Tue, 30 Oct 2018

Package shallot updated to version 0.4.5 with previous version 0.4.4 dated 2018-06-30

Title: Random Partition Distribution Indexed by Pairwise Information
Description: Implementations are provided for the models described in the paper D. B. Dahl, R. Day, J. Tsai (2017) <DOI:10.1080/01621459.2016.1165103>. The Ewens, Ewens-Pitman, Ewens attraction, Ewens-Pitman attraction, and ddCRP distributions are available for prior and posterior simulation. Posterior simulation is based on a user-supplied likelihood. Supporting functions for partition estimation and plotting are also provided.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between shallot versions 0.4.4 dated 2018-06-30 and 0.4.5 dated 2018-10-30

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Package malariaAtlas updated to version 0.0.3 with previous version 0.0.2 dated 2018-09-11

Title: An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'
Description: A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://map.ox.ac.uk/> servers as well as utility functions for plotting the downloaded data.
Author: Daniel Pfeffer [aut] (<https://orcid.org/0000-0002-2204-3488>), Tim Lucas [aut, cre] (<https://orcid.org/0000-0003-4694-8107>), Daniel May [aut] (<https://orcid.org/0000-0003-0005-2452>), Suzanne Keddie [aut] (<https://orcid.org/0000-0003-1254-7794>), Jen Rozier [aut] (<https://orcid.org/0000-0002-2610-7557>), Harry Gibson [aut] (<https://orcid.org/0000-0001-6779-3250>), Nick Golding [ctb], David Smith [ctb]
Maintainer: Tim Lucas <timcdlucas@gmail.com>

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Package jetpack updated to version 0.4.0 with previous version 0.3.1 dated 2018-07-25

Title: A Friendly Package Manager
Description: Manage project dependencies from your DESCRIPTION file. Create a reproducible virtual environment with minimal additional files in your project. Provides tools to add, remove, and update dependencies as well as install existing dependencies with a single function.
Author: Andrew Kane [aut, cre]
Maintainer: Andrew Kane <andrew@chartkick.com>

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Package filesstrings updated to version 3.0.0 with previous version 2.7.0 dated 2018-09-03

Title: Handy File and String Manipulation
Description: This started out as a package for file and string manipulation. Since then, the 'fs' and 'strex' packages emerged, offering functionality previously given by this package (but it's done better in these new ones). Those packages have hence almost pushed 'filesstrings' into extinction. However, it still has a small number of unique, handy file manipulation functions which can be seen in the vignette. One example is a function to remove spaces from all file names in a directory.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>), Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package rscorecard updated to version 0.11.0 with previous version 0.10.0 dated 2018-10-01

Title: A Method to Download Department of Education College Scorecard Data
Description: A method to download Department of Education College Scorecard data using the public API <https://collegescorecard.ed.gov/data/documentation/>. It is based on the 'dplyr' model of piped commands to select and filter data in a single chained function call. An API key from the U.S. Department of Education is required.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@virginia.edu>

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Package RCzechia updated to version 1.3.1 with previous version 1.3.0 dated 2018-08-07

Title: Spatial Objects of the Czech Republic
Description: Administrative regions, rivers and water bodies of the Czech Republic.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>

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Package lemon updated to version 0.4.2 with previous version 0.4.1 dated 2018-06-28

Title: Freshing Up your 'ggplot2' Plots
Description: Functions for working with legends and axis lines of 'ggplot2', facets that repeat axis lines on all panels, and some 'knitr' extensions.
Author: Stefan McKinnon Edwards [aut, ctb, cre] (<https://orcid.org/0000-0002-4628-8148>), Baptiste Auguie [ctb] (For g_legend and grid_arrange_shared_legend), Shaun Jackman [ctb] (For grid_arrange_shared_legend), Hadley Wickham [ctb] (ggplot2 functions), Winston Chang [ctb] (ggplot2 functions)
Maintainer: Stefan McKinnon Edwards <sme@iysik.com>

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New package matrixNormal with initial version 0.0.0
Package: matrixNormal
Version: 0.0.0
Date: 2018-10-26
Type: Package
Title: The Matrix Normal Distribution
Authors@R: person("Paul", "Hargarten", email = "hargartenp@vcu.edu", role = c("aut", "cre"))
Depends: R (>= 3.5.0)
Imports: mvtnorm (>= 1.0.8), utils (>= 3.5.0)
Suggests: datasets (>= 3.5.0), matrixcalc (>= 1.0.3), stats (>= 3.5.0), testthat (>= 2.0.1)
Description: Computes densities, probabilities, and random deviates of the Matrix Normal (Iranmanesh et.al. (2010) <doi:10.7508/ijmsi.2010.02.004>). Also includes simple but useful matrix functions. See R package help file for more information.
License: GPL-3
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/phargarten2/matrixNormal/issues
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-26 17:54:08 UTC; pablo
Author: Paul Hargarten [aut, cre]
Maintainer: Paul Hargarten <hargartenp@vcu.edu>
Repository: CRAN
Date/Publication: 2018-10-30 19:10:02 UTC

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New package LearningRlab with initial version 1.3
Package: LearningRlab
Version: 1.3
Date: 2018-10-23
Title: Statistical Learning Functions
Authors@R: c( person("Dennis","Monheimius", role = c("aut"), email = "dennis.monhemimius@edu.uah.es"), person("Eduardo","Benito", role = c("aut","cre"), email = "eduardo.benito@edu.uah.es"), person("Juan Jose Cuadrado", role = c("aut"), email = "jjcg@uah.es"), person("Universidad de Alcala de Henares", role = c("aut")) )
Author: Dennis Monheimius [aut], Eduardo Benito [aut, cre], Juan Jose Cuadrado [aut], Universidad de Alcala de Henares [aut]
Maintainer: Eduardo Benito <eduardo.benito@edu.uah.es>
Depends: magick, crayon
Suggests: knitr
Description: Aids in learning statistical functions incorporating the result of calculus done with each function and how they are obtained, that is, which equations and variables are used. Also for all these equations and their related variables detailed explanations and interactive exercises are also included. All these characteristics allow to the package user to improve the learning of statistics basics by means of their use.
License: Unlimited
VignetteBuilder: knitr
NeedsCompilation: yes
Type: Package
Packaged: 2018-10-27 14:55:01 UTC; edube
Repository: CRAN
Date/Publication: 2018-10-30 19:10:05 UTC

