116>), An The Truong Nguyen [ctb]
Maintainer: Juergen Niedballa <niedballa@izw-berlin.de>

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Package decon updated to version 1.3-4 with previous version 1.2-4 dated 2013-04-17

Title: Deconvolution Estimation in Measurement Error Models
Description: A collection of functions to deal with nonparametric measurement error problems using deconvolution kernel methods. We focus two measurement error models in the package: (1) an additive measurement error model, where the goal is to estimate the density or distribution function from contaminated data; (2) nonparametric regression model with errors-in-variables. The R functions allow the measurement errors to be either homoscedastic or heteroscedastic. To make the deconvolution estimators computationally more efficient in R, we adapt the "Fast Fourier Transform" (FFT) algorithm for density estimation with error-free data to the deconvolution kernel estimation. Several methods for the selection of the data-driven smoothing parameter are also provided in the package. See details in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.
Author: Xiao-Feng Wang, Bin Wang
Maintainer: Xiao-Feng Wang <wangx6@ccf.org>

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Package metapack updated to version 0.1.4 with previous version 0.1.3 dated 2021-07-20

Title: Bayesian Meta-Analysis and Network Meta-Analysis
Description: Contains functions performing Bayesian inference for meta-analytic and network meta-analytic models through Markov chain Monte Carlo algorithm. Currently, the package implements Hui Yao, Sungduk Kim, Ming-Hui Chen, Joseph G. Ibrahim, Arvind K. Shah, and Jianxin Lin (2015) <doi:10.1080/01621459.2015.1006065> and Hao Li, Daeyoung Lim, Ming-Hui Chen, Joseph G. Ibrahim, Sungduk Kim, Arvind K. Shah, Jianxin Lin (2021) <doi:10.1002/sim.8983>. For maximal computational efficiency, the Markov chain Monte Carlo samplers for each model, written in C++, are fine-tuned. This software has been developed under the auspices of the National Institutes of Health and Merck & Co., Inc., Kenilworth, NJ, USA.
Author: Daeyoung Lim [aut, cre], Ming-Hui Chen [ctb], Sungduk Kim [ctb], Joseph Ibrahim [ctb], Arvind Shah [ctb], Jianxin Lin [ctb]
Maintainer: Daeyoung Lim <daeyoung.lim@uconn.edu>

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Package anomaly updated to version 4.0.2 with previous version 4.0.1 dated 2021-01-21

Title: Detecting Anomalies in Data
Description: Implements Collective And Point Anomaly (CAPA) <arXiv:1806.01947>, Multi-Variate Collective And Point Anomaly (MVCAPA) <arXiv:1909.01691>, Proportion Adaptive Segment Selection (PASS) <doi:10.1093/biomet/ass059>, and Bayesian Abnormal Region Detector (BARD) <arXiv:1412.5565> methods for the detection of anomalies in time series data. Also includes sequential versions of CAPA and MVCAPA <arXiv:2009.06670>.
Author: Alex Fisch [aut], Daniel Grose [aut, cre], Lawrence Bardwell [aut, ctb], Idris Eckley [aut, ths], Paul Fearnhead [aut, ths]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>

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Package rgeolocate updated to version 1.4.1 with previous version 1.3.1 dated 2020-05-17

Title: IP Address Geolocation
Description: Connectors to online and offline sources for taking IP addresses and geolocating them to country, city, timezone and other geographic ranges. For individual connectors, see the package index.
Author: Os Keyes [aut, cre], Drew Schmidt [aut], David Robinson [ctb], Chris Davis [ctb], Bob Rudis [ctb], Maxmind, Inc. [cph], Pascal Gloor [cph], IP2Location.com [cph]
Maintainer: Os Keyes <ironholds@gmail.com>

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Package RPPASPACE updated to version 1.0.8 with previous version 1.0.7 dated 2020-12-10

Title: Reverse-Phase Protein Array Super Position and Concentration Evaluation
Description: Provides tools for the analysis of reverse-phase protein arrays (RPPAs), which are also known as "tissue lysate arrays" or simply "lysate arrays". The package's primary purpose is to input a set of quantification files representing dilution series of samples and control points taken from scanned RPPA slides and determine a relative log concentration value for each valid dilution series present in each slide and provide graphical visualization of the input and output data and their relationships. Other optional features include generation of quality control scores for judging the quality of the input data, spatial adjustment of sample points based on controls added to the slides, and various types of normalization of calculated values across a set of slides. The package was derived from a previous package named SuperCurve. For a detailed description of data inputs and outputs, usage information, and a list of related papers describing methods used in the package please review the vignette "Guide_to_RPPASPACE". Hu (2007) <doi:10.1093/bioinformatics/btm283>.
Author: James M. Melott [aut, cre], Paul Roebuck [aut], Kevin R. Coombes [aut], Shannon Neeley [aut], Corwin Joy [aut], Jianhua Hu [aut], Keith Baggerly [aut]
Maintainer: James M. Melott <jmmelott@mdanderson.org>

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Package IsoplotRgui updated to version 4.2 with previous version 4.1 dated 2021-07-10

Title: Web Interface to 'IsoplotR'
Description: Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Author: Pieter Vermeesch [aut, cre], Tim Band [ctb]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

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Package tLagPropOdds updated to version 1.1 with previous version 1.0 dated 2021-07-01

Title: Proportional Odds Model with Censored, Time-Lagged Categorical Outcome
Description: Implements a semiparametric estimator for the odds ratio model with censored, time-lagged, ordered categorical outcome in a randomized clinical trial that incorporates baseline and time-dependent information. Tsiatis, A. A. and Davidian, M. (2021) <arXiv:2106.15559>.
Author: Marie Davidian [aut], A. A. Tsiatis [aut], Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>

