Wed, 29 Jan 2020

Package statsExpressions updated to version 0.3.0 with previous version 0.2.1 dated 2020-01-23

Title: Expressions with Statistical Details
Description: Statistical processing backend for 'ggstatsplot', this package creates expressions with details from statistical tests. Currently, it supports only the most common types of statistical tests: parametric, nonparametric, robust, and bayesian versions of t-test/anova, correlation analyses, contingency table analysis, and meta-analysis.
Author: Indrajeet Patil [cre, aut, ctb] (<https://orcid.org/0000-0003-1995-6531>), Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

Diff between statsExpressions versions 0.2.1 dated 2020-01-23 and 0.3.0 dated 2020-01-29

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Package mcmcse updated to version 1.4-1 with previous version 1.3-2 dated 2017-07-04

Title: Monte Carlo Standard Errors for MCMC
Description: Provides tools for computing Monte Carlo standard errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. MCSE computation for expectation and quantile estimators is supported as well as multivariate estimations. The package also provides functions for computing effective sample size and for plotting Monte Carlo estimates versus sample size.
Author: James M. Flegal <jflegal@ucr.edu>, John Hughes <j.hughes@ucdenver.edu>, Dootika Vats <dootika@iitk.ac.in>, and Ning Dai <daixx224@umn.edu>
Maintainer: Dootika Vats <dootika@iitk.ac.in>

Diff between mcmcse versions 1.3-2 dated 2017-07-04 and 1.4-1 dated 2020-01-29

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Package clustree updated to version 0.4.2 with previous version 0.4.1 dated 2019-08-21

Title: Visualise Clusterings at Different Resolutions
Description: Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
Author: Luke Zappia [aut, cre] (<https://orcid.org/0000-0001-7744-8565>), Alicia Oshlack [aut] (<https://orcid.org/0000-0001-9788-5690>), Andrea Rau [ctb], Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>)
Maintainer: Luke Zappia <luke@lazappi.id.au>

Diff between clustree versions 0.4.1 dated 2019-08-21 and 0.4.2 dated 2020-01-29

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Package chest updated to version 0.3.1 with previous version 0.2.0 dated 2019-12-16

Title: Change-in-Estimate Approach to Assess Confounding Effects
Description: Applies the change-in-effect estimate method to assess confounding effects in medical and epidemiological research (Greenland & Pearce (2016) <doi:10.1146/annurev-publhealth-031914-122559> ). It starts with a crude model including only the outcome and exposure variables. At each of the subsequent steps, one variable which creates the largest change among the remaining variables is selected. This process is repeated until all variables have been entered into the model (Wang Z (2007) <doi:10.1177/1536867X0700700203> ). Currently, the 'chest' package has functions for linear regression, logistic regression, negative binomial regression, Cox proportional hazards model and conditional logistic regression.
Author: Zhiqiang Wang [aut, cre]
Maintainer: Zhiqiang Wang <zhiqiang.wang@menzies.edu.au>

Diff between chest versions 0.2.0 dated 2019-12-16 and 0.3.1 dated 2020-01-29

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Package ImpactEffectsize updated to version 0.3.1 with previous version 0.3.0 dated 2020-01-14

Title: Calculation and Visualization of the Impact Effect Size Measure
Description: A non-parametric effect size measure capturing changes in central tendency or shape of data distributions. The package provides the necessary functions to calculate and plot the Impact effect size measure between two groups.
Author: Jorn Lotsch[aut,cre], Alfred Ultsch[aut]
Maintainer: Jorn Lotsch <j.loetsch@em.uni-frankfurt.de>

Diff between ImpactEffectsize versions 0.3.0 dated 2020-01-14 and 0.3.1 dated 2020-01-29

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Package fable updated to version 0.1.2 with previous version 0.1.1 dated 2019-12-06

Title: Forecasting Models for Tidy Time Series
Description: Provides a collection of commonly used univariate and multivariate time series forecasting models including automatically selected exponential smoothing (ETS) and autoregressive integrated moving average (ARIMA) models. These models work within the 'fable' framework provided by the 'fabletools' package, which provides the tools to evaluate, visualise, and combine models in a workflow consistent with the tidyverse.
Author: Mitchell O'Hara-Wild [aut, cre], Rob Hyndman [aut], Earo Wang [aut], Gabriel Caceres [ctb] (NNETAR implementation)
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>

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More information about fable at CRAN
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Package distr6 updated to version 1.3.3 with previous version 1.3.2 dated 2020-01-12

Title: The Complete R6 Probability Distributions Interface
Description: An R6 object oriented distributions package. Unified interface for 42 probability distributions and 11 kernels including functionality for multiple scientific types. Additionally functionality for composite distributions and numerical imputation. Design patterns including wrappers and decorators are described in Gamma et al. (1994, ISBN:0-201-63361-2). For quick reference of probability distributions including d/p/q/r functions and results we refer to McLaughlin, M. P. (2001). Additionally Devroye (1986, ISBN:0-387-96305-7) for sampling the Dirichlet distribution, Gentle (2009) <doi:10.1007/978-0-387-98144-4> for sampling the Multivariate Normal distribution and Michael et al. (1976) <doi:10.2307/2683801> for sampling the Wald distribution.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>), Franz Kiraly [aut], Peter Ruckdeschel [ctb] (Author of distr), Matthias Kohl [ctb] (Author of distr), Shen Chen [ctb], Jordan Deenichin [ctb], Chengyang Gao [ctb], Chloe Zhaoyuan Gu [ctb], Yunjie He [ctb], Xiaowen Huang [ctb], Shuhan Liu [ctb], Runlong Yu [ctb], Chijing Zeng [ctb], Qian Zhou [ctb]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>

Diff between distr6 versions 1.3.2 dated 2020-01-12 and 1.3.3 dated 2020-01-29

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Package VeryLargeIntegers updated to version 0.1.8 with previous version 0.1.6 dated 2018-02-21

Title: Store and Operate with Arbitrarily Large Integers
Description: Multi-precision library that allows to store and operate with arbitrarily big integers without loss of precision. It includes a large list of tools to work with them, like: - Arithmetic and logic operators - Modular-arithmetic operators - Computer Number Theory utilities - Probabilistic primality tests - Factorization algorithms - Random generators of diferent types of integers.
Author: Javier Leiva Cuadrado
Maintainer: Javier Leiva Cuadrado <jleivacuadrado@gmail.com>

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Package RNeXML updated to version 2.4.2 with previous version 2.4.0 dated 2019-11-08

Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Hilmar Lapp [aut] (<https://orcid.org/0000-0001-9107-0714>), Kseniia Shumelchyk [aut], Rutger Vos [aut] (<https://orcid.org/0000-0001-9254-7318>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package RMaCzek updated to version 1.3 with previous version 1.2.0 dated 2020-01-21

Title: Czekanowski's Diagrams
Description: Allows for production of Czekanowski's Diagrams. See A. Vasterlund (2019) Master thesis, Linkoping University.
Author: Albin Vasterlund [aut], Krzysztof Bartoszek [cre, aut, ths]
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>

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Package av updated to version 0.5.0 with previous version 0.4.0 dated 2020-01-19

Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with audio and video in R. Generates high quality video from images or R graphics with custom audio. Also offers high performance tools for reading raw audio, creating 'spectrograms', and converting between countless audio / video formats. This package interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package airGR updated to version 1.4.3.60 with previous version 1.4.3.52 dated 2020-01-21

Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>), Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>), Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>), Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>), Claude Michel [aut, ths], Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>), François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>, 'Parameter estimation' vignettes), Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>), Nicolas Le Moine [ctb], Thibaut Mathevet [ctb] (<https://orcid.org/0000-0002-4142-4454>), Safouane Mouelhi [ctb], Ludovic Oudin [ctb] (<https://orcid.org/0000-0002-3712-0933>), Raji Pushpalatha [ctb], Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>

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Package icesTAF updated to version 3.3-3 with previous version 3.3-2 dated 2020-01-07

Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework <https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.
Author: Arni Magnusson [aut, cre], Colin Millar [aut], Alexandros Kokkalis [ctb], Ibrahim Umar [ctb]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>

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Package fabletools updated to version 0.1.2 with previous version 0.1.1 dated 2019-09-16

Title: Core Tools for Packages in the 'fable' Framework
Description: Provides tools, helpers and data structures for developing models and time series functions for 'fable' and extension packages. These tools support a consistent and tidy interface for time series modelling and analysis.
Author: Mitchell O'Hara-Wild [aut, cre], Rob Hyndman [aut], Earo Wang [aut], Di Cook [ctb], George Athanasopoulos [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>

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Package ExPanDaR updated to version 0.5.1 with previous version 0.5.0 dated 2020-01-10

Title: Explore Your Data Interactively
Description: Provides a shiny-based front end (the 'ExPanD' app) and a set of functions for exploratory data analysis. Run as a web-based app, 'ExPanD' enables users to assess the robustness of empirical evidence without providing them access to the underlying data. You can export a notebook containing the analysis of 'ExPanD' and/or use the functions of the package to support your exploratory data analysis workflow. Refer to the vignettes of the package for more information on how to use 'ExPanD' and/or the functions of this package.
Author: Joachim Gassen [aut, cre] (<https://orcid.org/0000-0003-4364-2911>)
Maintainer: Joachim Gassen <gassen@wiwi.hu-berlin.de>

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Package tibbleOne updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-28

Title: Table One for 'Latex', 'Word', and 'Html' 'R Markdown' Documents
Description: Table one is a tabular description of characteristics, e.g., demographics of patients in a clinical trial, presented overall and also stratified by a categorical variable, e.g. treatment group. There are many excellent packages available to create table one. This package focuses on providing table one objects that seamlessly fit into 'R Markdown' analyses.
Author: Byron Jaeger [aut, cre] (<https://orcid.org/0000-0001-7399-2299>), Boyi Guo [ctb]
Maintainer: Byron Jaeger <bcjaeger@uab.edu>

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Package readwritesqlite updated to version 0.1.0 with previous version 0.0.2 dated 2019-07-23

Title: Enhanced Reading and Writing for 'SQLite' Databases
Description: Reads and writes data frames to 'SQLite' databases while preserving time zones (for POSIXct columns), projections (for 'sfc' columns), units (for 'units' columns), levels (for factors and ordered factors) and classes for logical, Date and 'hms' columns. It also logs changes to tables and provides more informative error messages.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Sebastian Dalgarno [ctb] (<https://orcid.org/0000-0002-3658-4517>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package rbhl updated to version 0.9.0 with previous version 0.8.0 dated 2017-04-12

Title: Interface to the 'Biodiversity' 'Heritage' Library
Description: Interface to 'Biodiversity' 'Heritage' Library ('BHL') (<https://www.biodiversitylibrary.org/>) API (<https://www.biodiversitylibrary.org/docs/api3.html>). 'BHL' is a repository of 'digitized' literature on 'biodiversity' studies, including 'floras', research papers, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package pbdMPI updated to version 0.4-3 with previous version 0.4-2 dated 2019-12-08

Title: Programming with Big Data -- Interface to MPI
Description: An efficient interface to MPI by utilizing S4 classes and methods with a focus on Single Program/Multiple Data ('SPMD') parallel programming style, which is intended for batch parallel execution.
Author: Wei-Chen Chen [aut, cre], George Ostrouchov [aut], Drew Schmidt [aut], Pragneshkumar Patel [aut], Hao Yu [aut], Christian Heckendorf [ctb] (FreeBSD), Brian Ripley [ctb] (Windows HPC Pack 2012), R Core team [ctb] (some functions are modified from the base packages), Sebastien Lamy de la Chapelle [aut] (fix check type for send/recv long vectors)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>

Diff between pbdMPI versions 0.4-2 dated 2019-12-08 and 0.4-3 dated 2020-01-29

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Package imgw updated to version 0.3.0 with previous version 0.2.0 dated 2019-09-12

Title: Polish Meteorological and Hydrological Data
Description: Download Polish meteorological and hydrological data from the Institute of Meteorology and Water Management - National Research Institute (<https://dane.imgw.pl/>). This package also allows for adding geographical coordinates for each observation.
Author: Bartosz Czernecki [aut, cre] (<https://orcid.org/0000-0001-6496-1386>), Arkadiusz Głogowski [aut] (<https://orcid.org/0000-0002-7587-8892>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), IMGW-PIB [ctb] (source of the data)
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>

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Package SubgrPlots updated to version 0.1.3 with previous version 0.1.2 dated 2020-01-13

Title: Graphical Displays for Subgroup Analysis in Clinical Trials
Description: Provides functions for obtaining a variety of graphical displays that may be useful in the subgroup analysis setting. An example with a prostate cancer dataset is provided. The graphical techniques considered include level plots, mosaic plots, contour plots, bar charts, Venn diagrams, tree plots, forest plots, Galbraith plots, L'Abbé plots, the subpopulation treatment effect pattern plot, alluvial plots, circle plots and UpSet plots.
Author: Nicolas Ballarini [aut, cre], Yi-Da Chiu [aut], Jake Conway [ctb], Nils Gehlenborg [ctb], Michal Bojanowski [ctb], Robin Edwards [ctb]
Maintainer: Nicolas Ballarini <nicoballarini@gmail.com>

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Package etm updated to version 1.0.5.1 with previous version 1.0.5 dated 2019-05-28

Title: Empirical Transition Matrix
Description: The etm (empirical transition matrix) package permits to estimate the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator. Functions for data preparation and for displaying are also included (Allignol et al., 2011 <doi:10.18637/jss.v038.i04>). Functionals of the Aalen-Johansen estimator, e.g., excess length-of-stay in an intermediate state, can also be computed (Allignol et al. 2011 <doi:10.1007/s00180-010-0200-x>).
Author: Arthur Allignol
Maintainer: ORPHANED

Diff between etm versions 1.0.5 dated 2019-05-28 and 1.0.5.1 dated 2020-01-29

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Package abcrlda updated to version 1.0.2 with previous version 1.0.1 dated 2019-11-25

