Fri, 17 Jul 2020

Package pspline.inference updated to version 1.0.2 with previous version 0.24 dated 2020-07-08

Title: Estimation of Characteristics of Seasonal and Sporadic Infectious Disease Outbreaks Using Generalized Additive Modeling with Penalized Basis Splines
Description: Inference of infectious disease outcomes using generalized additive (mixed) models with penalized basis splines (P-Splines). See <https://medrxiv.org/cgi/content/short/2020.07.14.20138180v1>.
Author: Ben Artin [aut, cre, cph]
Maintainer: Ben Artin <ben@artins.org>

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Package ariExtra updated to version 0.2.10 with previous version 0.2.9 dated 2020-07-07

Title: Tools for Creating Automated Courses
Description: Leverages the 'ari' package and other tools to create automated courses from slides and a script. Also, uploads these to 'YouTube' and other services using 'tuber' package.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package RcppArmadillo updated to version 0.9.900.2.0 with previous version 0.9.900.1.0 dated 2020-06-09

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 SightabilityModel updated to version 1.4.0 with previous version 1.3 dated 2014-10-04

Title: Wildlife Sightability Modeling
Description: Uses logistic regression to model the probability of detection as a function of covariates. This model is then used with observational survey data to estimate population size, while accounting for uncertain detection. See Steinhorst and Samuel (1989).
Author: Fieberg John [aut], Schwarz Carl James [aut, cre]
Maintainer: Schwarz Carl James <cschwarz.stat.sfu.ca@gmail.com>

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Package etasFLP updated to version 2.1.0 with previous version 2.0.0 dated 2020-05-05

Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes for Earthquake Description
Description: Estimation of the components of an ETAS (Epidemic Type Aftershock Sequence) model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive). New version 2.0.0: covariates have been introduced to explain the effects of external factors on the induced seismicity; the parametrization has been changed; Chiodi, Adelfio (2017)<doi:10.18637/jss.v076.i03>.
Author: Marcello Chiodi [aut, cre], Giada Adelfio [aut]
Maintainer: Marcello Chiodi <marcello.chiodi@unipa.it>

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Package eatDB updated to version 0.4.1 with previous version 0.4.0 dated 2020-04-07

Title: Spreadsheet Interface for Relational Databases
Description: Use 'SQLite3' as a database system via a complete SQL free R interface, treating the data as if it was a single spreadsheet.
Author: Benjamin Becker [aut, cre]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>

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Package climaemet updated to version 0.2.0 with previous version 0.1.0 dated 2020-07-07

Title: Climate AEMET Tools
Description: Tools to download the climatic data of the Spanish Meteorological Agency (AEMET) directly from R using their API <https://opendata.aemet.es/> and create scientific graphs (climate charts, trend analysis of climate time series, temperature and precipitation anomalies maps, warming stripes graphics, climatograms, etc.).
Author: Manuel Pizarro [aut, cre]
Maintainer: Manuel Pizarro <m.pizarro@csic.es>

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Package specs updated to version 0.1.1 with previous version 0.1.0 dated 2020-07-06

Title: Single-Equation Penalized Error-Correction Selector (SPECS)
Description: Implementation of SPECS, your favourite Single-Equation Penalized Error-Correction Selector developed in Smeekes and Wijler (2020) <arXiv:1809.08889>. SPECS provides a fully automated estimation procedure for large and potentially (co)integrated datasets. The dataset in levels is converted to a conditional error-correction model, either by the user or by means of the functions included in this package, and various specialised forms of penalized regression can be applied to the model. Automated options for initializing and selecting a sequence of penalties, as well as the construction of penalty weights via an initial estimator, are available. Moreover, the user may choose from a number of pre-specified deterministic configurations to further simplify the model building process.
Author: Etienne Wijler [aut, cre], Stephan Smeekes [aut] (<https://orcid.org/0000-0002-0157-639X>)
Maintainer: Etienne Wijler <e.wijler@maastrichtuniversity.nl>

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Package set6 updated to version 0.1.6 with previous version 0.1.5 dated 2020-07-01