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Package graphframes updated to version 0.1.2 with previous version 0.1.1 dated 2018-06-21

Title: Interface for 'GraphFrames'
Description: A 'sparklyr' <https://spark.rstudio.com/> extension that provides an R interface for 'GraphFrames' <https://graphframes.github.io/>. 'GraphFrames' is a package for 'Apache Spark' that provides a DataFrame-based API for working with graphs. Functionality includes motif finding and common graph algorithms, such as PageRank and Breadth-first search.
Author: Kevin Kuo [aut, cre] (<https://orcid.org/0000-0001-7803-7901>)
Maintainer: Kevin Kuo <kevin.kuo@rstudio.com>

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Package GDINA updated to version 2.2.0 with previous version 2.1.15 dated 2018-06-07

Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling for both dichotomous and polytomous responses. Various cognitive diagnosis models can be estimated, include the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7>, the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070>, and many other models they subsume. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.
Author: Wenchao Ma [aut, cre, cph], Jimmy de la Torre [aut, cph], Miguel Sorrel [ctb]
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>

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Package chngpt updated to version 2018.10-17 with previous version 2018.7-25 dated 2018-08-07

Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong [cre], Zonglin He [aut], Adam Elder [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>

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New package biva with initial version 0.1.0
Package: biva
Type: Package
Title: Business Intelligence
Version: 0.1.0
Author: Kartikeya Bolar
Maintainer: Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>
Description: Interactive shiny application for working with different kinds of data. Visuals for data are provided. Runtime examples are provided.
License: GPL-2
Encoding: UTF-8
LazyData: FLASE
Depends: R (>= 3.0.3)
Imports: shiny,shinyAce,rpivotTable,corrgram
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-26 19:40:52 UTC; kartikeya.bolar
Repository: CRAN
Date/Publication: 2018-10-30 19:20:06 UTC

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Package aire.zmvm updated to version 0.8.0 with previous version 0.6.1 dated 2018-04-19

Title: Download Mexico City Pollution, Wind, and Temperature Data
Description: Tools for downloading hourly averages, daily maximums and minimums from each of the pollution, wind, and temperature measuring stations or geographic zones in the Mexico City metro area. The package also includes the locations of each of the stations and zones. See <http://aire.cdmx.gob.mx/> for more information.
Author: Diego Valle-Jones [aut, cre]
Maintainer: Diego Valle-Jones <diego@diegovalle.net>

Diff between aire.zmvm versions 0.6.1 dated 2018-04-19 and 0.8.0 dated 2018-10-30

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Package QDComparison updated to version 2.0 with previous version 1.0 dated 2018-10-06

Title: Modern Nonparametric Tools for Two-Sample Quantile and Distribution Comparisons
Description: Allows practitioners to determine (i) if two univariate distributions (which can be continuous, discrete, or even mixed) are equal, (ii) how two distributions differ (shape differences, e.g., location, scale, etc.), and (iii) where two distributions differ (at which quantiles), all using nonparametric LP statistics. The primary reference is Jungreis, D. and Mukhopadhyay, S. (2018, Technical Report).
Author: David Jungreis, Subhadeep Mukhopadhyay
Maintainer: David Jungreis <dbjungreis@gmail.com>

Diff between QDComparison versions 1.0 dated 2018-10-06 and 2.0 dated 2018-10-30

 DESCRIPTION                 |    8 ++++----
 MD5                         |   10 +++++-----
 R/LP.QDC.R                  |   22 +++++++++++++++-------
 R/QTE.Out.R                 |   15 ++++++++++++---
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 6 files changed, 49 insertions(+), 25 deletions(-)

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New package pksensi with initial version 1.0.0
Package: pksensi
Type: Package
Title: Global Sensitivity Analysis in Pharmacokinetic Modeling
Version: 1.0.0
Authors@R: c( person("Nan-Hung", "Hsieh", role = c("aut", "cre"), email = "nhsieh@cvm.tamu.edu", comment = c(ORCID = "0000-0003-0163-2766")), person("Brad", "Reisfeld", role = "aut"), person("Weihsueh A.", "Chiu", role = "aut", comment = c(ORCID = "0000-0002-7575-2368")))
Depends: R (>= 3.3.0)
Imports: data.table, deSolve, dplyr, getPass, ggplot2, magrittr, reshape
Description: Applying the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in pharmacokinetic (PK) models, especially the physiologically-based pharmacokinetic (PBPK) model with multivariate outputs. The package also provide some functions to check the sensitivity measures and its convergence of model parameters.
License: GPL (>= 3)
RoxygenNote: 6.1.0
Suggests: covr, knitr, rmarkdown, testthat, viridis
LazyData: true
URL: https://github.com/nanhung/pksensi
BugReports: https://github.com/nanhung/pksensi/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-10-30 17:46:51 UTC; nhsieh
Author: Nan-Hung Hsieh [aut, cre] (<https://orcid.org/0000-0003-0163-2766>), Brad Reisfeld [aut], Weihsueh A. Chiu [aut] (<https://orcid.org/0000-0002-7575-2368>)
Maintainer: Nan-Hung Hsieh <nhsieh@cvm.tamu.edu>
Repository: CRAN
Date/Publication: 2018-10-30 18:20:03 UTC

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New package pbv with initial version 0.1-17
Package: pbv
Type: Package
Title: Probabilities for Bivariate Normal Distribution
Version: 0.1-17
Date: 2018-10-25 10:31:08
Author: Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>)
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Description: Computes probabilities of the bivariate normal distribution in a vectorized R function (Drezner & Wesolowsky, 1990, <doi:10.1080/00949659008811236>).
Depends: R (>= 3.1)
Imports: Rcpp
Suggests: pbivnorm
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/alexanderrobitzsch/pbv, https://sites.google.com/site/alexanderrobitzsch2/software
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2018-10-25 08:31:31 UTC; sunpn563
Repository: CRAN
Date/Publication: 2018-10-30 18:50:03 UTC

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Package modeest updated to version 2.3.2 with previous version 2.1 dated 2012-10-15

Title: Mode Estimation
Description: Provides estimators of the mode of univariate unimodal data or univariate unimodal distributions.
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>