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Package superb updated to version 0.9.7.7 with previous version 0.9.7.6 dated 2021-10-04

Title: Summary Plots with Adjusted Error Bars
Description: Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superbPlot(), can either return a plot or a dataframe with the statistic and its precision interval so that other plotting package can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.
Author: Denis Cousineau [aut, cre], Bradley Harding [ctb], Marc-Andre Goulet [ctb], Jesika Walker [art, pre]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>

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Package relaimpo updated to version 2.2-6 with previous version 2.2-5 dated 2021-05-15

Title: Relative Importance of Regressors in Linear Models
Description: Provides several metrics for assessing relative importance in linear models. These can be printed, plotted and bootstrapped. The recommended metric is lmg, which provides a decomposition of the model explained variance into non-negative contributions. There is a version of this package available that additionally provides a new and also recommended metric called pmvd. If you are a non-US user, you can download this extended version from Ulrike Groempings web site.
Author: Ulrike Groemping [aut, cre], Lehrkamp Matthias [ctb]
Maintainer: Ulrike Groemping <ulrike.groemping@bht-berlin.de>

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Package FeatureImpCluster updated to version 0.1.5 with previous version 0.1.4 dated 2021-06-03

Title: Feature Importance for Partitional Clustering
Description: Implements a novel approach for measuring feature importance in k-means clustering. Importance of a feature is measured by the misclassification rate relative to the baseline cluster assignment due to a random permutation of feature values. An explanation of permutation feature importance in general can be found here: <https://christophm.github.io/interpretable-ml-book/feature-importance.html>.
Author: Oliver Pfaffel [aut, cre]
Maintainer: Oliver Pfaffel <opfaffel@gmail.com>

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Package naijR updated to version 0.3.2 with previous version 0.3.1 dated 2021-09-30

Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political data about Nigeria, aimed at simplifying work with data and information that are specific to the country.
Author: Victor Ordu [aut, cre] (<https://orcid.org/0000-0003-3716-0668>)
Maintainer: Victor Ordu <victorordu@outlook.com>

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Package MonteCarloSEM updated to version 0.0.3 with previous version 0.0.2 dated 2021-04-22

Title: Monte Carlo Data Simulation Package
Description: Monte Carlo simulation allows to test different conditions given to the correct structural equation models. This package runs Monte Carlo simulations under different conditions (such as sample size or normality of data). Within the package data sets can be simulated and run based on the given model. First, continuous and normal data sets are generated based on the given model. Later Fleishman's power method (1978) <DOI:10.1007/BF02293811> is used to add non-normality if exists. When data generation is completed (or when generated data sets are given) model test can also be run.
Author: Fatih Orcan [aut, cre] (<https://orcid.org/0000-0003-1727-0456>)
Maintainer: Fatih Orcan <fatihorcan84@gmail.com>

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Package casebase updated to version 0.10.1 with previous version 0.9.1 dated 2021-02-07

Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression
Description: Fit flexible and fully parametric hazard regression models to survival data with single event type or multiple competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the fitted hazard model, we provide functions to readily calculate and plot cumulative incidence and survival curves for a given covariate profile. This approach accommodates any log-linear hazard function of prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide a plot method for visualizing incidence density via population time plots. Based on the case-base sampling approach of Hanley and Miettinen (2009) <DOI:10.2202/1557-4679.1125>, Saarela and Arjas (2015) <DOI:10.1111/sjos.12125>, and Saarela (2015) <DOI:10.1007/s10985-015-9352-x>.
Author: Sahir Bhatnagar [aut, cre] (http://sahirbhatnagar.com/), Maxime Turgeon [aut] (<https://orcid.org/0000-0003-4863-6035>), Jesse Islam [aut] (https://www.jesseislam.com/), Olli Saarela [aut] (http://individual.utoronto.ca/osaarela/), James Hanley [aut] (http://www.medicine.mcgill.ca/epidemiology/hanley/)
Maintainer: Sahir Bhatnagar <sahir.bhatnagar@gmail.com>

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Package SPOTMisc updated to version 1.2.18 with previous version 1.2.11 dated 2021-08-04

Title: Misc Extensions for the 'SPOT' Package
Description: Implements additional models, simulation tools, and interfaces as extensions to 'SPOT'. It provides tools for hyperparameter tuning via 'keras/tensorflow', interfacing 'mlr', for performing Markov chain simulations, and for sensitivity analysis based on sequential bifurcation methods as described in Bettonvil and Kleijnen (1996). Furthermore, additional plotting functions for output from 'SPOT' runs are implemented. Bartz-Beielstein T, Lasarczyk C W G, Preuss M (2005) <doi:10.1109/CEC.2005.1554761>. Bartz-Beielstein T, Zaefferer M, Rehbach F (2021) <arXiv:1712.04076>. Bartz-Beielstein T, Rehbach F, Sen A, Zaefferer M <arXiv:2105.14625>. Bettonvil, B, Kleijnen JPC (1996) <doi:10.1016/S0377-2217(96)00156-7>.
Author: Thomas Bartz-Beielstein [aut, cre] (<https://orcid.org/0000-0002-5938-5158>), Martin Zaefferer [aut] (<https://orcid.org/0000-0003-2372-2092>), Frederik Rehbach [aut] (<https://orcid.org/0000-0003-0922-8629>)
Maintainer: Thomas Bartz-Beielstein <tbb@bartzundbartz.de>

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Package sensitivity updated to version 1.27.0 with previous version 1.26.1 dated 2021-09-02

Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and robustness analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Sebastien Da Veiga, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Thibault Delage, Reda El Amri, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Margot Herin, Marouane Il Idrissi, Loic Le Gratiet, Paul Lemaitre, Amandine Marrel, Anouar Meynaoui, Barry L. Nelson, Filippo Monari, Roelof Oomen, Oldrich Rakovec, Bernardo Ramos, Olivier Roustant, Eunhye Song, Jeremy Staum, Roman Sueur, Taieb Touati, Vanessa Verges, Frank Weber
Maintainer: Bertrand Iooss <biooss@yahoo.fr>

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Package IsoplotR updated to version 4.2 with previous version 4.1 dated 2021-07-09

Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

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Package rmytarget updated to version 2.4.0 with previous version 2.3.1 dated 2021-09-08

Title: Load Data from 'MyTarget API v2 and v3'
Description: Allows work with 'MyTarget Statistics API v2' <https://target.my.com/adv/api-marketing/doc/stat-v2> and 'MyTarget Statistics API v3' <https://target.my.com/adv/api-marketing/doc/stat-v2#statisticsv3> load data by ads, campaigns, agency clients and statistic from your ads account.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>), Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>

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Package bipartiteD3 updated to version 0.3.0 with previous version 0.2.0 dated 2019-03-28

Title: Interactive Bipartite Graphs
Description: Generates interactive bipartite graphs using the D3 library. Designed for use with the 'bipartite' analysis package. Sources open source 'viz-js' library Adapted from examples at <https://bl.ocks.org/NPashaP> (released under GPL-3).
Author: Chris Terry [aut, cre]
Maintainer: Chris Terry <christerry3@btinternet.com>

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Package rsimsum updated to version 0.11.0 with previous version 0.10.1 dated 2021-07-05

Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo standard errors of commonly used summary statistics. This package is modelled on the 'simsum' user-written command in 'Stata' (White I.R., 2010 <https://www.stata-journal.com/article.html?article=st0200>), further extending it with additional functionality.
Author: Alessandro Gasparini [aut, cre] (<https://orcid.org/0000-0002-8319-7624>), Ian R. White [aut]
Maintainer: Alessandro Gasparini <alessandro.gasparini@ki.se>

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Package NMOF updated to version 2.5-0 with previous version 2.4-1 dated 2021-04-10

Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the first and the second edition of "Numerical Methods and Optimization in Finance" by M. Gilli, D. Maringer and E. Schumann (2019, ISBN:978-0128150658). The package provides implementations of optimisation heuristics (Differential Evolution, Genetic Algorithms, Particle Swarm Optimisation, Simulated Annealing and Threshold Accepting), and other optimisation tools, such as grid search and greedy search. There are also functions for the valuation of financial instruments such as bonds and options, for portfolio selection and functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>

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Package lidR updated to version 3.2.2 with previous version 3.2.1 dated 2021-09-29

Title: Airborne LiDAR Data Manipulation and Visualization for Forestry Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data manipulation and visualization. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, artificial point reduction, classification from geographic data, normalization, individual tree segmentation and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph], David Auty [aut, ctb] (Reviews the documentation), Florian De Boissieu [ctb] (Fixed bugs and improved catalog features), Andrew Sánchez Meador [ctb] (Implemented wing2015() for segment_snags()), Bourdon Jean-François [ctb] (Contributed to Roussel2020() for track_sensor()), Gatziolis Demetrios [ctb] (Implemented Gatziolis2019() for track_sensor()), Leon Steinmeier [ctb] (Contributed to parallelization management), Stanislaw Adaszewski [cph] (Author of the C++ concaveman code)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

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Package roclang updated to version 0.1.2 with previous version 0.1.0 dated 2021-08-04

Title: Functions for Diffusing Function Documentations into 'Roxygen' Comments
Description: Efficient diffusing of content across function documentations. Sections, parameters or dot parameters are extracted from function documentations and turned into valid Rd character strings, which are ready to diffuse into the 'roxygen' comments of another function by inserting inline code.
Author: Xiurui Zhu [aut, cre]
Maintainer: Xiurui Zhu <zxr6@163.com>

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Package pyinit updated to version 1.1.2 with previous version 1.1.1 dated 2020-12-01

Title: Pena-Yohai Initial Estimator for Robust S-Regression
Description: Deterministic Pena-Yohai initial estimator for robust S estimators of regression. The procedure is described in detail in Pena, D., & Yohai, V. (1999) <doi:10.2307/2670164>.
Author: David Kepplinger [aut, cre], Matias Salibian-Barrera [aut], Gabriela Cohen Freue [aut]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>

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Package CMplot updated to version 3.7.0 with previous version 3.6.2 dated 2020-06-30

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

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Package CIMTx updated to version 1.0.0 with previous version 0.3.0 dated 2021-07-16

Title: Causal Inference for Multiple Treatments with a Binary Outcome
Description: Different methods to conduct causal inference for multiple treatments with a binary outcome, including regression adjustment, vector matching, Bayesian additive regression trees, targeted maximum likelihood and inverse probability of treatment weighting using different generalized propensity score models such as multinomial logistic regression, generalized boosted models and super learner. For more details, see the paper by Hu et al. <doi:10.1177/0962280220921909>.
Author: Liangyuan Hu [aut], Chenyang Gu [aut], Michael Lopez [aut], Jiayi Ji [aut, cre]
Maintainer: Jiayi Ji <Jiayi.Ji@mountsinai.org>

Diff between CIMTx versions 0.3.0 dated 2021-07-16 and 1.0.0 dated 2021-10-20

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Package cancensus updated to version 0.4.5 with previous version 0.4.4 dated 2021-10-19

Title: Access, Retrieve, and Work with Canadian Census Data and Geography
Description: Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer), Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for correspondence), Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>

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Package ATAforecasting updated to version 0.0.54 with previous version 0.0.53 dated 2021-10-11