Title: Asymptotically Bias-Corrected Regularized Linear Discriminant Analysis
Description: Offers methods to perform asymptotically bias-corrected regularized linear discriminant analysis (ABC_RLDA) for cost-sensitive binary classification. The bias-correction is an estimate of the bias term added to regularized discriminant analysis (RLDA) that minimizes the overall risk. The default magnitude of misclassification costs are equal and set to 0.5; however, the package also offers the options to set them to some predetermined values or, alternatively, take them as hyperparameters to tune. A. Zollanvari, M. Abdirash, A. Dadlani and B. Abibullaev (2019) <doi:10.1109/LSP.2019.2918485>.
Author: Dmitriy Fedorov [aut, cre], Amin Zollanvari [aut], Aresh Dadlani [aut], Berdakh Abibullaev [aut]
Maintainer: Dmitriy Fedorov <dmitriy.fedorov@nu.edu.kz>

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Tue, 28 Jan 2020

Package rsparkling updated to version 0.2.19 with previous version 0.2.18 dated 2019-01-30

Title: R Interface for H2O Sparkling Water
Description: An extension package for 'sparklyr' that provides an R interface to H2O Sparkling Water machine learning library (see <https://github.com/h2oai/sparkling-water> for more information).
Author: Jakub Hava [aut, cre], Navdeep Gill [aut], Erin LeDell [aut], Michal Malohlava [aut], JJ Allaire [aut], H2O.ai [cph], RStudio [cph]
Maintainer: Jakub Hava <jakub@h2o.ai>

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Package ncf updated to version 1.2-9 with previous version 1.2-8 dated 2019-03-22

Title: Spatial Covariance Functions
Description: Spatial (cross-)covariance and related geostatistical tools: the nonparametric (cross-)covariance function , the spline correlogram, the nonparametric phase coherence function, local indicators of spatial association (LISA), (Mantel) correlogram, (Partial) Mantel test.
Author: Ottar N. Bjornstad [aut, cre], Jun Cai [ctb]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>

Diff between ncf versions 1.2-8 dated 2019-03-22 and 1.2-9 dated 2020-01-28

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Package boral updated to version 1.8 with previous version 1.7 dated 2018-10-21

Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via Three. JAGS types of models may be fitted: 1) With explanatory variables only, boral fits independent column Generalized Linear Models (GLMs) to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui <fhui28@gmail.com>, with contributions from Wade Blanchard <wade.blanchard@anu.edu.au>
Maintainer: Francis Hui <fhui28@gmail.com>

Diff between boral versions 1.7 dated 2018-10-21 and 1.8 dated 2020-01-28

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Package rel updated to version 1.4.1 with previous version 1.4.0 dated 2020-01-19

Title: Reliability Coefficients
Description: Derives point estimates with confidence intervals for Bennett et als S, Cohen's kappa, Conger's kappa, Fleiss' kappa, Gwet's AC, intraclass correlation coefficients, Krippendorff's alpha, Scott's pi, the standard error of measurement, and weighted kappa.
Author: Riccardo LoMartire
Maintainer: Riccardo LoMartire <lomartire@kth.se>

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Package tidybayes updated to version 2.0.1 with previous version 1.1.0 dated 2019-06-02

Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided to help extract tidy data frames of draws from Bayesian models and that generate point summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre], Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@umich.edu>

Diff between tidybayes versions 1.1.0 dated 2019-06-02 and 2.0.1 dated 2020-01-28

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 tidybayes-2.0.1/tidybayes/DESCRIPTION                                                                             |   47 
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 tidybayes-2.0.1/tidybayes/NEWS.md                                                                                 |   49 
 tidybayes-2.0.1/tidybayes/R/add_draws.R                                                                           |   51 
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 tidybayes-2.0.1/tidybayes/R/combine_chains.R                                                                      |   22 
 tidybayes-2.0.1/tidybayes/R/compare_levels.R                                                                      |  104 
 tidybayes-2.0.1/tidybayes/R/compose_data.R                                                                        |  130 
 tidybayes-2.0.1/tidybayes/R/data.R                                                                                |    8 
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 tidybayes-2.0.1/tidybayes/R/fitted_draws.R                                                                        |    7 
 tidybayes-2.0.1/tidybayes/R/gather_draws.R                                                                        |    8 
 tidybayes-2.0.1/tidybayes/R/gather_emmeans_draws.R                                                                |   44 
 tidybayes-2.0.1/tidybayes/R/gather_pairs.R                                                                        |   28 
 tidybayes-2.0.1/tidybayes/R/gather_variables.R                                                                    |   48 
 tidybayes-2.0.1/tidybayes/R/geom.R                                                                                |  123 
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 tidybayes-2.0.1/tidybayes/R/geom_eye.R                                                                            |  155 
 tidybayes-2.0.1/tidybayes/R/geom_interval.R                                                                       |  163 
 tidybayes-2.0.1/tidybayes/R/geom_intervalh.R                                                                      |  102 
 tidybayes-2.0.1/tidybayes/R/geom_lineribbon.R                                                                     |   74 
 tidybayes-2.0.1/tidybayes/R/geom_pointinterval.R                                                                  |  187 
 tidybayes-2.0.1/tidybayes/R/geom_pointintervalh.R                                                                 |  103 
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 tidybayes-2.0.1/tidybayes/R/get_variables.R                                                                       |    8 
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Package oro.nifti updated to version 0.10.1 with previous version 0.9.1 dated 2017-10-26

Title: Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output
Description: Functions for the input/output and visualization of medical imaging data that follow either the 'ANALYZE', 'NIfTI' or 'AFNI' formats. This package is part of the Rigorous Analytics bundle.
Author: Brandon Whitcher [aut, cre], Volker Schmid [aut], Andrew Thornton [aut], Karsten Tabelow [ctb], Jon Clayden [ctb], John Muschelli [aut]
Maintainer: Brandon Whitcher <bwhitcher@gmail.com>

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 oro.nifti-0.10.1/oro.nifti/R/sform_code.R                   |   10 
 oro.nifti-0.10.1/oro.nifti/R/sizeof_hdr.R                   |   45 +
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Package httptest updated to version 3.3.0 with previous version 3.2.2 dated 2018-12-07

Title: A Test Environment for HTTP Requests
Description: Testing and documenting code that communicates with remote servers can be painful. Dealing with authentication, server state, and other complications can make testing seem too costly to bother with. But it doesn't need to be that hard. This package enables one to test all of the logic on the R sides of the API in your package without requiring access to the remote service. Importantly, it provides three contexts that mock the network connection in different ways, as well as testing functions to assert that HTTP requests were---or were not---made. It also allows one to safely record real API responses to use as test fixtures. The ability to save responses and load them offline also enables one to write vignettes and other dynamic documents that can be distributed without access to a live server.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>

Diff between httptest versions 3.2.2 dated 2018-12-07 and 3.3.0 dated 2020-01-28

 DESCRIPTION                            |   14 ++++-----
 MD5                                    |   50 ++++++++++++++++-----------------
 NEWS.md                                |    9 +++++
 R/capture-requests.R                   |   35 +++++------------------
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 tests/testthat/test-capture-requests.R |   25 +++++++---------
 tests/testthat/test-expect-header.R    |    9 +++++
 tests/testthat/test-find-redactor.R    |   38 ++++++++++++++++++-------
 tests/testthat/test-mock-api.R         |    5 +--
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 vignettes/redacting.Rmd                |    2 -
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More information about httptest at CRAN
Permanent link

Package gglogo updated to version 0.1.5 with previous version 0.1.4 dated 2019-06-28

Title: Geom for Logo Sequence Plots
Description: Visualize sequences in (modified) logo plots. The design choices used by these logo plots allow sequencing data to be more easily analyzed. Because it is integrated into the 'ggplot2' geom framework, these logo plots support native features such as faceting.
Author: Heike Hofmann [aut], Eric Hare [aut, cre], GGobi Foundation [aut]
Maintainer: Eric Hare <eric@oaiti.org>

Diff between gglogo versions 0.1.4 dated 2019-06-28 and 0.1.5 dated 2020-01-28

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Permanent link

Package ShinyItemAnalysis updated to version 1.3.2 with previous version 1.3.1 dated 2019-06-26

Title: Test and Item Analysis via Shiny
Description: Interactive shiny application for analysis of educational tests and their items.
Author: Patricia Martinkova [aut, cre], Adela Hladka [aut], Ondrej Leder [ctb], Jakub Houdek [ctb], Lubomir Stepanek [ctb], Tomas Jurica [ctb], Jana Vorlickova [ctb], Jan Netik [ctb]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>

Diff between ShinyItemAnalysis versions 1.3.1 dated 2019-06-26 and 1.3.2 dated 2020-01-28

 DESCRIPTION                                                        |   15 
 MD5                                                                |  154 
 NAMESPACE                                                          |   17 
 NEWS                                                               |  162 
 R/DDplot.R                                                         |  206 -
 R/DistractorAnalysis.R                                             |   87 
 R/HCI.R                                                            |   14 
 R/HCIkey.R                                                         |    8 
 R/HCItest.R                                                        |   14 
 R/ItemAnalysis.R                                                   |  145 
 R/LearningToLearn.R                                                |only
 R/Logistik_edited.R                                                |only
 R/dataMedical.R                                                    |   44 
 R/dataMedicalgraded.R                                              |   33 
 R/dataMedicalkey.R                                                 |   23 
 R/dataMedicaltest.R                                                |   29 
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 R/difMH_edited.R                                                   |only
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 R/gDisrim.R                                                        |   61 
 R/ggWrightMap.R                                                    |   52 
 R/onAttach.R                                                       |only
 R/plotAdjacent.R                                                   |   94 
 R/plotCumulative.R                                                 |  171 
 R/plotDIFLogistic.R                                                |  282 -
 R/plotDIFirt.R                                                     |  202 
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 R/plotMultinomial.R                                                |   87 
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 R/startShinyItemAnalysis.R                                         |    8 
 R/theme_app.R                                                      |   32 
 README.md                                                          |    9 
 data/HCI.rda                                                       |binary
 data/HCIkey.rda                                                    |binary
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 inst/CITATION                                                      |   12 
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 man/LearningToLearn.Rd                                             |only
 man/dataMedical.Rd                                                 |   89 
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 man/dataMedicalkey.Rd                                              |   76 
 man/dataMedicaltest.Rd                                             |   89 
 man/gDiscrim.Rd                                                    |  181 
 man/ggWrightMap.Rd                                                 |  128 
 man/plotAdjacent.Rd                                                |   98 
 man/plotCumulative.Rd                                              |  106 
 man/plotDIFLogistic.Rd                                             |  150 
 man/plotDIFirt.Rd                                                  |  156 
 man/plotDistractorAnalysis.Rd                                      |  203 
 man/plotMultinomial.Rd                                             |   97 
 man/startShinyItemAnalysis.Rd                                      |   54 
 man/theme_app.Rd                                                   |   71 
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Permanent link

Package rmapshaper updated to version 0.4.3 with previous version 0.4.2 dated 2020-01-17

Title: Client for 'mapshaper' for 'Geospatial' Operations
Description: Edit and simplify 'geojson', 'Spatial', and 'sf' objects. This is wrapper around the 'mapshaper' 'JavaScript' library by Matthew Bloch <https://github.com/mbloch/mapshaper/> to perform topologically-aware polygon simplification, as well as other operations such as clipping, erasing, dissolving, and converting 'multi-part' to 'single-part' geometries. It relies on the 'geojsonio' package for working with 'geojson' objects, the 'sf' package for working with 'sf' objects, and the 'sp' and 'rgdal' packages for working with 'Spatial' objects.
Author: Andy Teucher [aut, cre], Kenton Russell [aut] (JavaScript support), Matthew Bloch [cph] (mapshaper Javascript library)
Maintainer: Andy Teucher <andy.teucher@gmail.com>

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Package rlang updated to version 0.4.4 with previous version 0.4.3 dated 2020-01-24

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], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package fillr updated to version 1.0.0 with previous version 0.1.1 dated 2019-08-02

Title: Fill Missing Values in Vectors
Description: Edit vectors to fill missing values, based on the vector itself.
Author: Jelger van Zaane [aut, cre]
Maintainer: Jelger van Zaane <me@jelgervanzaane.nl>

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Package GeNetIt updated to version 0.1-3 with previous version 0.1-2 dated 2019-10-03

Title: Spatial Graph-Theoretic Genetic Gravity Modelling
Description: Implementation of spatial graph-theoretic genetic gravity models. The model framework is applicable for other types of spatial flow questions. Includes functions for constructing spatial graphs, sampling and summarizing associated raster variables and building unconstrained and singly constrained gravity models.
Author: Jeffrey S. Evans [aut, cre], Melanie Murphy [aut]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>

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Package corto updated to version 1.0.1 with previous version 0.99.10 dated 2019-10-30

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 package implements a similar pipeline as ARACNe-AP (Algorithm for the Reconstruction of Accurate Cellular Networks with Adaptive Partitioning) by Giorgi (2016) <doi:10.1093/bioinformatics/btw216>) with optimizations to run outside a computing cluster (most notably correlation to infer feature dependencies instead of Mutual Information).
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 mimsy updated to version 0.4.3 with previous version 0.4.2 dated 2019-03-10

Title: Calculate MIMS Dissolved Gas Concentrations Without Getting a Headache
Description: Calculate dissolved gas concentrations from raw MIMS (Membrane Inlet Mass Spectrometer) signal data. Use mimsy() on a formatted CSV file to return dissolved gas concentrations (mg and microMole) of N2, O2, Ar based on gas solubility at temperature, pressure, and salinity. See references Benson and Krause (1984) <DOI:10.4319/lo.1992.37.6.1307>, Garcia and Gordon (1992) <DOI:10.4319/lo.1984.29.3.0620>, Stull (1947) <DOI:10.1021/ie50448a022>, and Hamme and Emerson (2004) <DOI:10.1016/j.dsr.2004.06.009> for more information. Easily save the output to a nicely-formatted multi-tab 'Excel' workbook with mimsy.save(). Supports dual-temperature standard calibration for dual-bath MIMS setups.
Author: Michelle C. Kelly [aut, cre]
Maintainer: Michelle C. Kelly <michellecatherinekelly@gmail.com>

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Package rqPen updated to version 2.2.1 with previous version 2.2 dated 2019-12-10

Title: Penalized Quantile Regression
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood [aut, cre], Adam Maidman [ctb]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>

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Package rorcid updated to version 0.6.0 with previous version 0.5.0 dated 2019-06-07

Title: Interface to the 'Orcid.org' API
Description: Client for the 'Orcid.org' API (<https://orcid.org/>). Functions included for searching for people, searching by 'DOI', and searching by 'Orcid' 'ID'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package doRedis updated to version 2.0.0 with previous version 1.1.1 dated 2014-04-03