Diff between modeest versions 2.1 dated 2012-10-15 and 2.3.2 dated 2018-10-30

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New package namer with initial version 0.1.3
Package: namer
Title: Names Your 'R Markdown' Chunks
Version: 0.1.3
Authors@R: c(person(given = "Steph", family = "Locke", role = c("aut", "cre"), email = "steph@itsalocke.com"), person(given = "Maëlle", family = "Salmon", role = "aut", email = "maelle.salmon@yahoo.se", comment = c(ORCID = "0000-0002-2815-0399")), person(given = "Ellis", family = "Valentiner", role = "ctb"), person(given = "Locke Data", role = "fnd", comment = "https://itsalocke.com"))
Description: It names the 'R Markdown' chunks of files based on the filename.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: fs, glue, magrittr, purrr, tibble, dplyr, rstudioapi
RoxygenNote: 6.1.0.9000
Suggests: testthat, covr, rmarkdown, knitr, UNF
VignetteBuilder: knitr
URL: https://github.com/lockedata/namer
BugReports: https://github.com/lockedata/namer/issues
NeedsCompilation: no
Packaged: 2018-10-26 06:19:24 UTC; Maelle
Author: Steph Locke [aut, cre], Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>), Ellis Valentiner [ctb], Locke Data [fnd] (https://itsalocke.com)
Maintainer: Steph Locke <steph@itsalocke.com>
Repository: CRAN
Date/Publication: 2018-10-30 19:00:02 UTC

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Package mcmcr updated to version 0.0.2 with previous version 0.0.1 dated 2018-04-13

Title: Manipulate MCMC Samples
Description: Functions and classes to store, manipulate and summarise Monte Carlo Markov Chain (MCMC) samples.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between mcmcr versions 0.0.1 dated 2018-04-13 and 0.0.2 dated 2018-10-30

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 mcmcr-0.0.2/mcmcr/R/utils.R                 |    2 
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 13 files changed, 96 insertions(+), 70 deletions(-)

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New package ITRLearn with initial version 1.0
Package: ITRLearn
Type: Package
Title: Statistical Learning for Individualized Treatment Regime
Version: 1.0
Date: 2018-10-22
Author: Chengchun Shi, Rui Song, Wenbin Lu and Bo Fu
Maintainer: Chengchun Shi <cshi4@ncsu.edu>
Description: Maximin-projection learning (MPL, Shi, et al., 2018) is implemented for recommending a meaningful and reliable individualized treatment regime for future groups of patients based on the observed data from different populations with heterogeneity in individualized decision making. Q-learning and A-learning are implemented for estimating the groupwise contrast function that shares the same marginal treatment effects. The packages contains classical Q-learning and A-learning algorithms for a single stage study as a byproduct. More functions will be added at later versions.
Imports: Formula, kernlab
License: GPL-2
NeedsCompilation: yes
Repository: CRAN
Packaged: 2018-10-25 17:13:22 UTC; spring
Date/Publication: 2018-10-30 18:40:14 UTC

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New package gremlin with initial version 0.1.0.0
Package: gremlin
Type: Package
Title: Mixed-Effects REML Incorporating Generalized Inverses
Version: 0.1.0.0
Authors@R: person("Matthew", "Wolak", email = "matthewwolak@gmail.com", role = c("cre", "aut"), comment = c(ORCID="0000-0002-7962-0071"))
URL: http://github.com/matthewwolak/gremlin
BugReports: http://github.com/matthewwolak/gremlin/issues
Depends: Matrix
Imports: methods
Suggests: nadiv
LazyData: yes
NeedsCompilation: yes
Description: Fit linear mixed-effects models using restricted (or residual) maximum likelihood (REML) and with generalized inverse matrices to specify covariance structures for random effects. In particular, the package is suited to fit quantitative genetic mixed models, often referred to as 'animal models' (Kruuk. 2004 <DOI: 10.1098/rstb.2003.1437>). Implements the average information algorithm as the main tool to maximize the restricted likelihood, but with other algorithms available (Meyer. 1997. Genet Sel Evol 29:97; Meyer and Smith. 1998. Genet Sel Evol 28:23.).
License: GPL-3
RoxygenNote: 6.0.1
Packaged: 2018-10-25 17:36:51 UTC; matthew
Author: Matthew Wolak [cre, aut] (<https://orcid.org/0000-0002-7962-0071>)
Maintainer: Matthew Wolak <matthewwolak@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-30 18:30:02 UTC

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New package fabMix with initial version 4.3
Package: fabMix
Type: Package
Title: Overfitting Bayesian Mixtures of Factor Analyzers with Parsimonious Covariance and Unknown Number of Components
Version: 4.3
Date: 2018-10-25
Authors@R: c(person(given = "Panagiotis", family = "Papastamoulis", email = "papapast@yahoo.gr", role = c( "aut", "cre"), comment = c(ORCID = "0000-0001-9468-7613")))
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Description: Model-based clustering of multivariate continuous data using Bayesian mixtures of factor analyzers (Papastamoulis (2018) <DOI:10.1016/j.csda.2018.03.007>). The number of clusters is estimated using overfitting mixture models (Rousseau and Mengersen (2011) <DOI:10.1111/j.1467-9868.2011.00781.x>): suitable prior assumptions ensure that asymptotically the extra components will have zero posterior weight, therefore, the inference is based on the ``alive'' components. A Gibbs sampler is implemented in order to (approximately) sample from the posterior distribution of the overfitting mixture. A prior parallel tempering scheme is also available, which allows to run multiple parallel chains with different prior distributions on the mixture weights. These chains run in parallel and can swap states using a Metropolis-Hastings move. Eight different parameterizations give rise to parsimonious representations of the covariance per cluster (following Mc Nicholas and Murphy (2008) <DOI:10.1007/s11222-008-9056-0>). The model parameterization and number of factors is selected according to the Bayesian Information Criterion. Identifiability issues related to label switching are dealt by post-processing the simulated output with the Equivalence Classes Representatives algorithm (Papastamoulis and Iliopoulos (2010) <https://www.jstor.org/stable/25703571>, Papastamoulis (2016) <DOI:10.18637/jss.v069.c01>). Missing values are currently allowed for two model parameterizations.
License: GPL-2
URL: https://github.com/mqbssppe/overfittingFABMix
Imports: Rcpp (>= 0.12.17), MASS, doParallel, foreach, label.switching, mvtnorm, doRNG, RColorBrewer, corrplot, mclust, coda
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2018-10-25 15:55:42 UTC; panagiotis
Author: Panagiotis Papastamoulis [aut, cre] (<https://orcid.org/0000-0001-9468-7613>)
Repository: CRAN
Date/Publication: 2018-10-30 18:50:07 UTC