Title: Automatic Time Series Analysis and Forecasting Using the Ata Method
Description: The Ata method (Yapar et al. (2019) <doi:10.15672/hujms.461032>), an alternative to exponential smoothing (described in Yapar (2016) <doi:10.15672/HJMS.201614320580>, Yapar et al. (2017) <doi:10.15672/HJMS.2017.493>), is a new univariate time series forecasting method which provides innovative solutions to issues faced during the initialization and optimization stages of existing forecasting methods. Forecasting performance of the Ata method is superior to existing methods both in terms of easy implementation and accurate forecasting. It can be applied to non-seasonal or seasonal time series which can be decomposed into four components (remainder, level, trend and seasonal). This methodology performed well on the M3 and M4-competition data. This package was written based on Ali Sabri Taylan’s PhD dissertation.
Author: Ali Sabri Taylan [aut, cre, cph] (<https://orcid.org/0000-0001-9514-934X>), Hanife Taylan Selamlar [aut, cph] (<https://orcid.org/0000-0002-4091-884X>), Guckan Yapar [aut, ths, cph] (<https://orcid.org/0000-0002-0971-6676>)
Maintainer: Ali Sabri Taylan <alisabritaylan@gmail.com>

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Package l1spectral updated to version 0.99.4 with previous version 0.99.2 dated 2021-03-16

Title: An L1-Version of the Spectral Clustering
Description: Provides an l1-version of the spectral clustering algorithm devoted to robustly clustering highly perturbed graphs using l1-penalty. This algorithm is described with more details in the preprint C. Champion, M. Champion, M. Blazère, R. Burcelin and J.M. Loubes, "l1-spectral clustering algorithm: a robust spectral clustering using Lasso regularization" (2021).
Author: Camille Champion [aut], Magali Champion [aut, cre]
Maintainer: Magali Champion <magali.champion@u-paris.fr>

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Package WeMix updated to version 3.1.9 with previous version 3.1.8 dated 2021-06-06

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

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Package TRES updated to version 1.1.5 with previous version 1.1.4 dated 2021-06-25

Title: Tensor Regression with Envelope Structure
Description: Provides three estimators for tensor response regression (TRR) and tensor predictor regression (TPR) models with tensor envelope structure. The three types of estimation approaches are generic and can be applied to any envelope estimation problems. The full Grassmannian (FG) optimization is often associated with likelihood-based estimation but requires heavy computation and good initialization; the one-directional optimization approaches (1D and ECD algorithms) are faster, stable and does not require carefully chosen initial values; the SIMPLS-type is motivated by the partial least squares regression and is computationally the least expensive. For details of TRR, see Li L, Zhang X (2017) <doi:10.1080/01621459.2016.1193022>. For details of TPR, see Zhang X, Li L (2017) <doi:10.1080/00401706.2016.1272495>. For details of 1D algorithm, see Cook RD, Zhang X (2016) <doi:10.1080/10618600.2015.1029577>. For details of ECD algorithm, see Cook RD, Zhang X (2018) <doi:10.5705/ss.202016.0037>. For more details of the package, see Zeng J, Wang W, Zhang X (2021) <doi:10.18637/jss.v099.i12>.
Author: Wenjing Wang [aut], Jing Zeng [aut, cre], Xin Zhang [aut]
Maintainer: Jing Zeng <jing.zeng@stat.fsu.edu>

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Package spsurvey updated to version 5.0.1 with previous version 5.0.0 dated 2021-10-18

Title: Spatial Sampling Design and Analysis
Description: A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that are not spatially balanced, select panel samples, measure the amount of spatial balance in a sample, adjust design weights, and more.
Author: Michael Dumelle [aut, cre] (<https://orcid.org/0000-0002-3393-5529>), Tom Kincaid [aut], Tony Olsen [aut], Marc Weber [aut], Don Stevens [ctb], Denis White [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>

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Package rpf updated to version 1.0.11 with previous version 1.0.9 dated 2021-09-28

Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common to Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as core support code suitable for more specialized IRT packages to build upon. Complete access to optimized C functions are made available with R_RegisterCCallable(). This software is described in Pritikin & Falk (2020) <doi:10.1177/0146621620929431>.
Author: Joshua Pritikin [cre, aut], Jonathan Weeks [ctb], Li Cai [ctb], Carrie Houts [ctb], Phil Chalmers [ctb], Michael D. Hunter [ctb], Carl F. Falk [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>

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Package memuse updated to version 4.2-1 with previous version 4.1-0 dated 2020-02-17

Title: Memory Estimation Utilities
Description: How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is your current R session using? How much ram do you even have? Learn the scintillating answer to these and many more such questions with the 'memuse' package.
Author: Drew Schmidt [aut, cre], Christian Heckendorf [ctb] (FreeBSD improvements to meminfo), Wei-Chen Chen [ctb] (Windows build fixes), Dan Burgess [ctb] (donation of a Mac for development and testing)
Maintainer: Drew Schmidt <wrathematics@gmail.com>

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Package DEEVD updated to version 1.2.2 with previous version 1.2.1 dated 2020-07-22

Title: Density Estimation by Extreme Value Distributions
Description: Provides mean squared error (MSE) and plot the kernel densities related to extreme value distributions with their estimated values. By using Gumbel and Weibull Kernel. See Salha et al. (2014) <doi:10.4236/ojs.2014.48061> and Khan and Akbar (2021) <doi:10.4236/ojs.2021.112018 >.
Author: Javaria Ahmad Khan, Atif Akbar.
Maintainer: Javaria Ahmad Khan <jakhan0@yahoo.com>

Diff between DEEVD versions 1.2.1 dated 2020-07-22 and 1.2.2 dated 2021-10-20

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Package roger updated to version 0.99-1 with previous version 0.99-0 dated 2021-08-21