Title: 'Foreach' Parallel Adapter Using the 'Redis' Database
Description: A parallel back end for the 'foreach' package using the 'Redis' database.
Author: B. W. Lewis <blewis@illposed.net>
Maintainer: B. W. Lewis <blewis@illposed.net>

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Package updog updated to version 1.2.0 with previous version 1.1.3 dated 2019-11-21

Title: Flexible Genotyping for Polyploids
Description: Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allelic bias, overdispersion, and sequencing error. The main functions are flexdog() and multidog(), which allow the specification of many different genotype distributions. An experimental function that takes into account varying levels of relatedness is implemented in mupdog(). Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = "updog") in R for example usage. See Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and Gerard and Ferrao (2019) <doi:10.1093/bioinformatics/btz852> for details on the implemented methods.
Author: David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>

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Package tokenbrowser updated to version 0.1.2 with previous version 0.1.1 dated 2019-10-24

Title: Create Full Text Browsers from Annotated Token Lists
Description: Create browsers for reading full texts from a token list format. Information obtained from text analyses (e.g., topic modeling, word scaling) can be used to annotate the texts.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>

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Package Quartet updated to version 1.1.0 with previous version 1.0.3 dated 2019-12-30

Title: Comparison of Phylogenetic Trees Using Quartet and Split Measures
Description: Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>, and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157> for pairs of binary trees.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Andreas Sand [ant], Gerth Stølting Brodal [ant], Rolf Fagerberg [ant], Thomas Mailund [ant], Christian N. S. Pedersen [ant], Jens Johansen [ant], Morten K. Holt [ant]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between Quartet versions 1.0.3 dated 2019-12-30 and 1.1.0 dated 2020-01-28

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Package ragt2ridges updated to version 0.3.4 with previous version 0.3.3 dated 2019-12-05

Title: Ridge Estimation of Vector Auto-Regressive (VAR) Processes
Description: The ragt2ridges-package provides ridge maximum likelihood estimation of vector auto-regressive processes: the VAR(1), VAR(2) and VARX(1) model (more to be added). Prior knowledge may be incorporated in the estimation through a) specification of the edges believed to be absent in the time series chain graph, and b) a shrinkage target towards which the parameter estimate is shrunken for large penalty parameter values. Estimation functionality is accompanied by methodology for penalty parameter selection. In addition, the package offers supporting functionality for the exploitation of estimated models. Among others, i) a procedure to infer the support of the non-sparse ridge estimate (and thereby of the time series chain graph) is implemented, ii) a table of node-wise network summary statistics, iii) mutual information analysis, and iv) impulse response analysis. Cf. Miok et al. (2017) <DOI:10.1002/bimj.201500269> and Miok et al. (2019) <DOI:10.1002/bimj.201700195> for details on the implemented methods.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>

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Package TropFishR updated to version 1.6.2 with previous version 1.6.1 dated 2019-01-17

Title: Tropical Fisheries Analysis
Description: A compilation of fish stock assessment methods for the analysis of length-frequency data in the context of data-poor fisheries. Includes methods and examples included in the FAO Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish stock assessment" (<http://www.fao.org/documents/card/en/c/9bb12a06-2f05-5dcb-a6ca-2d6dd3080f65/>), as well as other more recent methods.
Author: Tobias K. Mildenberger, Marc H. Taylor, Matthias Wolff
Maintainer: Tobias K. Mildenberger <t.k.mildenberger@gmail.com>

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Package rankFD updated to version 0.0.5 with previous version 0.0.4 dated 2020-01-27

Title: Rank-Based Tests for General Factorial Designs
Description: The rankFD() function calculates the Wald-type statistic (WTS) and the ANOVA-type statistic (ATS) for nonparametric factorial designs, e.g., for count, ordinal or score data in a crossed design with an arbitrary number of factors.
Author: Frank Konietschke, Sarah Friedrich, Edgar Brunner, Markus Pauly
Maintainer: Frank Konietschke <frank.konietschke@charite.de>

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Package psychotools updated to version 0.5-1 with previous version 0.5-0 dated 2018-12-19

Title: Psychometric Modeling Infrastructure
Description: Infrastructure for psychometric modeling such as data classes (for item response data and paired comparisons), basic model fitting functions (for Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit, rating scale, multinomial processing tree models), extractor functions for different types of parameters (item, person, threshold, discrimination, guessing, upper asymptotes), unified inference and visualizations, and various datasets for illustration. Intended as a common lightweight and efficient toolbox for psychometric modeling and a common building block for fitting psychometric mixture models in package "psychomix" and trees based on psychometric models in package "psychotree".
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>), Carolin Strobl [aut], Florian Wickelmaier [aut], Basil Komboz [aut], Julia Kopf [aut], Lennart Schneider [aut], Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

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Package phenopix updated to version 2.4 with previous version 2.3.1 dated 2017-06-16

Title: Process Digital Images of a Vegetation Cover
Description: A collection of functions to process digital images, depict greenness index trajectories and extract relevant phenological stages.
Author: Gianluca Filippa, Edoardo Cremonese, Mirco Migliavacca, Marta Galvagno, Matthias Folker, Andrew D. Richardson, Enrico Tomelleri
Maintainer: Gianluca Filippa <gian.filippa@gmail.com>

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Package ggeffects updated to version 0.14.1 with previous version 0.14.0 dated 2019-12-16

Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Description: Compute marginal effects from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package ocedata updated to version 0.1.6 with previous version 0.1.5 dated 2018-12-19

Title: Oceanographic Data Sets for 'oce' Package
Description: Several Oceanographic data sets are provided for use by the 'oce' package and for other purposes.
Author: Dan Kelley [aut, cre] (<https://orcid.org/0000-0001-7808-5911>)
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>

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Package nomogramFormula updated to version 1.2.0.0 with previous version 1.1.0.0 dated 2019-09-02

Title: Calculate Total Points and Probabilities for Nomogram
Description: A nomogram, which can be carried out in 'rms' package, provides a graphical explanation of a prediction process. However, it is not very easy to draw straight lines, read points and probabilities accurately. Even, it is hard for users to calculate total points and probabilities for all subjects. This package provides formula_rd() and formula_lp() functions to fit the formula of total points with raw data and linear predictors respectively by polynomial regression. Function points_cal() will help you calculate the total points. prob_cal() can be used to calculate the probabilities after lrm(), cph() or psm() regression. For more complex condition, interaction or restricted cubic spine, TotalPoints.rms() can be used.
Author: Jing Zhang, Zhi Jin
Maintainer: Jing Zhang<zj391120@163.com>

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Package sjlabelled updated to version 1.1.3 with previous version 1.1.2 dated 2020-01-17

Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata', and working with labelled data. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), David Ranzolin [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package repr updated to version 1.1.0 with previous version 1.0.2 dated 2019-12-16

Title: Serializable Representations
Description: String and binary representations of objects for several formats / mime types.
Author: Philipp Angerer [aut, cre] (<https://orcid.org/0000-0002-0369-2888>), Thomas Kluyver [aut], Jan Schulz [aut], abielr [ctb], Denilson Figueiredo de Sa [ctb], Jim Hester [ctb], karldw [ctb], Dave Foster [ctb], Carson Sievert [ctb]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>

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Package bigutilsr updated to version 0.3.0 with previous version 0.2.2 dated 2019-11-04

Title: Utility Functions for Large-scale Data
Description: Utility functions for large-scale data. For now, package 'bigutilsr' mainly includes functions for outlier detection and PCA projection.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>

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Package staRdom updated to version 1.1.3 with previous version 1.1.1 dated 2019-11-27

Title: PARAFAC Analysis of EEMs from DOM
Description: This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.
Author: Matthias Pucher [aut, cre], Daniel Graeber [aut, ctb], Stefan Preiner [ctb], Renata Pinto [ctb]
Maintainer: Matthias Pucher <matthias.pucher@wcl.ac.at>

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Package sf updated to version 0.8-1 with previous version 0.8-0 dated 2019-09-17

Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial vector data. Binds to 'GDAL' for reading and writing data, to 'GEOS' for geometrical operations, and to 'PROJ' for projection conversions and datum transformations.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>), Etienne Racine [ctb], Michael Sumner [ctb], Ian Cook [ctb], Tim Keitt [ctb], Robin Lovelace [ctb], Hadley Wickham [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Kirill M<U+00FC>ller [ctb], Thomas Lin Pedersen [ctb], Dan Baston [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package difNLR updated to version 1.3.2 with previous version 1.3.1 dated 2020-01-27

Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Drabinova and Martinkova, 2017, doi:10.1111/jedm.12158).
Author: Adela Hladka [aut, cre], Patricia Martinkova [aut], Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>

Diff between difNLR versions 1.3.1 dated 2020-01-27 and 1.3.2 dated 2020-01-28

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Package bikm1 updated to version 1.0.0 with previous version 0.9.0 dated 2019-08-24

Title: Co-Clustering Adjusted Rand Index and Bikm1 Procedure for Contingency and Binary Data-Sets
Description: Co-clustering of the rows and columns of a contingency or binary matrix, or double binary matrices and model selection for the number of row and column clusters. Three models are considered: the Poisson latent block model for contingency matrix, the binary latent block model for binary matrix and a new model we develop: the multiple latent block model for double binary matrices. A new procedure named bikm1 is implemented to investigate more efficiently the grid of numbers of clusters. Then, the studied model selection criteria are the integrated completed likelihood (ICL) and the Bayesian integrated likelihood (BIC). Finally, the co-clustering adjusted Rand index (CARI) to measure agreement between co-clustering partitions is implemented. Robert Valerie and Vasseur Yann (2017) <arXiv:1705.06760>.
Author: Valerie Robert [aut, cre]
Maintainer: Valerie Robert <valerie.robert.math@gmail.com>

Diff between bikm1 versions 0.9.0 dated 2019-08-24 and 1.0.0 dated 2020-01-28

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Package bigassertr updated to version 0.1.2 with previous version 0.1.1 dated 2019-10-14

Title: Assertion and Message Functions
Description: Enhanced message functions (cat() / message() / warning() / error()) using wrappers around sprintf(). Also, multiple assertion functions (e.g. to check class, length, values, files, arguments, etc.).
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>

Diff between bigassertr versions 0.1.1 dated 2019-10-14 and 0.1.2 dated 2020-01-28

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Package rmumps updated to version 5.2.1-10 with previous version 5.2.1-7 dated 2019-12-06

Title: Wrapper for MUMPS Library
Description: Some basic features of 'MUMPS' (Multifrontal Massively Parallel sparse direct Solver) are wrapped in a class whose methods can be used for sequentially solving a sparse linear system (symmetric or not) with one or many right hand sides (dense or sparse). There is a possibility to do separately symbolic analysis, LU (or LDL^t) factorization and system solving. Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'. 'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194> and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre], Emmanuel Agullo [ctb], Patrick Amestoy [ctb, cph], Maurice Bremond [ctb], Alfredo Buttari [ctb], Philippe Combes [ctb], Marie Durand [ctb], Aurelia Fevre [ctb], Abdou Guermouche [ctb], Guillaume Joslin [ctb], Jacko Koster [ctb], Jean-Yves L'Excellent [ctb], Stephane Pralet [ctb], Chiara Puglisi [ctb], Francois-Henry Rouet [ctb], Wissam Sid-Lakhdar [ctb], Tzvetomila Slavova [ctb], Bora Ucar [ctb], Clement Weisbecker [ctb], Juergen Schulze [ctb], George Karypis [ctb], Douglas C. Schmidt [ctb], Isamu Hasegawa [ctb], Alexander Chemeris [ctb], Makoto Matsumoto [ctb], Takuji Nishimura [ctb], Francois Pellegrini [ctb], David Goudin [ctb], Pascal Henon [ctb], Pierre Ramet [ctb], Sebastien Fourestier [ctb], Jun-Ho Her [ctb], Cedric Chevalier [ctb], Timothy A. Davis [ctb, cph], Iain S. Duff [ctb, cph], John K. Reid [ctb, cph], Richard Stallman [ctb], Samuel Thibault [ctb, cph], CERFACS [cph], CNRS [cph], ENS Lyon [cph], INP Toulouse [cph], INRIA [cph], University of Bordeaux [cph], Regents of the University of Minnesota [cph], Free Software Foundation, Inc [cph], Alexander Chemeris [cph], Makoto Matsumoto [cph], Takuji Nishimura [cph], Universite de Bordeaux [cph], CNRS [cph], INRAE [cph]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>

Diff between rmumps versions 5.2.1-7 dated 2019-12-06 and 5.2.1-10 dated 2020-01-28

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Package lidR updated to version 2.2.2 with previous version 2.2.1 dated 2020-01-21

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 lassnags), Bourdon Jean-François [ctb] (Implemented sensor_tracking)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

Diff between lidR versions 2.2.1 dated 2020-01-21 and 2.2.2 dated 2020-01-28

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Package clubSandwich updated to version 0.4.1 with previous version 0.4.0 dated 2019-12-18

Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections
Description: Provides several cluster-robust variance estimators (i.e., sandwich estimators) for ordinary and weighted least squares linear regression models, including the bias-reduced linearization estimator introduced by Bell and McCaffrey (2002) <http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf> and developed further by Pustejovsky and Tipton (2017) <DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating the variance- covariance matrix and for testing single- and multiple- contrast hypotheses based on Wald test statistics. Tests of single regression coefficients use Satterthwaite or saddle-point corrections. Tests of multiple- contrast hypotheses use an approximation to Hotelling's T-squared distribution. Methods are provided for a variety of fitted models, including lm() and mlm objects, glm(), ivreg() (from package 'AER'), plm() (from package 'plm'), gls() and lme() (from 'nlme'), lmer() (from `lme4`), robu() (from 'robumeta'), and rma.uni() and rma.mv() (from 'metafor').
Author: James Pustejovsky [aut, cre] (<https://orcid.org/0000-0003-0591-9465>)
Maintainer: James Pustejovsky <jepusto@gmail.com>

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Package cartography updated to version 2.3.0 with previous version 2.2.1 dated 2019-09-27

Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package helps to design cartographic representations such as proportional symbols, choropleth, typology, flows or discontinuities maps. It also offers several features that improve the graphic presentation of maps, for instance, map palettes, layout elements (scale, north arrow, title...), labels or legends. See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>), Nicolas Lambert [aut], Ian Fellows [cph] (no overlap algorithm for labels, from wordcloud package)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>