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New package contextual with initial version 0.9.1
Package: contextual
Type: Package
Title: Simulation and Analysis of Contextual Multi-Armed Bandit Policies
Version: 0.9.1
Authors@R: c(person("Robin", "van Emden", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5820-8638"), email = "robinvanemden@gmail.com"), person("Maurits", "Kaptein", role = "ctb", email = "m.c.kaptein@tilburguniversity.edu", comment = c(ORCID = "0000-0002-6316-7524")))
Maintainer: Robin van Emden <robinvanemden@gmail.com>
Description: Facilitates the simulation and evaluation of context-free and contextual multi-Armed Bandit policies or algorithms to ease the implementation, evaluation, and dissemination of both existing and new bandit algorithms and policies.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: R6 (>= 2.3.0), data.table, R.devices, foreach, doParallel, itertools, iterators, nleqslv, checkmate
Suggests: testthat, vdiffr, covr, knitr, here, rmarkdown, devtools, ggplot2
VignetteBuilder: knitr
URL: https://github.com/Nth-iteration-labs/contextual
BugReports: https://github.com/Nth-iteration-labs/contextual/issues
NeedsCompilation: no
Packaged: 2018-10-25 13:46:38 UTC; robin
Author: Robin van Emden [aut, cre] (<https://orcid.org/0000-0001-5820-8638>), Maurits Kaptein [ctb] (<https://orcid.org/0000-0002-6316-7524>)
Repository: CRAN
Date/Publication: 2018-10-30 18:40:07 UTC

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Package REPLesentR updated to version 0.3.0 with previous version 0.2.0 dated 2018-10-16

Title: Presentations in the REPL
Description: Create presentations and display them inside the R 'REPL' (Read-Eval-Print loop), aka the R console. Presentations can be written in 'RMarkdown' or any other text format. A set of convenient navigation options as well as code evaluation during a presentation is provided. It is great for tech talks with live coding examples and tutorials. While this is not a replacement for standard presentation formats, it's old-school looks might just be what sets it apart. This project has been inspired by the 'REPLesent' project for presentations in the 'Scala' 'REPL'.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>

Diff between REPLesentR versions 0.2.0 dated 2018-10-16 and 0.3.0 dated 2018-10-30

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 tests/testthat/test-SlideDeck.R |    3 ++-
 7 files changed, 15 insertions(+), 12 deletions(-)

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New package PerseusR with initial version 0.3.3
Package: PerseusR
Title: Perseus R Interop
Version: 0.3.3
Author: Jan Rudolph <rudolph@biochem.mpg.de>
Maintainer: Jan Rudolph <rudolph@biochem.mpg.de>
Description: Enables the interoperability between the Perseus platform for omics data analysis (Tyanova et al. 2016) <doi:10.1038/nmeth.3901> and R. It provides the foundation for developing and running Perseus plugins implemented in R by providing all required input and output handling, including data and parameter parsing as described in Rudolph and Cox 2018 <doi:10.1101/447268>.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: utils, plyr, methods, XML, Biobase, stringr
Suggests: testthat, roxygen2, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-24 14:31:08 UTC; rudolph
Repository: CRAN
Date/Publication: 2018-10-30 18:00:02 UTC

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New package GHS with initial version 0.1
Package: GHS
Title: Graphical Horseshoe MCMC Sampler Using Data Augmented Block Gibbs Sampler
Version: 0.1
Author: Ashutosh Srivastava<srivas48@purdue.edu>, Anindya Bhadra<bhadra@purdue.edu>
Maintainer: Ashutosh Srivastava<srivas48@purdue.edu>
Description: Draw posterior samples to estimate the precision matrix for multivariate Gaussian data. Posterior means of the samples is the graphical horseshoe estimate by Li, Bhadra and Craig(2017) <arXiv:1707.06661>. The function uses matrix decomposition and variable change from the Bayesian graphical lasso by Wang(2012) <doi:10.1214/12-BA729>, and the variable augmentation for sampling under the horseshoe prior by Makalic and Schmidt(2016) <arXiv:1508.03884>. Structure of the graphical horseshoe function was inspired by the Bayesian graphical lasso function using blocked sampling, authored by Wang(2012) <doi:10.1214/12-BA729>.
Depends: R (>= 3.4.0), stats, MASS
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2018-10-24 16:05:44 UTC; Ashutosh Srivastava
Repository: CRAN
Date/Publication: 2018-10-30 18:00:07 UTC

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Package cpt updated to version 1.0.2 with previous version 1.0 dated 2018-02-27

Title: Classification Permutation Test
Description: Non-parametric test for equality of multivariate distributions. Trains a classifier to classify (multivariate) observations as coming from one of several distributions. If the classifier is able to classify the observations better than would be expected by chance (using permutation inference), then the null hypothesis that the distributions are equal is rejected.
Author: Johann Gagnon-Bartsch <johanngb@umich.edu>
Maintainer: Johann Gagnon-Bartsch <johanngb@umich.edu>

Diff between cpt versions 1.0 dated 2018-02-27 and 1.0.2 dated 2018-10-30

 DESCRIPTION            |    8 ++++----
 MD5                    |   10 +++++-----
 R/cpt.R                |    4 ++--
 R/getensemble.metric.R |    7 +++++++
 R/getmetric.R          |    6 ++++++
 man/cpt-package.Rd     |    4 ++--
 6 files changed, 26 insertions(+), 13 deletions(-)

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Package AMModels updated to version 0.1.4 with previous version 0.1.3 dated 2018-03-05

Title: Adaptive Management Model Manager
Description: Helps enable adaptive management by codifying knowledge in the form of models generated from numerous analyses and data sets. Facilitates this process by storing all models and data sets in a single object that can be updated and saved, thus tracking changes in knowledge through time. A shiny application called AM Model Manager (modelMgr()) enables the use of these functions via a GUI.
Author: Jon Katz <jonkatz4@gmail.com>, Therese Donovan <tdonovan@uvm.edu>
Maintainer: Jon Katz <jonkatz4@gmail.com>