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

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Tue, 19 Oct 2021

Package genSurv updated to version 1.0.4 with previous version 1.0.3 dated 2015-11-09

Title: Generating Multi-State Survival Data
Description: Generation of survival data with one (binary) time-dependent covariate. Generation of survival data arising from a progressive illness-death model.
Author: Artur Araujo [aut, cre] (<https://orcid.org/0000-0003-1419-4208>), Luis Meira-Machado [aut] (<https://orcid.org/0000-0002-8577-7665>), Susana Faria [aut] (<https://orcid.org/0000-0001-8014-9902>)
Maintainer: Artur Araujo <artur.stat@gmail.com>

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Package digitalDLSorteR updated to version 0.1.1 with previous version 0.1.0 dated 2021-10-08

Title: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
Description: Deconvolution of bulk RNA-Seq data using context-specific deconvolution models based on Deep Neural Networks using scRNA-Seq data as input. These models are able to make accurate estimates of the cell composition of bulk RNA-Seq samples from the same context using the advances provided by Deep Learning and the meaningful information provided by scRNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> for more details.
Author: Diego Mañanes [aut, cre] (<https://orcid.org/0000-0001-7247-6794>), Carlos Torroja [aut] (<https://orcid.org/0000-0001-8914-3400>), Fatima Sanchez-Cabo [aut] (<https://orcid.org/0000-0003-1881-1664>)
Maintainer: Diego Mañanes <dmananesc@cnic.es>

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Package pricesensitivitymeter updated to version 1.2.2 with previous version 1.2.1 dated 2021-03-21

Title: Van Westendorp Price Sensitivity Meter Analysis
Description: An implementation of the van Westendorp Price Sensitivity Meter in R, which is a survey-based approach to analyze consumer price preferences and sensitivity (van Westendorp 1976, isbn:9789283100386).
Author: Max Alletsee [aut, cre]
Maintainer: Max Alletsee <max.alletsee@gmail.com>

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Package graphicalVAR updated to version 0.3 with previous version 0.2.4 dated 2020-10-23

Title: Graphical VAR for Experience Sampling Data
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical vector autoregression model in combination with regularization. See also Epskamp, Waldorp, Mottus & Borsboom (2018) <doi:10.1080/00273171.2018.1454823>.
Author: Sacha Epskamp [aut, cre], Eren Asena [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package ARPALData updated to version 1.2.1 with previous version 1.2.0 dated 2021-09-12

Title: Retrieving, Managing and Analysing Air Quality and Weather Data for Lombardy (Italy) using ARPA Lombardia Open Database
Description: Contains functions for retrieving, managing and analysing air quality and weather data from Regione Lombardia open database (<https://www.dati.lombardia.it/>). Data are collected by ARPA Lombardia (Lombardia Environmental Protection Agency), Italy, through its ground monitoring network. See the webpage <https://www.arpalombardia.it/Pages/ARPA_Home_Page.aspx> for further information on ARPA Lombardia's activities and history. Data quality (e.g. missing values, exported values, graphical mapping) has been checked involving members of the ARPA Lombardia's office for air quality control. The package makes available observations since 1989 (for weather) and 1996 (for air quality) and are updated with daily frequency by the regional agency.
Author: Paolo Maranzano [aut, cre, cph] (<https://orcid.org/0000-0002-9228-2759>), Andrea Algieri [aut, cph]
Maintainer: Paolo Maranzano <pmaranzano.ricercastatistica@gmail.com>

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Package rcdd updated to version 1.4 with previous version 1.2-2 dated 2019-04-22

Title: Computational Geometry
Description: R interface to (some of) cddlib (<https://github.com/cddlib/cddlib>). Converts back and forth between two representations of a convex polytope: as solution of a set of linear equalities and inequalities and as convex hull of set of points and rays. Also does linear programming and redundant generator elimination (for example, convex hull in n dimensions). All functions can use exact infinite-precision rational arithmetic.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Glen D. Meeden <glen@stat.umn.edu>, incorporates code from cddlib (ver 0.94f) written by Komei Fukuda <fukuda@ifor.math.ethz.ch>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>

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Package SuperGauss updated to version 2.0.2 with previous version 2.0.1 dated 2020-10-03

Title: Superfast Likelihood Inference for Stationary Gaussian Time Series
Description: Likelihood evaluations for stationary Gaussian time series are typically obtained via the Durbin-Levinson algorithm, which scales as O(n^2) in the number of time series observations. This package provides a "superfast" O(n log^2 n) algorithm written in C++, crossing over with Durbin-Levinson around n = 300. Efficient implementations of the score and Hessian functions are also provided, leading to superfast versions of inference algorithms such as Newton-Raphson and Hamiltonian Monte Carlo. The C++ code provides a Toeplitz matrix class packaged as a header-only library, to simplify low-level usage in other packages and outside of R.
Author: Yun Ling [aut], Martin Lysy [aut, cre]
Maintainer: Martin Lysy <mlysy@uwaterloo.ca>

Diff between SuperGauss versions 2.0.1 dated 2020-10-03 and 2.0.2 dated 2021-10-19

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Package sumFREGAT updated to version 1.2.2 with previous version 1.2.1 dated 2021-02-28

Title: Fast Region-Based Association Tests on Summary Statistics
Description: An adaptation of classical region/gene-based association analysis techniques to the use of summary statistics (P values and effect sizes) and correlations between genetic variants as input. It is a tool to perform the most popular and efficient gene-based tests using the results of genome-wide association (meta-)analyses without having the original genotypes and phenotypes at hand.
Author: Nadezhda M. Belonogova <belon@bionet.nsc.ru> and Gulnara R. Svishcheva <gulsvi@bionet.nsc.ru> with contributions from: Seunggeun Lee (kernel functions), Pierre Lafaye de Micheaux ('davies' method), Minghui Wang, Yiyuan Liu, Shizhong Han (simpleM function), Yaowu Liu (ACAT function), Thomas Lumley ('kuonen' method), and James O. Ramsay (functional data analysis functions)
Maintainer: Nadezhda M. Belonogova <belon@bionet.nsc.ru>