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Package bssm updated to version 0.1.9 with previous version 0.1.8-1 dated 2020-01-07

Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space Models
Description: Efficient methods for Bayesian inference of state space models via particle Markov chain Monte Carlo and parallel importance sampling type weighted Markov chain Monte Carlo (Vihola, Helske, and Franks, 2017, <arXiv:1609.02541>). Gaussian, Poisson, binomial, or negative binomial observation densities and basic stochastic volatility models with Gaussian state dynamics, as well as general non-linear Gaussian models and discretised diffusion models are supported.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>), Matti Vihola [aut] (<https://orcid.org/0000-0002-8041-7222>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

Diff between bssm versions 0.1.8-1 dated 2020-01-07 and 0.1.9 dated 2020-01-28

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Package beam updated to version 2.0.1 with previous version 2.0.0 dated 2020-01-26

Title: Fast Bayesian Inference in Large Gaussian Graphical Models
Description: Fast Bayesian inference of marginal and conditional independence structures from high-dimensional data.
Author: Gwenael G.R. Leday [cre, aut], Ilaria Speranza [aut], Harry Gray [ctb]
Maintainer: Gwenael G.R. Leday <gwenael.leday@mrc-bsu.cam.ac.uk>

Diff between beam versions 2.0.0 dated 2020-01-26 and 2.0.1 dated 2020-01-28

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Package mlr3misc updated to version 0.1.7 with previous version 0.1.6 dated 2019-12-12

Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions used in 'mlr3' and its companion packages. Comes with helper functions for functional programming, for printing, to work with 'data.table', as well as some generally useful 'R6' classes. This package also supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3misc versions 0.1.6 dated 2019-12-12 and 0.1.7 dated 2020-01-28

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Package fingertipsR updated to version 1.0.1 with previous version 1.0.0 dated 2020-01-07

Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre], Julian Flowers [aut, ctb], Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>), Duncan Gormansway [ctb], Carl Ganz [ctb], David Whiting [ctb], Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>

Diff between fingertipsR versions 1.0.0 dated 2020-01-07 and 1.0.1 dated 2020-01-28

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Package rredlist updated to version 0.6.0 with previous version 0.5.0 dated 2018-07-19

Title: 'IUCN' Red List Client
Description: 'IUCN' Red List (<http://apiv3.iucnredlist.org/api/v3/docs>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.
Author: Scott Chamberlain [aut, cre], rOpenSci [fnd] (https://ropensci.org/), Maëlle Salmon [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rredlist versions 0.5.0 dated 2018-07-19 and 0.6.0 dated 2020-01-28

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Package pomp updated to version 2.5 with previous version 2.4 dated 2019-10-21

Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre], Edward L. Ionides [aut], Carles Breto [aut], Stephen P. Ellner [ctb], Matthew J. Ferrari [ctb], Bruce E. Kendall [ctb], Michael Lavine [ctb], Dao Nguyen [ctb], Daniel C. Reuman [ctb], Helen Wearing [ctb], Simon N. Wood [ctb], Sebastian Funk [ctb], Steven G. Johnson [ctb], Eamon O'Dea [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>

Diff between pomp versions 2.4 dated 2019-10-21 and 2.5 dated 2020-01-28

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More information about pomp at CRAN
Permanent link

Package emmeans updated to version 1.4.4 with previous version 1.4.3.01 dated 2019-11-28

Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph], Henrik Singmann [ctb], Jonathon Love [ctb], Paul Buerkner [ctb], Maxime Herve [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>

Diff between emmeans versions 1.4.3.01 dated 2019-11-28 and 1.4.4 dated 2020-01-28

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Package metamedian updated to version 0.1.5 with previous version 0.1.4 dated 2019-05-19

Title: Meta-Analysis of Medians
Description: Implements several methods to meta-analyze studies that report the sample median of the outcome. When the primary studies are one-group studies, the methods of McGrath et al. (2019) <doi:10.1002/sim.8013> can be applied to estimate the pooled median. In the two-group context, the methods of McGrath et al. (2020) <doi:10.1002/bimj.201900036> can be applied to estimate the pooled raw difference of medians across groups.
Author: Sean McGrath [aut, cre] (<https://orcid.org/0000-0002-7281-3516>), XiaoFei Zhao [aut], Russell Steele [aut], Andrea Benedetti [aut] (<https://orcid.org/0000-0002-8314-9497>)
Maintainer: Sean McGrath <sean.mcgrath@mail.mcgill.ca>

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Mon, 27 Jan 2020

Package R62S3 updated to version 1.4.0 with previous version 1.3.1 dated 2019-06-26

Title: Automatic Method Generation from R6
Description: After defining an R6 class, R62S3 is used to automatically generate optional S3/S4 generics and methods for dispatch. Also allows piping for R6 objects.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>

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Package ari updated to version 0.3.4 with previous version 0.3.3 dated 2020-01-12

Title: Automated R Instructor
Description: Create videos from 'R Markdown' documents, or images and audio files. These images can come from image files or HTML slides, and the audio files can be provided by the user or computer voice narration can be created using 'Amazon Polly'. The purpose of this package is to allow users to create accessible, translatable, and reproducible lecture videos. See <https://aws.amazon.com/polly/> for more information.
Author: Sean Kross [aut, cre], John Muschelli [ctb]
Maintainer: Sean Kross <sean@seankross.com>

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Package PLNmodels updated to version 0.9.5 with previous version 0.9.4 dated 2020-01-14

Title: Poisson Lognormal Models
Description: The Poisson-lognormal model and variants can be used for a variety of multivariate problems when count data are at play, including principal component analysis for count data (Chiquet, Mariadassou and Robin, 2018 <doi:10.1214/18-AOAS1177>), discriminant analysis and network inference (Chiquet, Mariadassou and Robin, 2018 <http://proceedings.mlr.press/v97/chiquet19a.html>). Implements variational algorithms to fit such models accompanied with a set of functions for visualization and diagnostic.
Author: Julien Chiquet [aut, cre] (<https://orcid.org/0000-0002-3629-3429>), Mahendra Mariadassou [aut] (<https://orcid.org/0000-0003-2986-354X>), Stéphane Robin [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>

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Package microdemic updated to version 0.5.0 with previous version 0.4.0 dated 2018-10-25

Title: 'Microsoft Academic' API Client
Description: The 'Microsoft Academic Knowledge' API provides programmatic access to scholarly articles in the 'Microsoft Academic Graph' (<https://academic.microsoft.com/>). Includes methods matching all 'Microsoft Academic' API routes, including search, graph search, text similarity, and interpret natural language query string.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Christopher Baker [aut], rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

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Package tidyselect updated to version 1.0.0 with previous version 0.2.5 dated 2018-10-11

Title: Select from a Set of Strings
Description: A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package Rtrack updated to version 0.9.6 with previous version 0.9.3 dated 2019-11-06

Title: Spatial Navigation Strategy Analysis
Description: A toolkit for the analysis of paths from spatial tracking experiments (such as the Morris water maze) and calculation of goal-finding strategies. This package is centered on an approach using machine learning for path classification.
Author: Rupert Overall [aut, cre] (<https://orcid.org/0000-0002-3882-6073>)
Maintainer: Rupert Overall <rtrack@rupertoverall.net>

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Package geomorph updated to version 3.2.1 with previous version 3.2.0 dated 2019-12-19

Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
Author: Dean Adams [aut, cre], Michael Collyer [aut], Antigoni Kaliontzopoulou [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>

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Package showtext updated to version 0.7-1 with previous version 0.7 dated 2019-06-11

Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType', 'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted into polygons or raster images, hence after the plot has been created, it no longer relies on the font files. No external software such as 'Ghostscript' is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

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Package SIS updated to version 0.8-8 with previous version 0.8-7 dated 2019-11-20

Title: Sure Independence Screening
Description: Variable selection techniques are essential tools for model selection and estimation in high-dimensional statistical models. Through this publicly available package, we provide a unified environment to carry out variable selection using iterative sure independence screening (SIS) (Fan and Lv (2008)<doi:10.1111/j.1467-9868.2008.00674.x>) and all of its variants in generalized linear models (Fan and Song (2009)<doi:10.1214/10-AOS798>) and the Cox proportional hazards model (Fan, Feng and Wu (2010)<doi:10.1214/10-IMSCOLL606>).
Author: Yang Feng [aut, cre], Jianqing Fan [aut], Diego Franco Saldana [aut], Yichao Wu [aut], Richard Samworth [aut]
Maintainer: Yang Feng <yangfengstat@gmail.com>

Diff between SIS versions 0.8-7 dated 2019-11-20 and 0.8-8 dated 2020-01-27

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Package seagull updated to version 1.0.4 with previous version 1.0.3 dated 2020-01-19

Title: Lasso, Group Lasso, and Sparse-Group Lasso for Mixed Models
Description: Proximal gradient descent solver for the operators lasso, group lasso, and sparse-group lasso. The implementation involves backtracking line search and warm starts. Input data needs to be clustered/grouped for the (sparse-)group lasso before calling these algorithms.
Author: Jan Klosa [aut, cre], Noah Simon [ths], Dörte Wittenburg [ths]
Maintainer: Jan Klosa <klosa@fbn-dummerstorf.de>

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Package esquisse updated to version 0.3.0 with previous version 0.2.3 dated 2020-01-09

Title: Explore and Visualize Your Data Interactively
Description: A 'shiny' gadget to create 'ggplot2' charts interactively with drag-and-drop to map your variables. You can quickly visualize your data accordingly to their type, export to 'PNG' or 'PowerPoint', and retrieve the code to reproduce the chart.
Author: Fanny Meyer [aut], Victor Perrier [aut, cre], Ian Carroll [ctb] (Faceting support)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package WR updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-06

Title: Win Ratio Analysis
Description: Contains win-ratio analysis routines for prioritized composite time-to-event outcomes, e.g., death and non-fatal events. These routines include functions to fit the proportional win-fractions (PW) model and to compute and plot the standardized score process to assess the proportionality assumption.
Author: Lu Mao and Tuo Wang
Maintainer: Lu Mao <lmao@biostat.wisc.edu>

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Package tidyquant updated to version 0.5.10 with previous version 0.5.9 dated 2019-12-15

Title: Tidy Quantitative Financial Analysis
Description: Bringing financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

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Package bestNormalize updated to version 1.4.3 with previous version 1.4.2 dated 2019-08-20

Title: Normalizing Transformation Functions
Description: Estimate a suite of normalizing transformations, including a new adaptation of a technique based on ranks which can guarantee normally distributed transformed data if there are no ties: ordered quantile normalization (ORQ). ORQ normalization combines a rank-mapping approach with a shifted logit approximation that allows the transformation to work on data outside the original domain. It is also able to handle new data within the original domain via linear interpolation. The package is built to estimate the best normalizing transformation for a vector consistently and accurately. It implements the Box-Cox transformation, the Yeo-Johnson transformation, three types of Lambert WxF transformations, and the ordered quantile normalization transformation. It also estimates the normalization efficacy of other commonly used transformations.
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>

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Package sociome updated to version 1.3.2 with previous version 1.3.0 dated 2019-11-06

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>

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Package sidrar updated to version 0.2.5 with previous version 0.2.4 dated 2017-07-25

Title: An Interface to IBGE's SIDRA API
Description: Allows the user to connect with IBGE's (Instituto Brasileiro de Geografia e Estatistica, see <http://www.ibge.gov.br/> for more information) SIDRA API in a flexible way. SIDRA is the acronym to "Sistema IBGE de Recuperacao Automatica" and is the system where IBGE turns available aggregate data from their researches.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>

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Package egor updated to version 0.20.01 with previous version 0.19.10 dated 2019-10-07

Title: Import and Analyse Ego-Centered Network Data
Description: Tools for importing, analyzing and visualizing ego-centered network data. Supports several data formats, including the export formats of 'EgoNet', 'EgoWeb 2.0' and 'openeddi'. An interactive (shiny) app for the intuitive visualization of ego-centered networks is provided. Also included are procedures for creating and visualizing Clustered Graphs (Lerner 2008 <DOI:10.1109/PACIFICVIS.2008.4475458>).
Author: Till Krenz [aut, cre], Pavel N. Krivitsky [aut], Raffaele Vacca [aut], Michal Bojanowski [aut], Markus Gamper [ctb], Andreas Herz [aut], Christopher McCarty [ctb]
Maintainer: Till Krenz <egor@tillt.net>

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Package cabinets updated to version 0.4.0 with previous version 0.3.1 dated 2019-11-01

Title: Project Specific Workspace Organization Templates
Description: Creates project specific directory and file templates that are written to a .Rprofile file. Upon starting a new R session, these templates can be used to streamline the creation of new directories that are standardized to the user's preferences.
Author: Nick Williams [aut, cre] (<https://orcid.org/0000-0002-1378-4831>)
Maintainer: Nick Williams <ntwilliams.personal@gmail.com>

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Package processR updated to version 0.2.3 with previous version 0.1.0 dated 2019-03-07

Title: Implementation of the 'PROCESS' Macro
Description: Perform moderation, mediation, moderated mediation and moderated moderation. Inspired from famous 'PROCESS' macro for 'SPSS' and 'SAS' created by Andrew Hayes.
Author: Keon-Woong Moon [aut, cre], Sokyoung Hong [ctb]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>

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Package statgenGWAS updated to version 1.0.3 with previous version 1.0.2 dated 2020-01-20

Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following the method described in Kang et al. (2010), <doi:10.1038/ng.548>. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre], Willem Kruijer [aut] (<https://orcid.org/0000-0001-7179-1733>), Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>), Martin Boer [ctb], Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>), Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>), Emilie Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>), Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>), Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>), Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>), Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>

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Package nlmixr updated to version 1.1.1-5 with previous version 1.1.1-3 dated 2019-11-13

Title: Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'RxODE' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>), Yuan Xiong [aut], Rik Schoemaker [aut] (<https://orcid.org/0000-0002-7538-3005>), Justin Wilkins [aut] (<https://orcid.org/0000-0002-7099-9396>), Richard Hooijmaijers [aut], Teun Post [aut], Wenping Wang [aut, cre], Robert Leary [ctb], Mirjam Trame [ctb], Hadley Wickham [ctb], Dirk Eddelbuettel [cph], Johannes Pfeifer [ctb], Robert B. Schnabel [ctb], Elizabeth Eskow [ctb], Emmanuelle Comets [ctb], Audrey Lavenu [ctb], Marc Lavielle [ctb], David Ardia [cph], Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>), Daniel C. Dillon [ctb], Katharine Mullen [cph], Ben Goodrich [ctb]
Maintainer: Wenping Wang <wwang8198@gmail.com>