Diff between AMModels versions 0.1.3 dated 2018-03-05 and 0.1.4 dated 2018-10-30

 DESCRIPTION               |   10 ++--
 MD5                       |   46 ++++++++++-----------
 NAMESPACE                 |    3 -
 R/AMModels-package.R      |    1 
 R/grepAMModelLib.R        |   23 +++++++++-
 R/insertAMModelLib.R      |    6 +-
 R/methods-amModel.R       |    1 
 R/methods-amModelLib.R    |    1 
 R/rmModelsData.R          |   19 ++++++++
 build/vignette.rds        |binary
 man/AMModels.Rd           |   99 ++++++++++++++++++++--------------------------
 man/amData.Rd             |   34 ++++++---------
 man/amModel.Rd            |   32 +++++---------
 man/amModelLib.Rd         |   52 +++++++++++-------------
 man/getters.Rd            |   72 ++++++++++++++++-----------------
 man/grepAMModelLib.Rd     |   68 +++++++++++++------------------
 man/insertAMModelLib.Rd   |   53 ++++++++++--------------
 man/lsModels.Rd           |   54 +++++++++++--------------
 man/methods-amModel.Rd    |   52 ++++++++++++------------
 man/methods-amModelLib.Rd |   50 +++++++++++------------
 man/modelMgr.Rd           |    5 --
 man/mymodels.Rd           |    7 ++-
 man/rmModel.Rd            |   55 ++++++++++---------------
 man/simCovariate.Rd       |   27 ++++++------
 24 files changed, 378 insertions(+), 392 deletions(-)

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Package tracerer (with last version 1.5.1) was removed from CRAN

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

2018-10-30 1.5.1

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New package zbank with initial version 0.1.0
Package: zbank
Type: Package
Title: 'ZooBank' API Client
Description: Interface to the 'ZooBank' API (<http://zoobank.org/Api>) client. 'ZooBank' (<http://zoobank.org/>) is the official registry of zoological nomenclature. Methods are provided for using each of the API endpoints, including for querying by author, querying for publications, get statistics on 'ZooBank' activity, and more.
Version: 0.1.0
Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "sckott@protonmail.com", comment = c(ORCID = "0000-0003-1444-9135")))
License: MIT + file LICENSE
URL: https://github.com/ropenscilabs/zbank
BugReports: https://github.com/ropenscilabs/zbank/issues
Encoding: UTF-8
Imports: crul (>= 0.5.0), jsonlite (>= 1.5), tibble
Suggests: testthat, vcr
RoxygenNote: 6.1.0
X-schema.org-applicationCategory: Taxonomy
X-schema.org-keywords: taxonomy, biology, nomenclature, JSON, API, web, api-client, ZooBank, Zoological, species, names
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
Packaged: 2018-10-23 02:10:53 UTC; sckott
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Repository: CRAN
Date/Publication: 2018-10-30 16:20:03 UTC

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New package ttestshiny with initial version 0.1.0
Package: ttestshiny
Type: Package
Title: Ttest Shiny
Version: 0.1.0
Author: Kartikeya Bolar
Maintainer: Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>
Description: Interactive shiny application for working with ttest on data. Results for analysis are provided.
License: GPL-2
Encoding: UTF-8
LazyData: FLASE
Depends: R (>= 3.0.3)
Imports: shiny,shinyAce,shinyjs,dplyr
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-23 06:48:21 UTC; kartikeya.bolar
Repository: CRAN
Date/Publication: 2018-10-30 16:30:03 UTC

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New package TSDT with initial version 1.0.0
Package: TSDT
Type: Package
Title: Treatment-Specific Subgroup Detection Tool
Version: 1.0.0
Date: 2018-10-29
Author: Chakib Battioui, Brian Denton, Lei Shen
Maintainer: Brian Denton <denton_brian_david@lilly.com>
Description: Implements a method for identifying subgroups with superior response relative to the overall sample.
Imports: methods, mlbench, hash, party, rpart, survival, survRM2, stats, modeltools, utils, parallel
LazyLoad: no
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-29 15:34:28 UTC; c065288
Repository: CRAN
Date/Publication: 2018-10-30 16:50:16 UTC

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New package tracerer with initial version 1.5.1
Package: tracerer
Type: Package
Title: Tracer from R
Version: 1.5.1
Authors@R: c( person("Richel J.C.", "Bilderbeek", email = "richel@richelbilderbeek.nl", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1107-7049")), person("Joelle", "Barido-Sottani", role = "rev", comment = "Joelle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209"), person("David", "Winter", role = "rev", comment = "David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209"))
Maintainer: Richel J.C. Bilderbeek <richel@richelbilderbeek.nl>
Description: 'BEAST2' (<http://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'Tracer' (<http://tree.bio.ed.ac.uk/software/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.
License: GPL-3 | file LICENSE
LazyData: TRUE
Imports: jsonlite, Rcpp, testit
Suggests: ape, geiger, ggplot2, hunspell, knitr, phangorn, rbenchmark, reshape2, rmarkdown, spelling, testthat
VignetteBuilder: knitr
RoxygenNote: 6.1.0
URL: https://github.com/richelbilderbeek/tracerer
BugReports: https://github.com/richelbilderbeek/tracerer
LinkingTo: Rcpp
Language: en-US
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2018-10-29 08:20:43 UTC; plaintext
Author: Richel J.C. Bilderbeek [aut, cre] (<https://orcid.org/0000-0003-1107-7049>), Joelle Barido-Sottani [rev] (Joelle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209), David Winter [rev] (David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209)
Repository: CRAN
Date/Publication: 2018-10-30 16:30:05 UTC

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New package tbltools with initial version 0.0.2
Package: tbltools
Title: Tools for Working with Tibbles
Version: 0.0.2
Authors@R: person(given = "Michael W.", family = "Kearney", role = c("aut", "cre"), email = "kearneymw@missouri.edu", comment = c(ORCID = "0000-0002-0730-4694"))
Description: Tools for working with tibbles, or data.frame-like objects generated by the 'tibble' package <https://tibble.tidyverse.org/>. Functions assist in converting objects to tibbles and creating frequency tables.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: tfse, tibble, rlang, tidyselect
Suggests: testthat, covr
RoxygenNote: 6.1.0.9000
URL: https://github.com/mkearney/tbltools
BugReports: https://github.com/mkearney/tbltools/issues
NeedsCompilation: no
Packaged: 2018-10-29 19:58:48 UTC; mwk
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>
Repository: CRAN
Date/Publication: 2018-10-30 16:50:03 UTC