Title: R6 Mathematical Sets Interface
Description: An object-oriented package for mathematical sets, upgrading the current gold-standard {sets}. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>), Franz Kiraly [aut]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>

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Package CAST updated to version 0.4.2 with previous version 0.4.1 dated 2020-05-19

Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. This package includes functions to improve spatial-temporal modelling tasks using 'caret'. It prepares data for Leave-Location-Out and Leave-Time-Out cross-validation which are target-oriented validation strategies for spatial-temporal models. To decrease overfitting and improve model performances, the package implements a forward feature selection that selects suitable predictor variables in view to their contribution to the target-oriented performance.
Author: Hanna Meyer [cre, aut], Chris Reudenbach [ctb], Marvin Ludwig [ctb], Thomas Nauss [ctb], Edzer Pebesma [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>

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Package leastcostpath updated to version 1.7.4 with previous version 1.3.6 dated 2020-05-15

Title: Modelling Pathways and Movement Potential Within a Landscape (Version 1.7.4)
Description: Provides functionality to calculate cost surfaces based on slope (e.g. Herzog, 2010; Llobera and Sluckin, 2007 <doi:10.1016/j.jtbi.2007.07.020>; París Roche, 2002; Tobler, 1993), traversing slope (Bell and Lock, 2000), and landscape features (Llobera, 2000) to be used when modelling pathways and movement potential within a landscape (e.g. Llobera, 2015; Verhagen, 2013; White and Barber, 2012 <doi:10.1016/j.jas.2012.04.017>).
Author: Joseph Lewis [aut, cre]
Maintainer: Joseph Lewis <josephlewis1992@gmail.com>

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Package dialrjars updated to version 8.12.6 with previous version 8.12.0 dated 2020-03-23

Title: Required 'libphonenumber' jars for the 'dialr' Package
Description: Collects 'libphonenumber' jars required for the 'dialr' package.
Author: Danny Smith [aut, cre], Google Inc. [ctb, cph] (libphonenumber), Vonage Holdings Corp. [ctb, cph] (libphonenumber), Ian Galpin [ctb, cph] (libphonenumber), Ben Gertzfield [ctb, cph] (libphonenumber)
Maintainer: Danny Smith <danny@gorcha.org>

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Package vdar updated to version 0.1.3 with previous version 0.1.2-1 dated 2020-03-19

Title: Discriminant Analysis Incorporating Individual Uncertainties
Description: The qda() function from package 'MASS' is extended to calculate a weighted linear (LDA) and quadratic discriminant analysis (QDA) by changing the group variances and group means based on cell-wise uncertainties. The uncertainties can be derived e.g. through relative errors for each individual measurement (cell), not only row-wise or column-wise uncertainties. The method can be applied compositional data (e.g. portions of substances, concentrations) and non-compositional data.
Author: Solveig Pospiech [aut, cre], K. Gerald van den Boogaart [ctb]
Maintainer: Solveig Pospiech <s.pospiech@hzdr.de>

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Package rehh updated to version 3.1.2 with previous version 3.1.1 dated 2020-06-19

Title: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests
Description: Population genetic data such as 'Single Nucleotide Polymorphisms' (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are also included to facilitate visualization and interpretation of these statistics. Due to changes in the API, albeit mostly minor, versions 3.X are not compatible with versions 2.0.X. Note: optionally, vcf files can be imported using package vcfR. That package is currently removed from CRAN, but can still be installed from <https://github.com/knausb/vcfR> following instructions there.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Alexander Klassmann <rehh@oneoverx.eu>

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Package configr updated to version 0.3.5 with previous version 0.3.4 dated 2018-11-13

Title: An Implementation of Parsing and Writing Configuration File (JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre] (<https://orcid.org/0000-0003-2349-208X>)
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>

Diff between configr versions 0.3.4 dated 2018-11-13 and 0.3.5 dated 2020-07-17

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Package sbm updated to version 0.2.1 with previous version 0.2.0 dated 2020-07-07