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Package qgraph updated to version 1.9 with previous version 1.6.9 dated 2021-01-28

Title: Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
Description: Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Author: Sacha Epskamp [aut, cre], Giulio Costantini [aut], Jonas Haslbeck [aut], Adela Isvoranu [aut], Angelique O. J. Cramer [ctb], Lourens J. Waldorp [ctb], Verena D. Schmittmann [ctb], Denny Borsboom [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package modeltime.ensemble updated to version 1.0.0 with previous version 0.4.2 dated 2021-07-16

Title: Ensemble Algorithms for Time Series Forecasting with Modeltime
Description: A 'modeltime' extension that implements time series ensemble forecasting methods including model averaging, weighted averaging, and stacking. These techniques are popular methods to improve forecast accuracy and stability. Refer to papers such as "Machine-Learning Models for Sales Time Series Forecasting" Pavlyshenko, B.M. (2019) <doi:10.3390>.
Author: Matt Dancho [aut, cre], Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>

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Package languageserver updated to version 0.3.12 with previous version 0.3.11 dated 2021-07-22

Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol/> for details.
Author: Randy Lai [aut, cre], Kun Ren [ctb]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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Package fairadapt updated to version 0.2.1 with previous version 0.2.0 dated 2021-07-28

Title: Fair Data Adaptation with Quantile Preservation
Description: An implementation of the fair data adaptation with quantile preservation described in Plecko & Meinshausen (2019) <arXiv:1911.06685>. The adaptation procedure uses the specified causal graph to pre-process the given training and testing data in such a way to remove the bias caused by the protected attribute. The procedure uses tree ensembles for quantile regression.
Author: Drago Plecko [aut, cre], Nicolas Bennett [aut]
Maintainer: Drago Plecko <drago.plecko@stat.math.ethz.ch>

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Package NetLogoR updated to version 0.3.9 with previous version 0.3.8 dated 2021-07-10

Title: Build and Run Spatially Explicit Agent-Based Models
Description: Build and run spatially explicit agent-based models using only the R platform. 'NetLogoR' follows the same framework as the 'NetLogo' software (Wilensky, 1999 <http://ccl.northwestern.edu/netlogo/>) and is a translation in R of the structure and functions of 'NetLogo'. 'NetLogoR' provides new R classes to define model agents and functions to implement spatially explicit agent-based models in the R environment. This package allows benefiting of the fast and easy coding phase from the highly developed 'NetLogo' framework, coupled with the versatility, power and massive resources of the R software. Examples of three models (Ants <http://ccl.northwestern.edu/netlogo/models/Ants>, Butterfly (Railsback and Grimm, 2012) and Wolf-Sheep-Predation <http://ccl.northwestern.edu/netlogo/models/WolfSheepPredation>) written using 'NetLogoR' are available. The 'NetLogo' code of the original version of these models is provided alongside. A programming guide inspired from the 'NetLogo' Programming Guide (<https://ccl.northwestern.edu/netlogo/docs/programming.html>) and a dictionary of 'NetLogo' primitives (<https://ccl.northwestern.edu/netlogo/docs/dictionary.html>) equivalences are also available. NOTE: To increment 'time', these functions can use a for loop or can be integrated with a discrete event simulator, such as 'SpaDES' (<https://cran.r-project.org/package=SpaDES>). The suggested package 'fastshp' can be installed with 'install.packages("fastshp", repos = "https://rforge.net", type = "source")'.
Author: Sarah Bauduin [aut] (<https://orcid.org/0000-0002-3252-5894>), Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>), Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>), Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>

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Package Langevin updated to version 1.3.1 with previous version 1.3.0 dated 2021-10-18

Title: Langevin Analysis in One and Two Dimensions
Description: Estimate drift and diffusion functions from time series and generate synthetic time series from given drift and diffusion coefficients.
Author: Philip Rinn [aut, cre], Pedro G. Lind [aut], David Bastine [ctb]
Maintainer: Philip Rinn <philip.rinn@uni-oldenburg.de>

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Package rWind updated to version 1.1.7 with previous version 1.1.5 dated 2020-02-17

Title: Download, Edit and Include Wind and Sea Currents Data in Ecological and Evolutionary Analysis
Description: Tools for download and manage surface wind and sea currents data from the Global Forecasting System <https://www.ncei.noaa.gov/products/weather-climate-models/global-forecast> and to compute connectivity between locations.
Author: Javier Fernández-López [aut, cre], Klaus Schliep [aut], Yurena Arjona [aut]
Maintainer: Javier Fernández-López <jflopez.bio@gmail.com>

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Package cancensus updated to version 0.4.4 with previous version 0.4.3 dated 2021-06-08

Title: Access, Retrieve, and Work with Canadian Census Data and Geography
Description: Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer), Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for correspondence), Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>

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Package Ravages updated to version 1.0.0 with previous version 0.1.5 dated 2021-05-12

Title: Rare Variant Analysis and Genetic Simulations
Description: Rare variant association tests: burden tests (Bocher et al. 2019 <doi:10.1002/gepi.22210>) and the Sequence Kernel Association Test (Bocher et al. 2021 <doi:10.1038/s41431-020-00792-8>) in the whole genome; and genetic simulations.
Author: Ozvan Bocher and Hervé Perdry
Maintainer: Ozvan Bocher <bocherozvan@gmail.com>