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New package sloop with initial version 1.0.0
Package: sloop
Title: Helpers for 'OOP' in R
Version: 1.0.0
Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut", "cre")), person("RStudio", role = "cph") )
Description: A collection of helper functions designed to help you to better understand object oriented programming in R, particularly using 'S3'.
License: GPL-3
URL: https://github.com/r-lib/sloop
BugReports: https://github.com/r-lib/sloop/issues
Depends: R (>= 3.3)
Imports: codetools, crayon, methods, purrr, rlang, tibble
Suggests: covr, testthat
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-23 15:07:46 UTC; hadley
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Repository: CRAN
Date/Publication: 2018-10-30 16:20:07 UTC

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New package siebanxicor with initial version 1.0.0
Package: siebanxicor
Type: Package
Title: Query Data Series from Bank of Mexico
Version: 1.0.0
Author: DGIE - Banco de México
Maintainer: Noé Palmerin <sie@banxico.org.mx>
Description: Allows to retrieve time series of all indicators available in the Bank of Mexico's Economic Information System (<http://www.banxico.org.mx/SieInternet/>).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: httr, jsonlite
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-10-29 19:23:46 UTC; D12465
Repository: CRAN
Date/Publication: 2018-10-30 16:40:02 UTC

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New package rpact with initial version 1.0.0
Package: rpact
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Version: 1.0.0
Date: 2018-10-22
Authors@R: c( person("Gernot", "Wassmer", email = "gernot.wassmer@rpact.com", role = c("aut")), person("Friedrich", "Pahlke", email = "friedrich.pahlke@rpact.com", role = c("aut", "cre")))
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Depends: R (>= 3.3.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://www.rpact.org
BugReports: https://bugreport.rpact.org
Imports: methods, stats, utils, graphics
Suggests: parallel, ggplot2 (>= 2.2.0), testthat (>= 2.0.0)
RoxygenNote: 6.0.1
Collate: 'f_core_constants.R' 'class_core_parameter_set.R' 'class_core_plot_settings.R' 'class_analysis_dataset.R' 'class_design.R' 'class_analysis_stage_results.R' 'class_analysis_results.R' 'class_design_plan.R' 'class_design_power_and_asn.R' 'class_design_set.R' 'f_analysis.R' 'f_analysis_means.R' 'f_analysis_rates.R' 'f_analysis_survival.R' 'f_core_assertions.R' 'f_core_output_formats.R' 'f_core_utilities.R' 'f_design_fisher_combination_test.R' 'f_design_group_sequential.R' 'f_design_sample_size_calculator.R' 'pkgname.R'
NeedsCompilation: yes
Packaged: 2018-10-22 14:33:56 UTC; Pahlke
Author: Gernot Wassmer [aut], Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Repository: CRAN
Date/Publication: 2018-10-30 16:10:03 UTC

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New package PROSPER with initial version 0.3.0
Package: PROSPER
Type: Package
Title: Simulation of Weed Population Dynamics
Version: 0.3.0
Date: 2018-10-05
Authors@R: c(person("Christoph", "v. Redwitz", role = c("aut", "cre"), email = "christoph.redwitz@posteo.de"), person("Friederike", "de Mol", role = "aut", email = "friederike.de-mol@uni-rostock.de"))
Maintainer: Christoph v. Redwitz <christoph.redwitz@posteo.de>
Description: An environment to simulate the development of annual plant populations with regard to population dynamics and genetics, especially herbicide resistance. It combines genetics on the individual level (Renton et al. 2011) with a stochastic development on the population level (Daedlow, 2015). Renton, M, Diggle, A, Manalil, S and Powles, S (2011) <doi:10.1016/j.jtbi.2011.05.010> Daedlow, Daniel (2015, doctoral dissertation: University of Rostock, Faculty of Agriculture and Environmental Sciences.)
License: GPL-3
LazyData: yes
Depends: data.table, methods
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-23 12:14:34 UTC; Christoph
Author: Christoph v. Redwitz [aut, cre], Friederike de Mol [aut]
Repository: CRAN
Date/Publication: 2018-10-30 16:30:20 UTC

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New package mudens with initial version 1.3.2
Package: mudens
Type: Package
Title: Density Estimate
Version: 1.3.2
Date: 2018-10-9
Author: Dick Herrick, Hans-Georg Mueller, Dan Serachitopal, Liangcai Zhang, Kenneth R. Hess
Description: Compute a density estimate from a vector of right-censored survival time using kernel functions.
Maintainer: Kenneth R. Hess <khess@mdanderson.org>
Imports: survival, Rcpp
RoxygenNote: 6.1.0
License: GPL (>= 2)
LinkingTo: Rcpp
NeedsCompilation: yes
Suggests: testthat
Encoding: UTF-8
Packaged: 2018-10-23 13:58:03 UTC; JSong1
Repository: CRAN
Date/Publication: 2018-10-30 16:20:11 UTC

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New package mapi with initial version 1.0.0-62
Package: mapi
Type: Package
Title: Mapping Averaged Pairwise Information
Version: 1.0.0-62
Date: 2018-10-14
Author: Sylvain Piry, Thomas Campolunghi, Florent Cestier, Karine Berthier
Maintainer: Sylvain Piry <sylvain.piry@inra.fr>
Description: Mapping Averaged Pairwise Information (MAPI) is an exploratory method providing graphical representations summarizing the spatial variation of pairwise metrics (eg. distance, similarity coefficient, ...) computed between georeferenced samples. Reference: Piry et al. (2016) <DOI:10.1111/2041-210X.12616>.
License: GPL (>= 2)
Imports: Rcpp (>= 0.10.0), data.table (>= 1.10), sf (>= 0.5), pbapply (>= 1.3), parallel (>= 3.3), stats (>= 3.1.1)
LinkingTo: Rcpp
Depends: R (>= 3.3)
Suggests: progress (>= 1.0), grDevices, sp (>= 1.3), latticeExtra
Encoding: UTF-8
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-10-14 17:33:34 UTC; piry
Repository: CRAN
Date/Publication: 2018-10-30 16:50:06 UTC