Title: Stochastic Blockmodels
Description: A collection of tools and function to adjust a variety of stochastic blockmodels (SBM). Support at the moment Simple and Bipartite SBM (undirected and directed) for Bernoulli, Poisson and Gaussian emission laws of the edges as described in Léger, 2016 <arxiv:1602.07587>.
Author: Julien Chiquet [aut, cre] (<https://orcid.org/0000-0002-3629-3429>), Sophie Donnet [aut], großBM team [ctb], Pierre Barbillon [ctb] (<https://orcid.org/0000-0002-7766-7693>)
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>

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Package mlr3misc updated to version 0.4.0 with previous version 0.3.0 dated 2020-06-03

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>

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Package graphsim updated to version 1.0.1 with previous version 1.0.0 dated 2020-07-02

Title: Simulate Expression Data from 'igraph' Networks
Description: Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to be considered as a confounding variable when simulating gene expression data to test the performance of genomic analyses.
Author: S. Thomas Kelly [ctb], S. Thomas Kelly [aut, cre], Michael A. Black [aut, ths], Robrecht Cannoodt [ctb], Jason Cory Brunson [ctb]
Maintainer: S. Thomas Kelly <tom.kelly@riken.jp>

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Package fDMA updated to version 2.2.6 with previous version 2.2.5 dated 2020-04-03

Title: Dynamic Model Averaging and Dynamic Model Selection for Continuous Outcomes
Description: Allows to estimate dynamic model averaging, dynamic model selection and median probability model. The original methods are implemented, as well as, selected further modifications of these methods. In particular the user might choose between recursive moment estimation and exponentially moving average for variance updating. Inclusion probabilities might be modified in a way using 'Google Trends'. The code is written in a way which minimises the computational burden (which is quite an obstacle for dynamic model averaging if many variables are used). For example, this package allows for parallel computations and Occam's window approach. The package is designed in a way that is hoped to be especially useful in economics and finance. Main reference: Raftery, A.E., Karny, M., Ettler, P. (2010) <doi:10.1198/TECH.2009.08104>.
Author: Krzysztof Drachal [aut, cre] (Faculty of Economic Sciences, University of Warsaw, Poland)
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>

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Package cumSeg updated to version 1.3 with previous version 1.2 dated 2019-01-18

Title: Change Point Detection in Genomic Sequences
Description: Estimation of number and location of change points in mean-shift (piecewise constant) models. Particularly useful (but not confined) to model genomic sequences of continuous measurements.
Author: Vito M.R. Muggeo
Maintainer: Vito M.R. Muggeo <vito.muggeo@unipa.it>

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Package boral updated to version 1.9 with previous version 1.8.1 dated 2020-06-05

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 [aut, cre], Wade Blanchard [aut]
Maintainer: Francis K.C. Hui <fhui28@gmail.com>

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Package rMVP updated to version 1.0.3 with previous version 1.0.0 dated 2020-05-07

Title: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool
Description: A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can (1) effectively process large data, (2) rapidly evaluate population structure, (3) efficiently estimate variance components several algorithms, (4) implement parallel-accelerated association tests of markers three methods, (5) globally efficient design on GWAS process computing, (6) enhance visualization of related information. 'rMVP' contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>) and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX (Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>, R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and 'SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/journal.pone.0107684>), and HE regression (Xiang Zhou (2017) <DOI:10.1214/17-AOAS1052>).
Author: Lilin Yin [aut], Haohao Zhang [aut], Zhenshuang Tang [aut], Jingya Xu [aut], Dong Yin [aut], Zhiwu Zhang [aut], Xiaohui Yuan [aut], Mengjin Zhu [aut], Shuhong Zhao [aut], Xinyun Li [aut], Qishan Wang [ctb], Feng Tian [ctb], Hyunmin Kang [ctb], Xiang Zhou [ctb], Xiaolei Liu [cre, aut, cph]
Maintainer: Xiaolei Liu <xiaoleiliu@mail.hzau.edu.cn>

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More information about rMVP at CRAN
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Package SDMtune updated to version 1.1.1 with previous version 1.1.0 dated 2020-03-11

Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the evaluation of species distribution models (SDMs). The package implements functions for data driven variable selection and model tuning and includes numerous utilities to display the results. All the functions used to select variables or to tune model hyperparameters have an interactive real-time chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>), Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>), Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>), Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>