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Package jstable updated to version 1.0.7 with previous version 1.0.6 dated 2021-07-25

Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>), Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package ggstatsplot updated to version 0.9.0 with previous version 0.8.0 dated 2021-06-09

Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It provides an easier syntax to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms, dot plots, dot-and-whisker plots) or categorical (pie and bar charts) data. Currently, it supports the most common types of statistical approaches and tests: parametric, nonparametric, robust, and Bayesian versions of t-test/ANOVA, correlation analyses, contingency table analysis, meta-analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, cph] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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More information about ggstatsplot at CRAN
Permanent link

Package crosstable updated to version 0.2.2 with previous version 0.2.1 dated 2021-03-08

Title: Crosstables for Descriptive Analyses
Description: Create descriptive tables for continuous and categorical variables. Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'. You can also compute statistical tests and effect sizes if needed.
Author: Dan Chaltiel [aut, cre] (<https://orcid.org/0000-0003-3488-779X>), David Hajage [ccp]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>

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Package pairwiseComparisons updated to version 3.2.0 with previous version 3.1.6 dated 2021-06-01

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>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package statsExpressions updated to version 1.2.0 with previous version 1.1.0 dated 2021-05-30

Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the most common types of statistical approaches and tests: parametric, nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation analyses, contingency table analyses, and meta-analyses. The functions are pipe-friendly and provide a consistent syntax to work with tidy data. These dataframes additionally contain expressions with statistical details, and can be used in graphing packages. This package also forms the statistical processing backend for 'ggstatsplot'.
Author: Indrajeet Patil [cre, aut, cph] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package PMwR updated to version 0.17-0 with previous version 0.16-1 dated 2021-09-18

Title: Portfolio Management with R
Description: Functions and examples for 'Portfolio Management with R': backtesting investment and trading strategies, computing profit/loss and returns, analysing trades, handling lists of transactions, reporting, and more.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>

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Package solaR updated to version 0.46 with previous version 0.45 dated 2020-01-19

Title: Radiation and Photovoltaic Systems
Description: Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
Author: Oscar Perpiñán Lamigueiro [cre, aut] (<https://orcid.org/0000-0002-4134-7196>)
Maintainer: Oscar Perpiñán Lamigueiro <oscar.perpinan@upm.es>

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Package Rd2roxygen updated to version 1.12 with previous version 1.11 dated 2020-06-24

Title: Convert Rd to 'Roxygen' Documentation
Description: Functions to convert Rd to 'roxygen' documentation. It can parse an Rd file to a list, create the 'roxygen' documentation and update the original R script (e.g. the one containing the definition of the function) accordingly. This package also provides utilities that can help developers build packages using 'roxygen' more easily. The 'formatR' package can be used to reformat the R code in the examples sections so that the code will be more readable.
Author: Hadley Wickham [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>)
Maintainer: Yihui Xie <xie@yihui.name>

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Package RcmdrPlugin.BWS1 updated to version 0.1-5 with previous version 0.1-4 dated 2020-12-17

Title: R Commander Plug-in for Case 1 (Object Case) Best-Worst Scaling
Description: Adds menu items to the R Commander for implementing case 1 (object case) best-worst scaling (BWS1) from designing choice sets to measuring preferences for items. BWS1 is a question-based survey method that constructs various combinations of items (choice sets) using the experimental designs, asks respondents to select the best and worst items in each choice set, and then measures preferences for the items by analyzing the responses. For details on BWS1, refer to Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>

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Package logger updated to version 0.2.2 with previous version 0.2.1 dated 2021-07-06

Title: A Lightweight, Modern and Flexible Logging Utility
Description: Inspired by the the 'futile.logger' R package and 'logging' Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.
Author: Gergely Daróczi [aut, cre] (<https://orcid.org/0000-0003-3149-8537>), System1 [fnd]
Maintainer: Gergely Daróczi <daroczig@rapporter.net>

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Package tidyseurat updated to version 0.3.0 with previous version 0.2.7 dated 2021-08-25

Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre], Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>

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Package lm.br updated to version 2.9.4 with previous version 2.9.3 dated 2017-04-27

Title: Linear Model with Breakpoint
Description: Exact significance tests for a changepoint in linear or multiple linear regression. Confidence regions with exact coverage probabilities for the changepoint. Based on Knowles, Siegmund and Zhang (1991) <doi:10.1093/biomet/78.1.15>.
Author: Marc Adams [aut, cre], authors of R function 'lm' [ctb] (general interface), authors of 'lm.gls' [ctb] (interface and R code for covariate weights), U.S. NIST [ctb] (C++ code for TNT::Vector template)
Maintainer: Marc Adams <lm.br.pkg@gmail.com>

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Mon, 18 Oct 2021

Package SPUTNIK updated to version 1.4 with previous version 1.3.3 dated 2021-05-17

Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry imaging data (MSI or IMS) based on spatial distribution of signal. Given a region-of-interest (ROI), representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimensionality and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimensionality and simplifying the chemical interpretation.
Author: Paolo Inglese [aut, cre], Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese@outlook.com>

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Package rlang updated to version 0.4.12 with previous version 0.4.11 dated 2021-04-30

Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], mikefc [cph] (Hash implementation based on Mike's xxhashlite), Yann Collet [cph] (Author of the embedded xxHash library), RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package parameters updated to version 0.15.0 with previous version 0.14.0 dated 2021-05-29

Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>, @strengejacke), Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>, @Dom_Makowski), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>), Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets), Søren Højsgaard [aut], Brenton M. Wiernik [aut] (<https://orcid.org/0000-0001-9560-6336>, @bmwiernik), Zen J. Lau [ctb], Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-1995-6531>, @vincentab), Jeffrey Girard [ctb] (<https://orcid.org/0000-0002-7359-3746>, @jeffreymgirard), Christina Maimone [rev], Niels Ohlsen [rev] (@Niels_Bremen)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package gimme updated to version 0.7-7 with previous version 0.7-6 dated 2021-08-19