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Package LPWC updated to version 0.99.4 with previous version 0.99.3 dated 2018-06-04

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 (2018) <doi:10.1101/292615>.
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>

Diff between LPWC versions 0.99.3 dated 2018-06-04 and 0.99.4 dated 2018-10-30

 DESCRIPTION                        |   31 ++++---
 MD5                                |   66 ++++++++--------
 NAMESPACE                          |   18 +++-
 R/bestlag.R                        |   29 +++++--
 R/comp_corr.R                      |   34 ++++++--
 R/corr_bestlag.R                   |   24 ++++--
 R/findC.R                          |   21 +++--
 R/prep_data.R                      |   26 ++++--
 R/score.R                          |    8 +-
 R/simdata.R                        |    2 
 R/weight.R                         |    7 +
 R/weight_lag.R                     |    5 +
 R/wt_corr.R                        |    6 +
 README.md                          |    6 +
 build/vignette.rds                 |binary
 inst/doc/LPWC.R                    |    8 +-
 inst/doc/LPWC.Rmd                  |   26 +++++-
 inst/doc/LPWC.html                 |  148 +++++++++++++++++++++----------------
 man/best.lag.Rd                    |   14 ++-
 man/comp.corr.Rd                   |   22 ++++-
 man/corr.bestlag.Rd                |   13 ++-
 man/findC.Rd                       |   10 +-
 man/prep.data.Rd                   |    8 +-
 man/score.Rd                       |    1 
 man/simdata.Rd                     |    2 
 man/weight.Rd                      |    1 
 man/weight.lag.Rd                  |    1 
 man/wt.corr.Rd                     |    1 
 tests/testthat/test_best_lag.R     |   21 +++--
 tests/testthat/test_corr_bestlag.R |   36 ++++++---
 tests/testthat/test_findC.R        |    7 +
 tests/testthat/test_weight.R       |    1 
 tests/testthat/test_wt_corr.R      |    1 
 vignettes/LPWC.Rmd                 |   26 +++++-
 34 files changed, 426 insertions(+), 204 deletions(-)

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New package lass0 with initial version 1.0.0
Package: lass0
Type: Package
Title: Lasso-Zero for (High-Dimensional) Linear Regression
Version: 1.0.0
Date: 2018-10-23
Author: Pascaline Descloux, Sylvain Sardy
Maintainer: Pascaline Descloux <pascaline.descloux@unige.ch>
Description: Model selection for the (possibly high-dimensional) linear regression model with Lasso-Zero, an L1-based methodology relying on the repeated use of noise dictionaries, as described by Descloux, P. and Sardy, S. (2018) <arXiv:1805.05133>.
Depends: stats, graphics
Imports: lpSolve (>= 5.6.13), ismev (>= 1.42), foreach (>= 1.4.4)
License: GPL-2
URL: http://arxiv.org/abs/1805.05133
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-23 14:50:16 UTC; Pascaline
Repository: CRAN
Date/Publication: 2018-10-30 16:30:09 UTC

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New package intoo with initial version 0.1.0
Package: intoo
Title: Object Oriented Intelligence
Version: 0.1.0
Date: 2018-10-23
License: GPL (>= 2)
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Author: Abby Spurdle [cre, aut], Emil Bode [ctb]
URL: https://sites.google.com/site/asrpws
Description: Implements %$% and %$%<- attribute operators and an object.info() function for printing objects with attributes, succinctly but informatively.
Suggests: zeallot, dub
NeedsCompilation: no
Packaged: 2018-10-23 00:50:15 UTC; Student9
Repository: CRAN
Date/Publication: 2018-10-30 16:20:14 UTC

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New package ibmsunburst with initial version 0.1.0
Package: ibmsunburst
Title: Generate Personality Insights Sunburst Diagrams
Version: 0.1.0
Authors@R: c(person(given = "Steph", family = "Locke", role = c("aut", "cre"), email = "steph@itsalocke.com", comment = c(ORCID = "0000-0002-2387-3723")), person(given = "IBM", role = "cph", comment = "IBM is author of the original JS code."), person(given = "Hendrik", family = "Feddersen", role = "fnd", comment = "https://www.ibm.com/"), person(given = "Kent", family = "Russell", role = "aut", email = "kent.russell@timelyportfolio.com"), person(given = "Locke Data", role = "fnd", comment = "https://itsalocke.com"), person(given = "Maëlle", family = "Salmon", role = "ctb", email = "maelle.salmon@yahoo.se", comment = c(ORCID = "0000-0002-2815-0399")))
Description: Generates Personality Insights sunburst diagrams based on 'IBM Watson' Personality Insights service output.
License: MIT + file LICENSE
Imports: jsonlite, htmlwidgets
Suggests: covr, testthat, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0.9000
URL: https://github.com/lockedata/ibmsunburst, https://lockedata.github.io/ibmsunburst/
BugReports: https://github.com/lockedata/ibmsunburst/issues
NeedsCompilation: no
Packaged: 2018-10-22 07:08:50 UTC; Maelle
Author: Steph Locke [aut, cre] (<https://orcid.org/0000-0002-2387-3723>), IBM [cph] (IBM is author of the original JS code.), Hendrik Feddersen [fnd] (https://www.ibm.com/), Kent Russell [aut], Locke Data [fnd] (https://itsalocke.com), Maëlle Salmon [ctb] (<https://orcid.org/0000-0002-2815-0399>)
Maintainer: Steph Locke <steph@itsalocke.com>
Repository: CRAN
Date/Publication: 2018-10-30 16:10:07 UTC

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New package hero with initial version 0.0.3
Package: hero
Type: Package
Title: Sandwich Smoother
Version: 0.0.3
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Description: Data and data-generating functions related to the paper 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.
Depends: R (>= 2.10)
License: GPL (>= 2)
LazyData: true
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-22 16:40:55 UTC; joshu
Repository: CRAN
Date/Publication: 2018-10-30 16:30:12 UTC