Diff between SDMtune versions 1.1.0 dated 2020-03-11 and 1.1.1 dated 2020-07-17

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Package RCzechia updated to version 1.5.1 with previous version 1.5.0 dated 2020-05-04

Title: Spatial Objects of the Czech Republic
Description: Administrative regions and other spatial objects of the Czech Republic.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>

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Package raster updated to version 3.3-13 with previous version 3.3-7 dated 2020-06-27

Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of spatial data. The package implements basic and high-level functions for raster data and for vector data operations such as intersections. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>), Jacob van Etten [ctb], Michael Sumner [ctb], Joe Cheng [ctb], Dan Baston [ctb], Andrew Bevan [ctb], Roger Bivand [ctb], Lorenzo Busetto [ctb], Mort Canty [ctb], David Forrest [ctb], Aniruddha Ghosh [ctb], Duncan Golicher [ctb], Josh Gray [ctb], Jonathan A. Greenberg [ctb], Paul Hiemstra [ctb], Kassel Hingee [ctb], Institute for Mathematics Applied Geosciences [cph], Charles Karney [ctb], Matteo Mattiuzzi [ctb], Steven Mosher [ctb], Jakub Nowosad [ctb], Edzer Pebesma [ctb], Oscar Perpinan Lamigueiro [ctb], Etienne B. Racine [ctb], Barry Rowlingson [ctb], Ashton Shortridge [ctb], Bill Venables [ctb], Rafael Wueest [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

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Package assertive updated to version 0.3-5.1 with previous version 0.3-5 dated 2016-12-30

Title: Readable Check Functions to Ensure Code Integrity
Description: Lots of predicates (is_* functions) to check the state of your variables, and assertions (assert_* functions) to throw errors if they aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: ORPHANED

Diff between assertive versions 0.3-5 dated 2016-12-30 and 0.3-5.1 dated 2020-07-17

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Package runittotestthat (with last version 0.0-2) was removed from CRAN

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

2015-06-24 0.0-2

Permanent link
Package Require updated to version 0.0.5 with previous version 0.0.4 dated 2020-06-05

Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that wraps 'install.packages', 'remotes::install_github', 'versions::install.versions', and 'base::require' that allows for reproducible workflows. As with other functions in a reproducible workflow, this package emphasizes functions that return the same result whether it is the first or subsequent times running the function.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>), Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>

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Package hR updated to version 0.2.2 with previous version 0.2.1 dated 2019-11-10

Title: Toolkit for Data Analytics in Human Resources
Description: Transform and analyze workforce data in meaningful ways for human resources (HR) analytics. Get started with workforce planning using a simple Shiny app.
Author: Dale Kube [aut, cre]
Maintainer: Dale Kube <dkube@uwalumni.com>

Diff between hR versions 0.2.1 dated 2019-11-10 and 0.2.2 dated 2020-07-17

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Package dipsaus updated to version 0.0.9 with previous version 0.0.8 dated 2020-06-23

Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using 'RcppParallel' and 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <zhengjia.wang@rice.edu>

Diff between dipsaus versions 0.0.8 dated 2020-06-23 and 0.0.9 dated 2020-07-17

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Package MultiMeta (with last version 0.1) was removed from CRAN

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

2015-01-15 0.1

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Package TKF (with last version 0.0.8) was removed from CRAN

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

2015-04-18 0.0.8
2015-02-10 0.0.3

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Package assertive.reflection updated to version 0.0-4.1 with previous version 0.0-4 dated 2016-12-30

Title: Assertions for Checking the State of R
Description: A set of predicates and assertions for checking the state and capabilities of R, the operating system it is running on, and the IDE being used. This is mainly for use by other package developers who want to include run-time testing features in their own packages. End-users will usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: ORPHANED

Diff between assertive.reflection versions 0.0-4 dated 2016-12-30 and 0.0-4.1 dated 2020-07-17

 DESCRIPTION                              |   11 +++++------
 MD5                                      |    4 ++--
 tests/testthat/test-r-has-capabilities.R |    8 +++++++-
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Package goxygen (with last version 1.0.2) was removed from CRAN

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

2020-07-03 1.0.2

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