Sat, 14 Dec 2019

New package RLumModel with initial version 0.2.5
Package: RLumModel
Type: Package
Title: Solving Ordinary Differential Equations to Understand Luminescence
Version: 0.2.5
Date: 2019-12-11
Author: Johannes Friedrich [aut, trl, cre] (<https://orcid.org/0000-0002-0805-9547>), Sebastian Kreutzer [aut, ths] (<https://orcid.org/0000-0002-0734-2199>), Christoph Schmidt [aut, ths] (<https://orcid.org/0000-0002-2309-3209>)
Authors@R: c( person("Johannes", "Friedrich", role = c("aut","trl","cre"), comment = c(ORCID = "0000-0002-0805-9547"), email = "johannes.friedrich@posteo.de"), person("Sebastian", "Kreutzer", role = c("aut", "ths"), comment = c(ORCID = "0000-0002-0734-2199")), person("Christoph", "Schmidt", role = c("aut", "ths"), comment = c(ORCID = "0000-0002-2309-3209")) )
Maintainer: Johannes Friedrich <johannes.friedrich@posteo.de>
Description: A collection of functions to simulate luminescence signals in quartz and Al2O3 based on published models.
Contact: Package Developer Team <developer@model.r-luminescence.de>
License: GPL-3
Depends: R (>= 3.4.0), utils, Luminescence (>= 0.9.0)
Imports: deSolve (>= 1.21), methods, Rcpp (>= 1.0.1)
Suggests: knitr (>= 1.22), kableExtra (>= 1.1.0), testthat (>= 2.1.1), rmarkdown (>= 1.12)
URL: https://CRAN.R-project.org/package=RLumModel
Collate: RLumModel-package.R RcppExports.R calc_signal.R calc_concentrations.R create_DRT.sequence.R create_SAR.sequence.R extract_pars.R model_LuminescenceSignals.R read_SEQ2R.R set_pars.R simulate_CW_OSL.R simulate_heating.R simulate_illumination.R simulate_irradiation.R simulate_LM_OSL.R simulate_pause.R simulate_RF.R simulate_RF_and_heating.R simulate_TL.R translate_sequence.R
RoxygenNote: 7.0.2
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
LinkingTo: Rcpp (>= 1.0.1), RcppArmadillo (>= 0.9.400.2.0)
NeedsCompilation: yes
Packaged: 2019-12-11 21:50:27 UTC; kreutzer
Repository: CRAN
Date/Publication: 2019-12-15 00:10:03 UTC

More information about RLumModel at CRAN
Permanent link

Package Rdpack updated to version 0.11-1 with previous version 0.11-0 dated 2019-04-14

Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.
Author: Georgi N. Boshnakov [aut, cre], Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package BayesPostEst updated to version 0.2.0 with previous version 0.1.0 dated 2019-10-06

Title: Generate Postestimation Quantities for Bayesian MCMC Estimation
Description: An implementation of functions to generate and plot postestimation quantities after estimating Bayesian regression models using Markov chain Monte Carlo (MCMC). Functionality includes the estimation of the Precision-Recall curves (see Beger, 2016 <doi:10.2139/ssrn.2765419>), the implementation of the observed values method of calculating predicted probabilities by Hanmer and Kalkan (2013) <doi:10.1111/j.1540-5907.2012.00602.x>, the implementation of the average value method of calculating predicted probabilities (see King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>), and the generation and plotting of first differences to summarize typical effects across covariates (see Long 1997, ISBN:9780803973749; King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>). This package can be used with MCMC output generated by any Bayesian estimation tool including 'JAGS', 'BUGS', 'MCMCpack', and 'Stan'.
Author: Johannes Karreth [aut] (<https://orcid.org/0000-0003-4586-7153>), Shana Scogin [aut, cre] (<https://orcid.org/0000-0002-7801-853X>), Rob Williams [aut] (<https://orcid.org/0000-0001-9259-3883>), Andreas Beger [aut] (<https://orcid.org/0000-0003-1883-3169>), Myunghee Lee [ctb], Neil Williams [ctb]
Maintainer: Shana Scogin <shanarscogin@gmail.com>