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Package lightr updated to version 1.0 with previous version 0.1 dated 2019-11-19

Title: Read Spectrometric Data and Metadata
Description: Parse various reflectance/transmittance/absorbance spectra file formats to extract spectral data and metadata, as described in Gruson, White & Maia (2019) <doi:10.21105/joss.01857>. This package has been peer-reviewed by rOpenSci (v. 0.1).
Author: Hugo Gruson [cre, aut] (<https://orcid.org/0000-0002-4094-1476>), Rafael Maia [aut] (<https://orcid.org/0000-0002-7563-9795>), Thomas White [aut] (<https://orcid.org/0000-0002-3976-1734>), Kotya Karapetyan [cph] (Author of the MATLAB script to read Avantes binary files (CC-BY))
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>

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Package restriktor updated to version 0.2-600 with previous version 0.2-500 dated 2019-12-09

Title: Restricted Statistical Estimation and Inference for Linear Models
Description: Allow for easy-to-use testing or evaluating of linear equality and inequality restrictions about parameters and effects in (generalized) linear statistical models.
Author: Leonard Vanbrabant [aut, cre], Yves Rosseel [ctb]
Maintainer: Leonard Vanbrabant <info@restriktor.org>

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Package difNLR updated to version 1.3.1 with previous version 1.3.0 dated 2019-08-20

Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Drabinova and Martinkova, 2017, doi:10.1111/jedm.12158).
Author: Adela Hladka [aut, cre], Patricia Martinkova [aut], Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>

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Package tfprobability updated to version 0.9.0.0 with previous version 0.8.0.0 dated 2019-10-30

Title: Interface to 'TensorFlow Probability'
Description: Interface to 'TensorFlow Probability', a 'Python' library built on 'TensorFlow' that makes it easy to combine probabilistic models and deep learning on modern hardware ('TPU', 'GPU'). 'TensorFlow Probability' includes a wide selection of probability distributions and bijectors, probabilistic layers, variational inference, Markov chain Monte Carlo, and optimizers such as Nelder-Mead, BFGS, and SGLD.
Author: Sigrid Keydana [aut, cre], Daniel Falbel [ctb], Kevin Kuo [ctb] (<https://orcid.org/0000-0001-7803-7901>), RStudio [cph]
Maintainer: Sigrid Keydana <sigrid@rstudio.com>

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Package ctsem updated to version 3.1.0 with previous version 3.0.9 dated 2019-12-18

Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous time state space modelling, for linear and nonlinear systems measured by continuous variables, with limited support for binary data. The subject specific dynamic system is modelled as a stochastic differential equation (SDE), measurement models are typically multivariate normal factor models. Using the original ctsem formulation based on OpenMx, described in the JSS paper "Continuous Time Structural Equation Modeling with R Package ctsem", with updated version as CRAN vignette <https://cran.r-project.org/package=ctsem/vignettes/ctsem.pdf> , linear mixed effects SDE's estimated via maximum likelihood and optimization are possible. Using the Stan based formulation, described in <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf> , nonlinearity (state dependent parameters) and random effects on all parameters are possible, using either optimization (with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling. Priors may be used. For the conceptual overview of the hierarchical Bayesian linear SDE approach, see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Modeling>. Exogenous inputs may also be included, for an overview of such possibilities see <https://www.researchgate.net/publication/328221807_Understanding_the_Time_Course_of_Interventions_with_Continuous_Time_Dynamic_Models> . Stan based functions are not available on 32 bit Windows systems at present.
Author: Charles Driver [aut, cre, cph], Manuel Voelkle [aut, cph], Han Oud [aut, cph], Trustees of Columbia University [cph]
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>

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Package clustermole updated to version 1.0.1 with previous version 1.0.0 dated 2020-01-20

Title: Unbiased Single-Cell Transcriptomic Data Cell Type Identification
Description: Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>

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Package archetypal updated to version 1.1.0 with previous version 1.0.0 dated 2019-06-13

Title: Finds the Archetypal Analysis of a Data Frame
Description: Performs archetypal analysis by using Principal Convex Hull Analysis (PCHA) under a full control of all algorithmic parameters. It contains a set of functions for determining the initial solution, the optimal algorithmic parameters and the optimal number of archetypes. Post run tools are also available for the assessment of the derived solution. Morup, M., Hansen, LK (2012) <doi:10.1016/j.neucom.2011.06.033>. Hochbaum, DS, Shmoys, DB (1985) <doi:10.1287/moor.10.2.180>. Eddy, WF (1977) <doi:10.1145/355759.355768>. Barber, CB, Dobkin, DP, Huhdanpaa, HT (1996) <doi:10.1145/235815.235821>. Christopoulos, DT (2016) <doi:10.2139/ssrn.3043076>. Christopoulos, DT (2015) <doi:10.1016/j.jastp.2015.03.009> . Falk, A. et al. (2018), <doi:10.1093/qje/qjy013> .
Author: Demetris Christopoulos [aut, cre], David Midgley [ctb], Sunil Venaik [ctb], INSEAD Fontainebleau France [fnd, cph]
Maintainer: Demetris Christopoulos <dchristop@econ.uoa.gr>

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Package rankFD updated to version 0.0.4 with previous version 0.0.3 dated 2019-05-10

Title: Rank-Based Tests for General Factorial Designs
Description: The rankFD() function calculates the Wald-type statistic (WTS) and the ANOVA-type statistic (ATS) for nonparametric factorial designs, e.g., for count, ordinal or score data in a crossed design with an arbitrary number of factors.
Author: Frank Konietschke, Sarah Friedrich, Edgar Brunner, Markus Pauly
Maintainer: Frank Konietschke <frank.konietschke@charite.de>

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Package mev updated to version 1.13.1 with previous version 1.13 dated 2019-12-17

Title: Multivariate Extreme Value Distributions
Description: Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes [Dombry, Engelke and Oesting (2016) <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.
Author: Leo Belzile [aut, cre] (<https://orcid.org/0000-0002-9135-014X>), Jennifer L. Wadsworth [aut], Paul J. Northrop [aut], Scott D. Grimshaw [aut], Jin Zhang [ctb], Michael A. Stephens [ctb], Art B. Owen [ctb], Raphael Huser [aut]
Maintainer: Leo Belzile <belzilel@gmail.com>

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Package effectsize updated to version 0.1.1 with previous version 0.0.1 dated 2019-11-15

Title: Indices of Effect Size and Standardized Parameters
Description: Provide utilities to work with indices of effect size and standardized parameters for a wide variety of models (see support list of insight; Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), allowing computation and conversion of indices such as Cohen's d, r, odds, etc.
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>), Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>), Ken Kelley [ctb], David Stanley [ctb]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

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Package doRNG updated to version 1.8.2 with previous version 1.7.1 dated 2018-06-22

Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform reproducible parallel foreach loops, using independent random streams as generated by L'Ecuyer's combined multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>]. It enables to easily convert standard %dopar% loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>

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Package broom updated to version 0.5.4 with previous version 0.5.3 dated 2019-12-14

Title: Convert Statistical Analysis Objects into Tidy Tibbles
Description: Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.
Author: David Robinson [aut], Alex Hayes [aut, cre] (<https://orcid.org/0000-0002-4985-5160>), Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb]
Maintainer: Alex Hayes <alexpghayes@gmail.com>

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Package bayestestR updated to version 0.5.1 with previous version 0.5.0 dated 2020-01-18

Title: Understand and Describe Bayesian Models and Posterior Distributions
Description: Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>), Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>), Michael D. Wilson [aut] (<https://orcid.org/0000-0003-4143-7308>), Paul-Christian Bürkner [rev], Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>), Quentin F. Gronau [ctb] (<https://orcid.org/0000-0001-5510-6943>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

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Package AzureRMR updated to version 2.3.1 with previous version 2.3.0 dated 2019-10-31

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 <hongooi@microsoft.com>

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Sun, 26 Jan 2020

Package rvg updated to version 0.2.3 with previous version 0.2.2 dated 2019-11-11

Title: R Graphics Devices for Vector Graphics Output
Description: Vector Graphics devices for Microsoft PowerPoint and Excel. Functions extending package 'officer' are provided to embed 'DrawingML' graphics into 'Microsoft PowerPoint' presentations and 'Microsoft Excel' workbooks.
Author: David Gohel [aut, cre], Bob Rudis [ctb] (the javascript code used by function set_attr), Francois Brunetti [ctb] (clipping algorithms)
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package psychonetrics updated to version 0.5.1 with previous version 0.5.0 dated 2020-01-25

Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package modelbased updated to version 0.1.1 with previous version 0.1.0 dated 2020-01-12

Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations for a wide variety of models (see support list of insight; Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), used in the computation of marginal means, contrast analysis and predictions.
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>), Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

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Package altmeta updated to version 2.3 with previous version 2.2 dated 2016-09-13

Title: Alternative Meta-Analysis Methods
Description: Provides alternative statistical methods for meta-analysis, including new heterogeneity tests and measures that are robust to outliers, measures of publication bias, and models for multivariate meta-analysis.
Author: Lifeng Lin [aut, cre] (<https://orcid.org/0000-0002-3562-9816>), Haitao Chu [aut] (<https://orcid.org/0000-0003-0932-598X>)
Maintainer: Lifeng Lin <linl@stat.fsu.edu>

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Package beam updated to version 2.0.0 with previous version 1.0.2 dated 2018-05-06

Title: Fast Bayesian Inference in Large Gaussian Graphical Models
Description: Fast Bayesian inference of marginal and conditional independence structures from high-dimensional data.
Author: Gwenael G.R. Leday [cre, aut], Ilaria Speranza [aut], Harry Gray [ctb]
Maintainer: Gwenael G.R. Leday <gwenael.leday@mrc-bsu.cam.ac.uk>

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Package wiesbaden updated to version 1.2.1 with previous version 1.2.0 dated 2019-11-10

Title: Access Databases from the Federal Statistical Office of Germany
Description: Retrieve and import data from different databases of the Federal Statistical Office of Germany (DESTATIS) using their SOAP XML web service.
Author: Moritz Marbach <moritz.marbach@gess.ethz.ch> [aut, cre]
Maintainer: Moritz Marbach <moritz.marbach@gess.ethz.ch>

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Package respirometry updated to version 1.0.2 with previous version 1.0.1 dated 2019-09-27

Title: Tools for Conducting and Analyzing Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct respirometry experiments. Strong emphasis is on aquatic respirometry. Tools focus on helping the researcher setup and conduct experiments. Functions for analysis of resulting respirometry data are also provided. This package provides tools for intermittent, flow-through, and closed respirometry techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>

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Package treedater updated to version 0.5.0 with previous version 0.3.0 dated 2019-01-16

Title: Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation
Description: Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. The methods are described in Volz, E.M. and S.D.W. Frost (2017) <doi:10.1093/ve/vex025>.
Author: Erik Volz [aut, cre]
Maintainer: Erik Volz <erik.volz@gmail.com>

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Package RRPP updated to version 0.5.2 with previous version 0.5.1 dated 2020-01-19

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], Dean Adams [aut]
Maintainer: Michael Collyer <mlcollyer@gmail.com>

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Package fastshap updated to version 0.0.4 with previous version 0.0.3 dated 2019-12-03

Title: Fast Approximate Shapley Values
Description: Computes fast (relative to other implementations) approximate Shapley values for any supervised learning model. Shapley values help to explain the predictions from any black box model using ideas from game theory; see Strumbel and Kononenko (2014) <doi:10.1007/s10115-013-0679-x> for details.
Author: Brandon Greenwell [aut, cre] (<https://orcid.org/0000-0002-8120-0084>)
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>

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Package leaftime updated to version 0.2.0 with previous version 0.1.2 dated 2019-12-02

Title: 'Leaflet-timeline' Plugin for Leaflet
Description: Use the 'leaflet-timeline' plugin with a leaflet widget to add an interactive slider with play, pause, and step buttons to explore temporal geographic spatial data changes.
Author: Jonathan Skeate [aut] (leaflet-timeline library, https://github.com/skeate/Leaflet.timeline), Kent Russell [aut, cre] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

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Package webr updated to version 0.1.5 with previous version 0.1.0 dated 2018-05-07

Title: Data and Functions for Web-Based Analysis
Description: Several analysis-related functions for the book entitled "Web-based Analysis without R in Your Computer"(written in Korean, ISBN 978-89-5566-185-9) by Keon-Woong Moon. The main function plot.htest() shows the distribution of statistic for the object of class 'htest'.
Author: Keon-Woong Moon [aut, cre], Tommaso Martino [ctb]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>

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Package RgoogleMaps updated to version 1.4.5.2 with previous version 1.4.5.1 dated 2020-01-08

Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>

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Package wrapr updated to version 1.9.6 with previous version 1.9.5 dated 2020-01-19

Title: Wrap R Tools for Debugging and Parametric Programming
Description: Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to, (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools:strmacro()' and 'base::bquote()'), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()', and more.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package stplanr updated to version 0.5.0 with previous version 0.4.1 dated 2019-11-23

Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. Enables common transport planning tasks including: downloading and cleaning transport datasets; creating geographic "desire lines" from origin-destination (OD) data; route assignment, locally and via interfaces to routing services such as <http://cyclestreets.net/>; calculation of route segment attributes such as bearing and aggregate flow; and 'travel watershed' analysis. See Lovelace and Ellison (2018) <doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Richard Ellison [aut], Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>), Barry Rowlingson [ctb] (Author of overline), Nick Bearman [ctb] (Co-author of gclip), Nikolai Berkoff [ctb] (Co-author of line2route), Scott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10), Mark Padgham [ctb], Andrea Gilardi [ctb] (<https://orcid.org/0000-0002-9424-7439>)
Maintainer: Robin Lovelace <rob00x@gmail.com>

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Package spatstat.data updated to version 1.4-3 with previous version 1.4-0 dated 2018-10-04

Title: Datasets for 'spatstat'
Description: Contains all the datasets for the 'spatstat' package.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>), Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>), Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package RcppAlgos updated to version 2.3.5 with previous version 2.3.4 dated 2019-07-03