Title: Group Iterative Multiple Model Estimation
Description: Data-driven approach for arriving at person-specific time series models. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. See Gates & Molenaar (2012) <doi:10.1016/j.neuroimage.2012.06.026>.
Author: Stephanie Lane [aut, trl], Kathleen Gates [aut, cre, ccp], Zachary Fisher [aut], Cara Arizmendi [aut], Peter Molenaar [aut, ccp], Michael Hallquist [ctb], Hallie Pike [ctb], Teague Henry [ctb], Kelly Duffy [ctb], Lan Luo [ctb], Adriene Beltz [csp], Aidan Wright [csp], Jonathan Park [ctb], Sebastian Castro Alvarez [ctb]
Maintainer: Kathleen M Gates <gateskm@email.unc.edu>

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Package ecocomDP updated to version 1.2.0 with previous version 1.1.0 dated 2021-07-31

Title: Tools to Create, Use, and Convert ecocomDP Data
Description: Work with the Ecological Community Data Design Pattern. 'ecocomDP' is a flexible data model for harmonizing ecological community surveys, in a research question agnostic format, from source data published across repositories, and with methods that keep the derived data up-to-date as the underlying sources change. Described in O'Brien et al. (2021), <doi:10.1016/j.ecoinf.2021.101374>.
Author: Colin Smith [aut, cre, cph] (<https://orcid.org/0000-0003-2261-9931>), Eric Sokol [aut] (<https://orcid.org/0000-0001-5923-0917>), Margaret O'Brien [aut] (<https://orcid.org/0000-0002-1693-8322>), Matt Bitters [ctb], Melissa Chen [ctb], Savannah Gonzales [ctb], Matt Helmus [ctb], Brendan Hobart [ctb], Ruvi Jaimes [ctb], Lara Janson [ctb], Marta Jarzyna [ctb], Michael Just [ctb], Daijiang Li [ctb], Wynne Moss [ctb], Kari Norman [ctb], Stephanie Parker [ctb], Natalie Robinson [ctb], Thilina Surasinghe [ctb], Kyle Zollo-Venecek [ctb] (<https://orcid.org/0000-0002-1615-590X>)
Maintainer: Colin Smith <colin.smith@wisc.edu>

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Package CLVTools updated to version 0.8.1 with previous version 0.8.0 dated 2021-03-23

Title: Tools for Customer Lifetime Value Estimation
Description: A set of state-of-the-art probabilistic modeling approaches to derive estimates of individual customer lifetime values (CLV). Commonly, probabilistic approaches focus on modelling 3 processes, i.e. individuals' attrition, transaction, and spending process. Latent customer attrition models, which are also known as "buy-'til-you-die models", model the attrition as well as the transaction process. They are used to make inferences and predictions about transactional patterns of individual customers such as their future purchase behavior. Moreover, these models have also been used to predict individuals’ long-term engagement in activities such as playing an online game or posting to a social media platform. The spending process is usually modelled by a separate probabilistic model. Combining these results yields in lifetime values estimates for individual customers. This package includes fast and accurate implementations of various probabilistic models for non-contractual settings (e.g., grocery purchases or hotel visits). All implementations support time-invariant covariates, which can be used to control for e.g., socio-demographics. If such an extension has been proposed in literature, we further provide the possibility to control for time-varying covariates to control for e.g., seasonal patterns. Currently, the package includes the following latent attrition models to model individuals' attrition and transaction process: [1] Pareto/NBD model (Pareto/Negative-Binomial-Distribution), [2] the Extended Pareto/NBD model (Pareto/Negative-Binomial-Distribution with time-varying covariates), [3] the BG/NBD model (Beta-Gamma/Negative-Binomial-Distribution) and the [4] GGom/NBD (Gamma-Gompertz/Negative-Binomial-Distribution). Further, we provide an implementation of the Gamma/Gamma model to model the spending process of individuals.
Author: Patrick Bachmann [cre, aut], Niels Kuebler [aut], Markus Meierer [aut], Jeffrey Naef [aut], Elliot Oblander [aut], Patrik Schilter [aut]
Maintainer: Patrick Bachmann <patrick.bachmann@business.uzh.ch>

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Package abstr updated to version 0.4.0 with previous version 0.3.0 dated 2021-08-19

Title: R Interface to the A/B Street Transport System Simulation Software
Description: Provides functions to convert origin-destination data, represented as straight 'desire lines' in the 'sf' Simple Features class system, into JSON files that can be directly imported into A/B Street <https://www.abstreet.org>, a free and open source tool for simulating urban transport systems and scenarios of change <doi:10.1007/s10109-020-00342-2>.
Author: Nathanael Sheehan [aut, cre] (<https://orcid.org/0000-0002-2779-0976>), Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>), Trevor Nederlof [aut], Lucas Dias [ctb], Dustin Carlino [aut]
Maintainer: Nathanael Sheehan <nathanaelsheehan@gmail.com>

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Package xfun updated to version 0.27 with previous version 0.26 dated 2021-09-14

Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>), Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package Langevin updated to version 1.3.0 with previous version 1.2.1 dated 2019-01-02

Title: Langevin Analysis in One and Two Dimensions
Description: Estimate drift and diffusion functions from time series and generate synthetic time series from given drift and diffusion coefficients.
Author: Philip Rinn [aut, cre], Pedro G. Lind [aut], David Bastine [ctb]
Maintainer: Philip Rinn <philip.rinn@uni-oldenburg.de>

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