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Package ushr updated to version 0.2.0 with previous version 0.1.0 dated 2019-10-09

Title: Understanding Suppression of HIV
Description: Analyzes longitudinal data of HIV decline in patients on antiretroviral therapy using the canonical biphasic exponential decay model (pioneered, for example, by work in Perelson et al. (1997) <doi:10.1038/387188a0>; and Wu and Ding (1999) <doi:10.1111/j.0006-341X.1999.00410.x>). Model fitting and parameter estimation are performed, with additional options to calculate the time to viral suppression. Plotting and summary tools are also provided for fast assessment of model results.
Author: Sinead E. Morris [aut, cre] (<https://orcid.org/0000-0001-8626-1698>), Luise Dziobek-Garrett [ctb], Andrew Yates [ctb]
Maintainer: Sinead E. Morris <sinead.morris@columbia.edu>

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Package comperes updated to version 0.2.3 with previous version 0.2.2 dated 2019-01-12

Title: Manage Competition Results
Description: Tools for storing and managing competition results. Competition is understood as a set of games in which players gain some abstract scores. There are two ways for storing results: in long (one row per game-player) and wide (one row per game with fixed amount of players) formats. This package provides functions for creation and conversion between them. Also there are functions for computing their summary and Head-to-Head values for players. They leverage grammar of data manipulation from 'dplyr'.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>

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Package rcheology updated to version 3.6.2.0 with previous version 3.6.1.0 dated 2019-07-07

Title: Data on Base Packages for Current and Previous Versions of R
Description: Provides a dataset of functions in all base packages of R versions 1.0.1 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

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Package tidytree updated to version 0.3.1 with previous version 0.3.0 dated 2019-11-21

Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Bradley Jones [ctb], Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package SPOT updated to version 2.0.5 with previous version 2.0.4 dated 2019-05-17

Title: Sequential Parameter Optimization Toolbox
Description: A set of tools for model based optimization and tuning of algorithms. It includes surrogate models, optimizers and design of experiment approaches. The main interface is spot, which uses sequentially updated surrogate models for the purpose of efficient optimization. The main goal is to ease the burden of objective function evaluations, when a single evaluation requires a significant amount of resources.
Author: Thomas Bartz-Beielstein [aut], Joerg Stork [aut], Martin Zaefferer [aut, cre], Margarita Rebolledo [ctb], Christian Lasarczyk [ctb], Joerg Ziegenhirt [ctb], Wolfgang Konen [ctb], Oliver Flasch [ctb], Patrick Koch [ctb], Martina Friese [ctb], Lorenzo Gentile [ctb], Frederik Rehbach [aut]
Maintainer: Martin Zaefferer <martin.zaefferer@gmx.de>

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Package robustHD updated to version 0.6.1 with previous version 0.6.0 dated 2019-12-09

Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear model selection techniques based on least angle regression and sparse regression.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>

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Package RMySQL updated to version 0.10.18 with previous version 0.10.17 dated 2019-03-04

Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), David James [aut], Saikat DebRoy [aut], Hadley Wickham [aut], Jeffrey Horner [aut], RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package RDS updated to version 0.9-2 with previous version 0.9-0 dated 2019-05-31

Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation with data collected using Respondent-Driven Sampling. This includes Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential Sampling estimator. The package is part of the "RDS Analyst" suite of packages for the analysis of respondent-driven sampling data. See Gile and Handcock (2010) <doi:10.1111/j.1467-9531.2010.01223.x> and Gile and Handcock (2015) <doi:10.1111/rssa.12091>.
Author: Mark S. Handcock [aut, cre], Krista J. Gile [aut], Ian E. Fellows [aut], W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>

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Package osmdata updated to version 0.1.2 with previous version 0.1.1 dated 2019-05-22