Title: High Performance Tools for Combinatorics and Computational Mathematics
Description: Provides optimized functions implemented in C++ with 'Rcpp' for solving problems in combinatorics and computational mathematics. Utilizes parallel programming via 'RcppThread' for maximal performance. Also makes use of the RMatrix class from the 'RcppParallel' library. There are combination/permutation functions with constraint parameters that allow for generation of all combinations/permutations of a vector meeting specific criteria (e.g. generating integer partitions/compositions or finding all combinations such that the sum is between two bounds). Capable of generating specific combinations/permutations (e.g. retrieve only the nth lexicographical result) which sets up nicely for parallelization as well as random sampling. Gmp support permits exploration where the total number of results is large (e.g. comboSample(10000, 500, n = 4)). Additionally, there are several high performance number theoretic functions that are useful for problems common in computational mathematics. Some of these functions make use of the fast integer division library 'libdivide'. The primeSieve function is based on the segmented sieve of Eratosthenes implementation by Kim Walisch. It is also efficient for large numbers by using the cache friendly improvements originally developed by Tomás Oliveira. Finally, there is a prime counting function that implements Legendre's formula based on the work of Kim Walisch.
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>

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Package english updated to version 1.2-5 with previous version 1.2-4 dated 2019-12-08

Title: Translate Integers into English
Description: Allow numbers to be presented in an English language version, one, two, three, ... Ordinals are also available, first, second, third, ... and indefinite article choice, "a" or "an".
Author: John Fox, Bill Venables, Anthony Damico and Anne Pier Salverda
Maintainer: Bill Venables <Bill.Venables@gmail.com>

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Package akc updated to version 0.9.3 with previous version 0.9.1 dated 2020-01-09

Title: Automatic Knowledge Classification
Description: A tidy framework for automatic knowledge classification and visualization. Currently, the core functionality of the framework is mainly supported by modularity-based clustering (community detection) in keyword co-occurrence network, and focuses on co-word analysis of bibliometric research. However, the designed functions in 'akc' are general, and could be extended to solve other tasks in text mining as well.
Author: Tian-Yuan Huang [aut, cre] (<https://orcid.org/0000-0002-3591-4203>)
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>

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Package synthACS updated to version 1.5.3 with previous version 1.5.2 dated 2019-07-22

Title: Synthetic Microdata and Spatial MicroSimulation Modeling for ACS Data
Description: Provides access to curated American Community Survey (ACS) base tables via a wrapper to library(acs). Builds synthetic micro-datasets at any user-specified geographic level with ten default attributes; and, conducts spatial microsimulation modeling (SMSM) via simulated annealing. SMSM is conducted in parallel by default. Lastly, we provide functionality for data-extensibility of micro-datasets.
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>

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Sat, 25 Jan 2020

Package tidyUSDA updated to version 0.2.6 with previous version 0.2.5 dated 2020-01-09

Title: A Minimal Tool Set for Gathering USDA Quick Stat Data for Analysis and Visualization
Description: Provides a consistent API to pull United States Department of Agriculture census and survey data from the National Agricultural Statistics Service (NASS) QuickStats service <https://quickstats.nass.usda.gov>.
Author: Brad Lindblad [aut, cre], Michael Thomas [ctb], Alex Mindeman [ctb]
Maintainer: Brad Lindblad <bradley.lindblad@gmail.com>

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Package tidycensus updated to version 0.9.6 with previous version 0.9.5 dated 2020-01-20

Title: Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for many geographies.
Author: Kyle Walker [aut, cre], Kris Eberwein [ctb], Matt Herman [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>

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Package LPM updated to version 2.8 with previous version 2.7 dated 2018-01-16

Title: Linear Parametric Models Applied to Hydrological Series
Description: Apply Univariate Long Memory Models, Apply Multivariate Short Memory Models To Hydrological Dataset, Estimate Intensity Duration Frequency curve to rainfall series.
Author: Corrado Tallerini [aut, cre], Salvatore Grimaldi [aut]
Maintainer: Corrado Tallerini <corrado.tallerini@email.it>

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Package rayshader updated to version 0.13.7 with previous version 0.13.2 dated 2019-12-18

Title: Create Maps and Visualize Data in 2D and 3D
Description: Uses a combination of raytracing and multiple hill shading methods to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hill shading, 2D and 3D plotting options, a built-in path tracer, 'Wavefront' OBJ file export, and the ability to save 3D visualizations to a 3D printable format.
Author: Tyler Morgan-Wall
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

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Package geiger updated to version 2.0.6.4 with previous version 2.0.6.3 dated 2020-01-23

Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Author: Luke Harmon, Matthew Pennell, Jason Weir, Chad Brock, Rich Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman
Maintainer: Luke Harmon <lukeh@uidaho.edu>

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Package eurostat updated to version 3.5.2 with previous version 3.4.20002 dated 2019-12-20

Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database <http://ec.europa.eu/eurostat> together with search and manipulation utilities.
Author: Leo Lahti [aut, cre] (<https://orcid.org/0000-0001-5537-637X>), Janne Huovari [aut], Markus Kainu [aut], Przemyslaw Biecek [aut], Joona Lehtomaki [ctb], Francois Briatte [ctb], Oliver Reiter [ctb]
Maintainer: Leo Lahti <leo.lahti@iki.fi>

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Package febr updated to version 1.0.3 with previous version 1.0.2 dated 2019-05-06

Title: Free Brazilian Repository for Open Soil Data
Description: Making the access to the Free Brazilian Repository for Open Soil Data <http://www.ufsm.br/febr/> as easy as possible.
Author: Alessandro Samuel-Rosa [aut, cre] (<https://orcid.org/0000-0003-0877-1320>), Universidade Federal de Santa Maria [fnd], Universidade Tecnológica Federal do Paraná [fnd]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>

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Package IsingSampler updated to version 0.2.1 with previous version 0.2 dated 2015-03-02

Title: Sampling Methods and Distribution Functions for the Ising Model
Description: Sample states from the Ising model and compute the probability of states. Sampling can be done for any number of nodes, but due to the intractibility of the Ising model the distribution can only be computed up to ~10 nodes.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package gghighlight updated to version 0.2.0 with previous version 0.1.0 dated 2018-07-04

Title: Highlight Lines and Points in 'ggplot2'
Description: Make it easier to explore data with highlights.
Author: Hiroaki Yutani [aut, cre] (<https://orcid.org/0000-0002-3385-7233>)
Maintainer: Hiroaki Yutani <yutani.ini@gmail.com>

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Package psychonetrics updated to version 0.5.0 with previous version 0.4 dated 2019-12-17

Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package PakPMICS2018 updated to version 1.0.0 with previous version 0.1.0 dated 2019-06-25

Title: Multiple Indicator Cluster Survey (MICS) 2017-18 Data for Punjab, Pakistan
Description: Provides data set and function for exploration of Multiple Indicator Cluster Survey (MICS) 2017-18 data for Punjab, Pakistan. The results of the present survey are critically important for the purposes of SDG monitoring, as the survey produces information on 32 global SDG indicators. The data was collected from 53,840 households selected at the second stage with systematic random sampling out of a sample of 2,692 clusters selected using Probability Proportional to size sampling. Six questionnaires were used in the survey: (1) a household questionnaire to collect basic demographic information on all de jure household members (usual residents), the household, and the dwelling; (2) a water quality testing questionnaire administered in three households in each cluster of the sample; (3) a questionnaire for individual women administered in each household to all women age 15-49 years; (4) a questionnaire for individual men administered in every second household to all men age 15-49 years; (5) an under-5 questionnaire, administered to mothers (or caretakers) of all children under 5 living in the household; and (6) a questionnaire for children age 5-17 years, administered to the mother (or caretaker) of one randomly selected child age 5-17 years living in the household (<http://www.mics.unicef.org/surveys>).
Author: Muhammad Yaseen [aut, cre] (<https://orcid.org/0000-0002-5923-1714>)
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>

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Package ether updated to version 0.1.6 with previous version 0.1.5 dated 2018-09-22

Title: Interaction with the 'Ethereum' Blockchain
Description: Interacts with the open-source, public 'Ethereum' <https://www.ethereum.org/> blockchain. It provides a distributed computing platform via smart contracts. This package provides functions which interrogate blocks and transactions in the 'Ethereum' blockchain.
Author: Andrew Collier [aut, cre]
Maintainer: Andrew Collier <andrew@exegetic.biz>

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Package rtsplot updated to version 0.1.2 with previous version 0.1.1 dated 2018-09-15

Title: Time Series Plot
Description: A fast and elegant time series visualization package. In addition to the standard R plot types, this package supports candle sticks, open-high-low-close, and volume plots. Useful for visualizing any time series data, e.g., stock prices and technical indicators.
Author: RTSVizTeam [aut, cph], Irina Kapler [cre]
Maintainer: Irina Kapler <irkapler@gmail.com>

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Package epimdr updated to version 0.6-5 with previous version 0.6-4 dated 2019-08-26

Title: Functions and Data for "Epidemics: Models and Data in R"
Description: Functions, data sets and shiny apps for "Epidemics: Models and Data in R" by Ottar N. Bjornstad (ISBN 978-3-319-97487-3) <https://www.springer.com/gp/book/9783319974866>. The package contains functions to study the S(E)IR model, spatial and age-structured SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the coursera Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Author: Ottar N. Bjornstad [aut, cre]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>

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Fri, 24 Jan 2020

Package TestDesign updated to version 1.0.1 with previous version 1.0.0 dated 2019-11-04

Title: Optimal Test Design Approach to Fixed and Adaptive Test Construction
Description: Use the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and van der Linden (2018) <doi:10.1201/9781315117430> in constructing fixed and adaptive tests. Supports the following mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package is not available from CRAN; see <https://www.gurobi.com/downloads>. See vignette for installing 'Rsymphony' package on Mac systems.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>), Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>)
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>

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Package RcppArmadillo updated to version 0.9.800.4.0 with previous version 0.9.800.3.0 dated 2019-12-07

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that Armadillo requires a fairly recent compiler; for the g++ family at least version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package lpSolve updated to version 5.6.15 with previous version 5.6.13.3 dated 2019-08-19

Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between lpSolve versions 5.6.13.3 dated 2019-08-19 and 5.6.15 dated 2020-01-24

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Package dixonTest updated to version 1.0.2 with previous version 1.0.1 dated 2020-01-12

Title: Dixon's Ratio Test for Outlier Detection
Description: For outlier detection in small and normally distributed samples the ratio test of Dixon (Q-test) can be used. Density, distribution function, quantile function and random generation for Dixon's ratio statistics are provided as wrapper functions. The core applies McBane's Fortran functions <doi:10.18637/jss.v016.i03> that use Gaussian quadrature for a numerical solution.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>), George C. McBane [ctb]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>

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Package ssdtools updated to version 0.1.1 with previous version 0.1.0 dated 2020-01-13

Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability distributions which are fitted to toxicity concentrations for different species as described by Posthuma et al. (2001) <isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to fit distributions such as the log-normal, gamma, burr Type-III, log-logistic, log-Gumbel, Gompertz and Weibull. The user can provide custom distributions. Multiple distributions can be averaged using Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by parametric bootstrapping.
Author: Joe Thorley [aut, cre, ctr] (<https://orcid.org/0000-0002-7683-4592>), Carl Schwarz [aut, ctr], Angeline Tillmanns [ctb], Ali Azizishirazi [ctb], Rebecca Fisher [ctb], David Fox [ctb], Kathleen McTavish [ctb], Heather Thompson [ctb], Andy Teucher [ctb], Emilie Doussantousse [ctb], Stephanie Hazlitt [ctb], Nan-Hung Hsieh [ctb], Sergio Ibarra Espinosa [ctb], Province of British Columbia [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package robustrao updated to version 1.0-5 with previous version 1.0-4 dated 2020-01-22

Title: An Extended Rao-Stirling Diversity Index to Handle Missing Data
Description: A collection of functions to compute the Rao-Stirling diversity index (Porter and Rafols, 2009) <DOI:10.1007/s11192-008-2197-2> and its extension to acknowledge missing data (i.e., uncategorized references) by calculating its interval of uncertainty using mathematical optimization as proposed in Calatrava et al. (2016) <DOI:10.1007/s11192-016-1842-4>. The Rao-Stirling diversity index is a well-established bibliometric indicator to measure the interdisciplinarity of scientific publications. Apart from the obligatory dataset of publications with their respective references and a taxonomy of disciplines that categorizes references as well as a measure of similarity between the disciplines, the Rao-Stirling diversity index requires a complete categorization of all references of a publication into disciplines. Thus, it fails for a incomplete categorization; in this case, the robust extension has to be used, which encodes the uncertainty caused by missing bibliographic data as an uncertainty interval. Classification / ACM - 2012: Information systems ~ Similarity measures, Theory of computation ~ Quadratic programming, Applied computing ~ Digital libraries and archives.
Author: Maria del Carmen Calatrava Moreno [aut, cre], Thomas Auzinger [aut]
Maintainer: Maria del Carmen Calatrava Moreno <mc.calatrava.moreno@gmail.com>

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Package iCellR updated to version 1.3.0 with previous version 1.2.9 dated 2020-01-16

Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq. Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Li F, et al (2019) <doi:10.1158/2159-8290.CD-19-0780> for more details.
Author: Alireza Khodadadi-Jamayran [aut, cre] (<https://orcid.org/0000-0003-2495-7504>), Joseph Pucella [ctb], Hua Zhou [ctb], Nicole Doudican [ctb], John Carucci [ctb], Adriana Heguy [ctb], Boris Reizis [ctb], Aristotelis Tsirigos [aut, ctb] (<https://orcid.org/0000-0002-7512-8477>)
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>

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Package HydroCode updated to version 1.0.1 with previous version 1.0.0 dated 2019-12-18

Title: Hydrological Codes
Description: Pfafstetter Hydrological Codes as cited in Verdin and Verdin (1999) <doi: 10.1016/S0022-1694(99)00011-6> are decoded for upstream or downstream queries.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>

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Package hero updated to version 0.4.7 with previous version 0.0.3 dated 2018-10-30

Title: Spatio-Temporal (Hero) Sandwich Smoother
Description: An implementation of the sandwich smoother proposed in Fast Bivariate Penalized Splines by Xiao et al. (2012) <doi:10.1111/rssb.12007>. A hero is a specific type of sandwich. Dictionary.com (2018) <https://www.dictionary.com> describes a hero as: a large sandwich, usually consisting of a small loaf of bread or long roll cut in half lengthwise and containing a variety of ingredients, as meat, cheese, lettuce, and tomatoes.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>

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Package jtools updated to version 2.0.2 with previous version 2.0.1 dated 2019-04-08

Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools that the author (Jacob) has written for the purpose of more efficiently understanding and sharing the results of (primarily) regression analyses. There are also a number of miscellaneous functions for statistical and programming purposes. Just about everything supports models from the survey package.
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <long.1377@osu.edu>

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Package bacondecomp updated to version 0.1.1 with previous version 0.1.0 dated 2020-01-16

Title: Goodman-Bacon Decomposition
Description: Decomposition for differences-in-differences with variation in treatment timing from Goodman-Bacon (2018) <doi:10.3386/w25018>.
Author: Evan Flack [aut, cre], Edward Jee [aut]
Maintainer: Evan Flack <evanjflack@gmail.com>

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Package tnet updated to version 3.0.14.1 with previous version 3.0.14 dated 2015-11-18

Title: Software for Analysis of Weighted, Two-Mode, and Longitudinal Networks
Description: R package for analyzing weighted, two-mode, and longitudinal networks.
Author: Tore Opsahl
Maintainer: ORPHANED

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Package Map2NCBI updated to version 1.4 with previous version 1.3 dated 2019-05-15

Title: Mapping Markers to the Nearest Genomic Feature
Description: Allows the user to generate a list of features (gene, pseudo, RNA, CDS, and/or UTR) directly from NCBI database for any species with a current build available. Option to save downloaded and formatted files is available, and the user can prioritize the feature list based on type and assembly builds present in the current build used. The user can then use the list of features generated or provide a list to map a set of markers (designed for SNP markers with a single base pair position available) to the closest feature based on the map build. This function does require map positions of the markers to be provided and the positions should be based on the build being queried through NCBI.
Author: Lauren L. Hulsman Hanna and David G. Riley
Maintainer: Lauren Hanna <Lauren.Hanna@ndsu.edu>

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Package ChemoSpec updated to version 5.2.12 with previous version 5.1.48 dated 2019-07-25

Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>), Mike Bostock [cph, ctb] (author of the d3.js library used by plotSpectraJS, http://d3js.org), Matt Keinsley [ctb] (author of initial AOV-PCA code)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

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Package cder updated to version 0.2-2 with previous version 0.2-1 dated 2020-01-13

Title: Interface to the California Data Exchange Center
Description: Connect to the California Data Exchange Center (CDEC) Web Service <http://cdec.water.ca.gov/>. 'CDEC' provides a centralized database to store, process, and exchange real-time hydrologic information gathered by various cooperators throughout California. The 'CDEC' Web Service <http://cdec.water.ca.gov/dynamicapp/wsSensorData> provides a data download service for accessing historical records.
Author: Michael Koohafkan [aut, cre]
Maintainer: Michael Koohafkan <michael.koohafkan@gmail.com>

Diff between cder versions 0.2-1 dated 2020-01-13 and 0.2-2 dated 2020-01-24

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Package aqp updated to version 1.19 with previous version 1.18.1 dated 2019-12-06

Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps/>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>

Diff between aqp versions 1.18.1 dated 2019-12-06 and 1.19 dated 2020-01-24

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Permanent link

Package vctrs updated to version 0.2.2 with previous version 0.2.1 dated 2019-12-17

Title: Vector Helpers
Description: Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut, cre], Lionel Henry [aut], Davis Vaughan [aut], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between vctrs versions 0.2.1 dated 2019-12-17 and 0.2.2 dated 2020-01-24

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Package timeSeries updated to version 3062.100 with previous version 3042.102 dated 2017-11-17

Title: Financial Time Series Objects (Rmetrics)
Description: 'S4' classes and various tools for financial time series: Basic functions such as scaling and sorting, subsetting, mathematical operations and statistical functions.
Author: Diethelm Wuertz [aut] (original code), Tobias Setz [cre], Yohan Chalabi [ctb], Martin Maechler [ctb] (<https://orcid.org/0000-0002-8685-9910>)
Maintainer: Tobias Setz <tobias.setz@live.com>

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Package MomTrunc updated to version 5.69 with previous version 5.63 dated 2020-01-19

Title: Moments of Folded and Doubly Truncated Multivariate Distributions
Description: It computes arbitrary products moments (mean vector and variance-covariance matrix), for some double truncated (and folded) multivariate distributions. These distributions belong to the family of selection elliptical distributions, which includes well known skewed distributions as the unified skew-t distribution (SUT) and its particular cases as the extended skew-t (EST), skew-t (ST) and the symmetric student-t (T) distribution. Analogous normal cases unified skew-normal (SUN), extended skew-normal (ESN), skew-normal (SN), and symmetric normal (N) are also included. Density, probabilities and random deviates are also offered for these members. References used for this package: Arellano-Valle, R. B. & Genton, M. G. (2005). On fundamental skew distributions. Journal of Multivariate Analysis, 96, 93-116. Galarza C.E., Matos L.A., Dey D.K. & Lachos V.H. (2019) On Moments of Folded and Truncated Multivariate Extended Skew-Normal Distributions. Technical report. ID 19-14. University of Connecticut. <https://stat.uconn.edu/tech-reports-2019/>.
Author: Christian E. Galarza, Raymond Kan and Victor H. Lachos
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>

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Package fracdiff updated to version 1.5-1 with previous version 1.5-0 dated 2020-01-16

Title: Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models
Description: Maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989); including inference and basic methods. Some alternative algorithms to estimate "H".
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Chris Fraley [ctb, cph] (S original; Fortran code), Friedrich Leisch [ctb] (R port, <https://orcid.org/0000-0001-7278-1983>), Valderio Reisen [ctb] (fdGPH() & fdSperio()), Artur Lemonte [ctb] (fdGPH() & fdSperio()), Rob Hyndman [ctb] (residuals() & fitted(), <https://orcid.org/0000-0002-2140-5352>)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package RATest updated to version 0.1.7 with previous version 0.1.6 dated 2019-07-18

Title: Randomization Tests
Description: A collection of randomization tests, data sets and examples. The current version focuses on three testing problems and their implementation in empirical work. First, it facilitates the empirical researcher to test for particular hypotheses, such as comparisons of means, medians, and variances from k populations using robust permutation tests, which asymptotic validity holds under very weak assumptions, while retaining the exact rejection probability in finite samples when the underlying distributions are identical. Second, the description and implementation of a permutation test for testing the continuity assumption of the baseline covariates in the sharp regression discontinuity design (RDD) as in Canay and Kamat (2017) <https://goo.gl/UZFqt7>. More specifically, it allows the user to select a set of covariates and test the aforementioned hypothesis using a permutation test based on the Cramer-von Miss test statistic. Graphical inspection of the empirical CDF and histograms for the variables of interest is also supported in the package. Third, it provides the practitioner with an effortless implementation of a permutation test based on the martingale decomposition of the empirical process for testing for heterogeneous treatment effects in the presence of an estimated nuisance parameter.
Author: Mauricio Olivares [aut, cre], Ignacio Sarmiento-Barbieri [aut]
Maintainer: Mauricio Olivares <maurice.olivares@gmail.com>

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Package jubilee updated to version 0.3.3 with previous version 0.3.1 dated 2019-07-19

Title: Forecasting Long-Term Growth of the U.S. Stock Market and Business Cycles
Description: A long-term forecast model called "Jubilee-Tectonic model" is implemented to forecast future returns of the U.S. stock market, Treasury yield, and gold price. The five-factor model forecasts the 10-year and 20-year future equity returns with high R-squared above 80 percent. It is based on linear growth and mean reversion characteristics in the U.S. stock market. This model also enhances the CAPE model by introducing the hypothesis that there are fault lines in the historical CAPE, which can be calibrated and corrected through statistical learning. In addition, it contains a module for business cycles, optimal interest rate, and recession forecasts.
Author: Stephen H-T. Lihn [aut, cre]
Maintainer: Stephen H-T. Lihn <stevelihn@gmail.com>

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Package irtplay updated to version 1.4.0 with previous version 1.3.0 dated 2019-11-18

Title: Online Item Calibration, Scoring, and Evaluation of Model-Data Fit in Item Response Theory (IRT) and Useful Functions Related to IRT Models
Description: Calibrate online item parameters (i.e., pretest and operational items), estimate examinees abilities, and examine the IRT model-data fit on item-level in different ways as well as provide useful functions related to unidimensional item response theory (IRT) models. For the online calibration, Stocking's Method A (Ban, Hanson, Wang, Yi, & Harris (2011) <doi:10.1111/j.1745-3984.2001.tb01123.x>) is provided. More methods of online calibration (e.g., fixed item parameter calibration) will be included in the future updated version. For the ability estimation, several popular scoring methods (e.g., MLE, EAP, and MAP) are implemented. In terms of assessing the IRT model-data fit, one of distinguished features of this package is that it gives not only well-known item fit statistics (e.g., chi-square (X2), likelihood ratio chi-square (G2), infit and oufit statistics, and S-X2 statistic (Ames & Penfield (2015) <doi:10.1111/emip.12067>)) but also graphical displays to look at residuals between between the observed data and model-based predictions (Hambleton, Swaminathan, & Rogers (1991, ISBN:9780803936478)). In addition, there are many useful functions such as computing asymptotic variance-covariance matrices of item parameter estimates (Li & Lissitz (2004) <doi:10.1111/j.1745-3984.2004.tb01109.x>), importing item and/or ability parameters from popular IRT software, generating simulated data, computing the conditional distribution of observed scores using the Lord-Wingersky recursion formula (Lord & Wingersky (1984) <doi:10.1207/s15324818ame1002_1>), computing the loglikelihood of individual items, computing the loglikelihood of abilities, computing item and test information functions, computing item and test characteristic curve functions, and plotting item and test characteristic curves and item and test information functions.
Author: Hwanggyu Lim [aut, cre], Craig S. Wells [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>

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Package callr updated to version 3.4.1 with previous version 3.4.0 dated 2019-12-09

Title: Call R from R
Description: It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>), Winston Chang [aut], RStudio [cph, fnd], Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package tidyr updated to version 1.0.2 with previous version 1.0.0 dated 2019-09-11

Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).
Author: Hadley Wickham [aut, cre], Lionel Henry [aut], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package robcp updated to version 0.2.5 with previous version 0.2.4 dated 2019-06-03

Title: Robust Change-Point Tests
Description: Provides robust methods to detect change-points in uni- or multivariate time series. They can cope with corrupted data and heavy tails. One can detect changes in location, scale and dependence structure of a possibly multivariate time series. Procedures are based on Huberized versions of CUSUM tests proposed in Duerre and Fried (2019) <arXiv:1905.06201>.
Author: Sheila Goerz [aut, cre], Alexander Duerre [ctb]
Maintainer: Sheila Goerz <sheila.goerz@tu-dortmund.de>

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Package Rmpfr updated to version 0.8-1 with previous version 0.7-2 dated 2019-01-22

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)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package rlang updated to version 0.4.3 with previous version 0.4.2 dated 2019-11-23

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], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between rlang versions 0.4.2 dated 2019-11-23 and 0.4.3 dated 2020-01-24

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Package joineRmeta updated to version 0.1.2 with previous version 0.1.1 dated 2018-03-09

Title: Joint Modelling for Meta-Analytic (Multi-Study) Data
Description: Fits joint models of the type proposed by Henderson and colleagues (2000) <doi:10.1093/biostatistics/1.4.465>, but extends to the multi-study, meta-analytic case. Functions for meta-analysis of a single longitudinal and a single time-to-event outcome from multiple studies using joint models. Options to produce plots for multi study joint data, to pool joint model fits from 'JM' and 'joineR' packages in a two stage meta-analysis, and to model multi-study joint data in a one stage meta-analysis.
Author: Maria Sudell [cre, aut] (<https://orcid.org/0000-0002-7919-4981>), Ruwanthi Kolamunnage-Dona [aut] (<https://orcid.org/0000-0003-3886-6208>), Catrin Tudur Smith [aut]
Maintainer: Maria Sudell <mesudell@liverpool.ac.uk>

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Package gWQSRS updated to version 1.1.0 with previous version 1.0.0 dated 2019-08-30

Title: Generalized Weighted Quantile Sum Regression Random Subset
Description: Fits Weighted Quantile Sum Random Subset (WQSRS) regressions for continuous, binomial, multinomial and count outcomes. Paul Curtin, Joshua Kellogg, Nadja Cech, Chris Gennings (2019) <doi:10.1080/03610918.2019.1577971>.
Author: Stefano Renzetti, Paul Curtin, Chris Gennings
Maintainer: Stefano Renzetti <stefano.renzetti88@gmail.com>

Diff between gWQSRS versions 1.0.0 dated 2019-08-30 and 1.1.0 dated 2020-01-24

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Package gmp updated to version 0.5-13.6 with previous version 0.5-13.5 dated 2019-03-11

Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme <rb-gmp@reflex-studio.de>, Sylvain Jasson <jasson@toulouse.inra.fr>, Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>

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Package cobs updated to version 1.3-4 with previous version 1.3-3 dated 2020-01-16

Title: Constrained B-Splines (Sparse Matrix Based)
Description: Qualitatively Constrained (Regression) Smoothing Splines via Linear Programming and Sparse Matrices.
Author: Pin T. Ng <Pin.Ng@nau.edu> and Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package GLMMadaptive updated to version 0.6-8 with previous version 0.6-5 dated 2019-09-26

Title: Generalized Linear Mixed Models using Adaptive Gaussian Quadrature
Description: Fits generalized linear mixed models for a single grouping factor under maximum likelihood approximating the integrals over the random effects with an adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates (1995) <doi:10.1080/10618600.1995.10474663>.
Author: Dimitris Rizopoulos [aut, cre] (<https://orcid.org/0000-0001-9397-0900>)
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>

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Package riceidconverter updated to version 1.0.6 with previous version 1.0.5 dated 2020-01-09