Title: Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server and processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre], Bob Rudis [aut], Robin Lovelace [aut], Maƫlle Salmon [aut], Andrew Smith [ctb], James Smith [ctb], Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Finkelstein Noam [ctb, cph] (Author of included stub.R code), Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>

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Package multinets updated to version 0.2.2 with previous version 0.2.1 dated 2018-07-07

Title: Multilevel Networks Analysis
Description: Analyze multilevel networks as described in Lazega et al (2008) <doi:10.1016/j.socnet.2008.02.001> and in Lazega and Snijders (2016, ISBN:978-3-319-24520-1). The package was developed essentially as an extension to 'igraph'.
Author: Neylson Crepalde [aut, cre]
Maintainer: Neylson Crepalde <neylsoncrepalde@gmail.com>

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Package MPTinR updated to version 1.12.0 with previous version 1.11.0 dated 2018-06-23

Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre], David Kellen [aut], Quentin Gronau [aut], Christian Mueller [ctb], Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>

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Package caseMatch updated to version 1.0.8 with previous version 1.0.7 dated 2017-01-06

Title: Identify Similar Cases for Qualitative Case Studies
Description: Allows users to identify similar cases for qualitative case studies using statistical matching methods.
Author: Rich Nielsen
Maintainer: Rich Nielsen <rnielsen@mit.edu>

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Package broom updated to version 0.5.3 with previous version 0.5.2 dated 2019-04-07

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 QuantumOps updated to version 3.0.0 with previous version 2.5.3 dated 2019-08-30

Title: Performs Common Linear Algebra Operations Used in Quantum Computing and Implements Quantum Algorithms
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help learn quantum mechanics and algorithms. Can create arbitrarily sized kets and bras and implements quantum gates, inner products, and tensor products. Creates arbitrarily controlled versions of all gates and can simulate complete or partial measurements of kets. Has functionality to convert functions into equivalent quantum gates and model quantum noise. Includes larger applications, such as Steane error correction <DOI:10.1103/physrevlett.77.793>, Quantum Fourier Transform and Shor's algorithm (Shor 1999), Grover's algorithm (1996), Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018) <arXiv:1804.00633>.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>

Diff between QuantumOps versions 2.5.3 dated 2019-08-30 and 3.0.0 dated 2019-12-14

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Package pca3d updated to version 0.10.1 with previous version 0.10 dated 2017-02-17

Title: Three Dimensional PCA Plots
Description: Functions simplifying presentation of PCA models in a 3D interactive representation using 'rgl'.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>

Diff between pca3d versions 0.10 dated 2017-02-17 and 0.10.1 dated 2019-12-14

 DESCRIPTION        |    7 ++++---
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 R/pca2d.R          |    2 +-
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 inst/doc/pca3d.pdf |binary
 9 files changed, 35 insertions(+), 31 deletions(-)

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Package Numero updated to version 1.4.0 with previous version 1.3.3 dated 2019-10-31

Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut], Stefan Mutter [aut], Aaron E. Casey [aut], Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>

Diff between Numero versions 1.3.3 dated 2019-10-31 and 1.4.0 dated 2019-12-14

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Package MetStaT (with last version 1.0) was removed from CRAN

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

2013-11-18 1.0

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Package highlight updated to version 0.4.7.4 with previous version 0.4.7.3 dated 2019-12-01

Title: Syntax Highlighter
Description: Syntax highlighter for R code based on the results of the R parser. Rendering in HTML and latex markup. Custom Sweave driver performing syntax highlighting of R code chunks.
Author: Romain Francois [aut, cre], Andre Simon [ctb]
Maintainer: ORPHANED

Diff between highlight versions 0.4.7.3 dated 2019-12-01 and 0.4.7.4 dated 2019-12-14

 DESCRIPTION      |    6 +++---
 MD5              |    6 +++---
 src/Makevars     |    1 +
 src/Makevars.win |    1 +
 4 files changed, 8 insertions(+), 6 deletions(-)

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