Title: Convert Biological ID from RAP or MSU to SYMBOL for Oryza Sativa
Description: Convert one biological ID to another of rice (Oryza sativa). Rice(Oryza sativa) has more than one form gene ID for the genome. The two main gene ID for rice genome are the RAP (The Rice Annotation Project, <https://rapdb.dna.affrc.go.jp/>, and the MSU(The Rice Genome Annotation Project, <http://rice.plantbiology.msu.edu/>. All RAP rice gene IDs are of the form Os##g####### as explained on the website <https://rapdb.dna.affrc.go.jp/>. All MSU rice gene IDs are of the form LOC_Os##g##### as explained on the website <http://rice.plantbiology.msu.edu/analyses_nomenclature.shtml>. All SYMBOL rice gene IDs are the unique name on the NCBI(National Center for Biotechnology Information, <https://www.ncbi.nlm.nih.gov/>. The TRANSCRIPTID, is the transcript id of rice, are of the form Os##t#######. The researchers usually need to converter between various IDs. Such as converter RAP to SYMBOLS for function searching on NCBI. There are a lot of websites with the function for converting RAP to MSU or MSU to RA, such as 'ID Converter' <https://rapdb.dna.affrc.go.jp/tools/converter>. But it is difficult to convert super multiple IDs on these websites. The package can convert all IDs between the three IDs (RAP, MSU and SYMBOL) regardless of the number.
Author: Xiang LI
Maintainer: Xiang LI <ynaulx@gmail.com>

Diff between riceidconverter versions 1.0.5 dated 2020-01-09 and 1.0.6 dated 2020-01-24

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Package cleaner updated to version 1.3.0 with previous version 1.2.0 dated 2019-11-05

Title: Fast and Easy Data Cleaning
Description: Data cleaning functions for classes logical, factor, numeric, character, currency and Date to make data cleaning fast and easy. Relying on very few dependencies, it provides smart guessing, but with user options to override anything if needed.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

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Package GSODR updated to version 2.0.1 with previous version 2.0.0 dated 2019-09-04

Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
Description: Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from the from the USA National Centers for Environmental Information ('NCEI'). Units are converted from from United States Customary System ('USCS') units to International System of Units ('SI'). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure ('es'), actual vapour pressure ('ea') and relative humidity are calculated from the original data and included in the final data set. The resulting metadata include station identification information, country, state, latitude, longitude, elevation, weather observations and associated flags. For information on the 'GSOD' data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from, <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Tomislav Hengl [aut] (<https://orcid.org/0000-0002-9921-5129>), Andrew Nelson [aut] (<https://orcid.org/0000-0002-7249-3778>), Hugh Parsonage [cph, ctb] (<https://orcid.org/0000-0003-4055-0835>), Taras Kaduk [ctb] (Suggestion for handling bulk station downloads more efficiently), Gwenael Giboire [ctb] (Several bug reports in early versions and testing feedback), Łukasz Pawlik [ctb] (Reported bug in windspeed conversion calculation), Ross Darnell [ctb] (Reported bug in 'Windows OS' versions causing 'GSOD' data untarring to fail)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

Diff between GSODR versions 2.0.0 dated 2019-09-04 and 2.0.1 dated 2020-01-24

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Package charlatan updated to version 0.4.0 with previous version 0.3.0 dated 2018-10-18

Title: Make Fake Data
Description: Make fake data, supporting addresses, person names, dates, times, colors, coordinates, currencies, digital object identifiers ('DOIs'), jobs, phone numbers, 'DNA' sequences, doubles and integers from distributions and within a range.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Kyle Voytovich [aut], Martin Pedersen [ctb], Brooke Anderson [rev] (Brooke Anderson reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/94), Tristan Mahr [rev] (Tristan Mahr reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/94), rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

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Package rtsdata updated to version 0.1.2 with previous version 0.1.1 dated 2018-10-26

Title: R Time Series Intelligent Data Storage
Description: A tool that allows to download and save historical time series data for future use offline. The intelligent updating functionality will only download the new available information; thus, saving you time and Internet bandwidth. It will only re-download the full data-set if any inconsistencies are detected. This package supports following data provides: 'Yahoo' (<https://finance.yahoo.com>), 'FRED' (<https://fred.stlouisfed.org>), 'Quandl' (<https://www.quandl.com>), 'AlphaVantage' (<https://www.alphavantage.co>), 'Tiingo' (<https://www.tiingo.com>).
Author: RTSVizTeam [aut, cph], Irina Kapler [cre]
Maintainer: Irina Kapler <irkapler@gmail.com>

Diff between rtsdata versions 0.1.1 dated 2018-10-26 and 0.1.2 dated 2020-01-24

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Package reactR updated to version 0.4.2 with previous version 0.4.1 dated 2019-07-07

Title: React Helpers
Description: Make it easy to use 'React' in R with 'htmlwidget' scaffolds, helper dependency functions, an embedded 'Babel' 'transpiler', and examples.
Author: Facebook Inc [aut, cph] (React library in lib, https://facebook.github.io/react; see AUTHORS for full list of contributors), Michel Weststrate [aut, cph] (mobx library in lib, https://github.com/mobxjs), Kent Russell [aut, cre] (R interface), Alan Dipert [aut] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

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Package prettyunits updated to version 1.1.1 with previous version 1.1.0 dated 2020-01-09

Title: Pretty, Human Readable Formatting of Quantities
Description: Pretty, human readable formatting of quantities. Time intervals: '1337000' -> '15d 11h 23m 20s'. Vague time intervals: '2674000' -> 'about a month ago'. Bytes: '1337' -> '1.34 kB'.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

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Package nipals updated to version 0.7 with previous version 0.5 dated 2018-10-24

Title: Principal Components Analysis using NIPALS or Weighted EMPCA, with Gram-Schmidt Orthogonalization
Description: Principal Components Analysis of a matrix using Non-linear Iterative Partial Least Squares or weighted Expectation Maximization PCA with Gram-Schmidt orthogonalization of the scores and loadings. Optimized for speed. See Andrecut (2009) <doi:10.1089/cmb.2008.0221>.
Author: Kevin Wright [aut, cre] (<https://orcid.org/0000-0002-0617-8673>)
Maintainer: Kevin Wright <kw.stat@gmail.com>

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Package magick updated to version 2.3 with previous version 2.2 dated 2019-08-26

Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package gh updated to version 1.1.0 with previous version 1.0.1 dated 2017-07-16

Title: 'GitHub' 'API'
Description: Minimal client to access the 'GitHub' 'API'.
Author: Gábor Csárdi [cre, ctb], Jennifer Bryan [aut], Hadley Wickham [aut]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package FSelectorRcpp updated to version 0.3.3 with previous version 0.3.1 dated 2019-04-22

Title: 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature Selection Algorithms with a Sparse Matrix Support
Description: 'Rcpp' (free of 'Java'/'Weka') implementation of 'FSelector' entropy-based feature selection algorithms based on an MDL discretization (Fayyad U. M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning. In 13'th International Joint Conference on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf> with a sparse matrix support.
Author: Zygmunt Zawadzki [aut, cre], Marcin Kosinski [aut], Krzysztof Slomczynski [ctb], Damian Skrzypiec [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>

Diff between FSelectorRcpp versions 0.3.1 dated 2019-04-22 and 0.3.3 dated 2020-01-24

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Package ca updated to version 0.71.1 with previous version 0.71 dated 2018-10-10

Title: Simple, Multiple and Joint Correspondence Analysis
Description: Computation and visualization of simple, multiple and joint correspondence analysis.
Author: Michael Greenacre [aut], Oleg Nenadic [aut, cre], Michael Friendly [ctb]
Maintainer: Oleg Nenadic <onenadi@uni-goettingen.de>

Diff between ca versions 0.71 dated 2018-10-10 and 0.71.1 dated 2020-01-24

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Package IrregLong updated to version 0.2.0 with previous version 0.1.0 dated 2019-02-11

Title: Analysis of Longitudinal Data with Irregular Observation Times
Description: Analysis of longitudinal data for which the times of observation are random variables that are potentially associated with the outcome process. The package includes inverse-intensity weighting methods (Lin H, Scharfstein DO, Rosenheck RA (2004) <doi:10.1111/j.1467-9868.2004.b5543.x>) and multiple outputation (Pullenayegum EM (2016) <doi:10.1002/sim.6829>).
Author: Eleanor Pullenayegum
Maintainer: Eleanor Pullenayegum <eleanor.pullenayegum@sickkids.ca>

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Package cheese updated to version 0.0.2 with previous version 0.0.1 dated 2019-04-01

Title: Tools for Intuitive and Flexible Statistical Analysis Workflows
Description: Contains flexible and intuitive functions to assist in carrying out tasks in a statistical analysis and to get from the raw data to presentation-ready results. A user-friendly interface is used in specialized functions that are aimed at common tasks such as building a univariate descriptive table for variables in a dataset. These high-level functions are built on a collection of low(er)-level functions that may be useful for aspects of a custom statistical analysis workflow or for general programming use.
Author: Alex Zajichek [aut, cre]
Maintainer: Alex Zajichek <alexzajichek@gmail.com>

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Package CGE updated to version 0.2.8 with previous version 0.2.5 dated 2019-12-07

Title: Computing General Equilibrium
Description: Developing general equilibrium models, computing general equilibrium and simulating economic dynamics with structural dynamic models in LI (2019, ISBN: 9787521804225) "General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press".
Author: LI Wu <liwu@staff.shu.edu.cn>
Maintainer: LI Wu <liwu@staff.shu.edu.cn>

Diff between CGE versions 0.2.5 dated 2019-12-07 and 0.2.8 dated 2020-01-24

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Thu, 23 Jan 2020

Package rngtools updated to version 1.5 with previous version 1.4 dated 2019-07-01

Title: Utility Functions for Working with Random Number Generators
Description: Provides a set of functions for working with Random Number Generators (RNGs). In particular, a generic S4 framework is defined for getting/setting the current RNG, or RNG data that are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.
Author: Renaud Gaujoux [aut, cre], Max Kuhn [ctb]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>

Diff between rngtools versions 1.4 dated 2019-07-01 and 1.5 dated 2020-01-23

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Package TcGSA updated to version 0.12.7 with previous version 0.12.4 dated 2019-04-30

Title: Time-Course Gene Set Analysis
Description: Implementation of Time-course Gene Set Analysis (TcGSA), a method for analyzing longitudinal gene-expression data at the gene set level. Method is detailed in: Hejblum, Skinner & Thiebaut (2015) <doi: 10.1371/journal.pcbi.1004310>.
Author: Boris P Hejblum [aut, cre], Damien Chimits [aut], Anthony Devaux [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>

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Package smoothr updated to version 0.1.2 with previous version 0.1.1 dated 2018-12-11

Title: Smooth and Tidy Spatial Features
Description: Tools for smoothing and tidying spatial features (i.e. lines and polygons) to make them more aesthetically pleasing. Smooth curves, fill holes, and remove small fragments from lines and polygons.
Author: Matthew Strimas-Mackey [aut, cre] (<https://orcid.org/0000-0001-8929-7776>)
Maintainer: Matthew Strimas-Mackey <mstrimas@gmail.com>

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Package primerTree updated to version 1.0.5 with previous version 1.0.4 dated 2018-12-19

Title: Visually Assessing the Specificity and Informativeness of Primer Pairs
Description: Identifies potential target sequences for a given set of primers and generates phylogenetic trees annotated with the taxonomies of the predicted amplification products.
Author: Jim Hester
Maintainer: Jim Hester <james.f.hester@gmail.com>

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Package LPWC updated to version 1.0.0 with previous version 0.99.5 dated 2019-03-12

Title: Lag Penalized Weighted Correlation for Time Series Clustering
Description: Computes a time series distance measure for clustering based on weighted correlation and introduction of lags. The lags capture delayed responses in a time series dataset. The timepoints must be specified. T. Chandereng, A. Gitter (2020) <doi:10.1186/s12859-019-3324-1>.
Author: Thevaa Chandereng [aut, cre, cph] (<https://orcid.org/0000-0003-4078-9176>), Anthony Gitter [aut, cph] (<https://orcid.org/0000-0002-5324-9833>)
Maintainer: Thevaa Chandereng <chandereng@wisc.edu>

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Package gllvm updated to version 1.2.1 with previous version 1.2.0 dated 2019-12-20

Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm). Estimation is performed using either Laplace approximation method or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>). For details see Niku et al. (2019) <doi:10.1371/journal.pone.0216129>.
Author: Jenni Niku, Wesley Brooks, Riki Herliansyah, Francis K.C. Hui, Sara Taskinen, David I. Warton
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>

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Package epiR updated to version 1.0-11 with previous version 1.0-10 dated 2019-11-24

Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp, Mathew Jay and Charles Reynard.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>

Diff between epiR versions 1.0-10 dated 2019-11-24 and 1.0-11 dated 2020-01-23

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Package butcher updated to version 0.1.2 with previous version 0.1.1 dated 2020-01-07

Title: Model Butcher
Description: Provides a set of five S3 generics to axe components of fitted model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut, cre] (<https://orcid.org/0000-0001-7217-4702>), Davis Vaughan [aut], Max Kuhn [aut], Alex Hayes [aut]
Maintainer: Joyce Cahoon <joyceyu48@gmail.com>

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Package colourvalues updated to version 0.3.2 with previous version 0.3.1 dated 2019-11-15

Title: Assigns Colours to Values
Description: Maps one of the viridis colour palettes, or a user-specified palette to values. Viridis colour maps are created by Stéfan van der Walt and Nathaniel Smith, and were set as the default palette for the 'Python' 'Matplotlib' library <https://matplotlib.org/>. Other palettes available in this library have been derived from 'RColorBrewer' <https://CRAN.R-project.org/package=RColorBrewer> and 'colorspace' <https://CRAN.R-project.org/package=colorspace> packages.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>

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Package yardstick updated to version 0.0.5 with previous version 0.0.4 dated 2019-08-26

Title: Tidy Characterizations of Model Performance
Description: Tidy tools for quantifying how well model fits to a data set such as confusion matrices, class probability curve summaries, and regression metrics (e.g., RMSE).
Author: Max Kuhn [aut], Davis Vaughan [aut, cre], RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>

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Package SamplingStrata updated to version 1.5 with previous version 1.4-1 dated 2019-04-22

Title: Optimal Stratification of Sampling Frames for Multipurpose Sampling Surveys
Description: In the field of stratified sampling design, this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample cost under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated applying the Bethel-Chromy algorithm to calculate the sampling size satisfying precision constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. Functions for the execution of the genetic algorithm are a modified version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Marco Ballin, Hanjo Odendaal, Daniela Pagliuca, Egon Willighagen, Diego Zardetto
Maintainer: Giulio Barcaroli <gbarcaroli@gmail.com>

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