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New package export with initial version 0.2.2
Package: export
Type: Package
Title: Streamlined Export of Graphs and Data Tables
Version: 0.2.2
Date: 2018-09-18
Authors@R: c(person("Tom", "Wenseleers", role = c("aut", "cre"), email = "tom.wenseleers@kuleuven.be"), person("Christophe", "Vanderaa", role = c("aut"), email = "christophe.vanderaa@kuleuven.be"))
Depends: R (>= 3.0)
Imports: stats, utils, datasets, grDevices, officer (>= 0.2.2), rvg (>= 0.1.8), xtable (>= 1.8-2), flextable (>= 0.4.3), rgl (>= 0.99.16), xml2 (>= 1.2.0), stargazer (>= 5.2.1), openxlsx (>= 4.0.17), broom (>= 0.4.4)
Suggests: ggplot2 (>= 1.0)
Description: Easily export 'R' graphs and statistical output to 'Microsoft Office' / 'LibreOffice', 'Latex' and 'HTML' Documents, using sensible defaults that result in publication-quality output with simple, straightforward commands. Output to 'Microsoft Office' is in editable 'DrawingML' vector format for graphs, and can use corporate template documents for styling. This enables the production of standardized reports and also allows for manual tidy-up of the layout of 'R' graphs in 'Powerpoint' before final publication. Export of graphs is flexible, and functions enable the currently showing R graph or the currently showing 'R' stats object to be exported, but also allow the graphical or tabular output to be passed as objects. The package relies on package 'officer' for export to 'Office' documents,and output files are also fully compatible with 'LibreOffice'. Base 'R', 'ggplot2' and 'lattice' plots are supported, as well as a wide variety of 'R' stats objects, via wrappers to xtable(), broom::tidy() and stargazer(), including aov(), lm(), glm(), lme(), glmnet() and coxph() as well as matrices and data frames and many more...
License: GPL-2
BugReports: https://github.com/tomwenseleers/export/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-10-22 15:51:22 UTC; Ento
Author: Tom Wenseleers [aut, cre], Christophe Vanderaa [aut]
Maintainer: Tom Wenseleers <tom.wenseleers@kuleuven.be>
Repository: CRAN
Date/Publication: 2018-10-30 16:30:15 UTC

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Package vennLasso updated to version 0.1.3 with previous version 0.1.2 dated 2018-03-25

Title: Variable Selection for Heterogeneous Populations
Description: Provides variable selection and estimation routines for models with main effects stratified on multiple binary factors. The 'vennLasso' package is an implementation of the method introduced in Huling, et al. (2017) <doi:10.1111/biom.12769>.
Author: Jared Huling [aut, cre] (<https://orcid.org/0000-0003-0670-4845>), Muxuan Liang [ctb], Yixuan Qiu [cph], Gael Guennebaud [cph], Ray Gardner [cph], Jitse Niesen [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>

Diff between vennLasso versions 0.1.2 dated 2018-03-25 and 0.1.3 dated 2018-10-30

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Package Ternary updated to version 1.0.2 with previous version 1.0.1 dated 2018-07-05

Title: An R Package for Creating Ternary Plots
Description: Plots ternary diagrams using the standard graphics functions. An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between Ternary versions 1.0.1 dated 2018-07-05 and 1.0.2 dated 2018-10-30

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New package temperatureresponse with initial version 0.2
Package: temperatureresponse
Version: 0.2
Date: 2018-10-14
Title: Temperature Response
Authors@R: person("Etienne", "Low-Decarie", email = "etienne.decarie@gmail.com", role = c("aut", "cre"))
Depends: R (>= 3.1.0)
Description: Fits temperature response models to rate measurements taken at different temperatures. Etienne Low-Decarie,Tobias G. Boatman, Noah Bennett,Will Passfield,Antonio Gavalas-Olea,Philipp Siegel, Richard J. Geider (2017) <doi:10.1002/ece3.3576> .
License: GPL-3
URL: https://github.com/low-decarie/temperatureresponse
RoxygenNote: 6.0.1
LazyData: true
Imports: graphics, stats, broom, dplyr, rootSolve, minpack.lm, AICcmodavg, numDeriv
NeedsCompilation: no
Packaged: 2018-10-30 01:20:11 UTC; LowDecarie
Author: Etienne Low-Decarie [aut, cre]
Maintainer: Etienne Low-Decarie <etienne.decarie@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-30 15:50:07 UTC

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New package sleepr with initial version 0.3.0
Package: sleepr
Title: Analyse Activity and Sleep Behaviour
Date: 2018-10-04
Version: 0.3.0
Authors@R: c( person("Quentin", "Geissmann", role = c("aut", "cre"), email = "qgeissmann@gmail.com") )
Description: Use behavioural variables to score activity and infer sleep from bouts of immobility. It is primarily designed to score sleep in fruit flies from Drosophila Activity Monitor (TriKinetics) and Ethoscope data. It implements sleep scoring using the "five-minute rule" (Hendricks et al. (2000) <DOI:10.1016/S0896-6273(00)80877-6>), activity classification for Ethoscopes (Geissmann et al. (2017) <DOI:10.1371/journal.pbio.2003026>) and a new algorithm to detect when animals are dead.
Depends: R (>= 3.00), behavr
Imports: data.table
Suggests: testthat, covr, knitr
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/rethomics/sleepr
BugReports: https://github.com/rethomics/sleepr/issues
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-22 01:02:57 UTC; quentin
Author: Quentin Geissmann [aut, cre]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-30 15:50:10 UTC

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New package RcppEnsmallen with initial version 0.1.10.0.1
Package: RcppEnsmallen
Title: Header-Only C++ Mathematical Optimization Library for 'Armadillo'
Version: 0.1.10.0.1
Authors@R: c( person("James", "Balamuta", email = "balamut2@illinois.edu", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-2826-8458")), person("Dirk", "Eddelbuettel", email = "edd@debian.org", role = c("aut", "cph"), comment = c(ORCID = "0000-0001-6419-907X")) )
Description: 'Ensmallen' is a templated C++ mathematical optimization library (by the 'MLPACK' team) that provides a simple set of abstractions for writing an objective function to optimize. Provided within are various standard and cutting-edge optimizers that include full-batch gradient descent techniques, small-batch techniques, gradient-free optimizers, and constrained optimization. The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library and pairs the appropriate header files from 'armadillo' through the 'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor 'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under 3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2, 'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under similar terms. Note that 'Ensmallen' requires a compiler that supports 'C++11' and 'Armadillo' 6.500 or later.
Depends: R (>= 3.3.0)
License: GPL (>= 2)
URL: https://github.com/coatless/rcppensmallen, https://github.com/mlpack/ensmallen, http://ensmallen.org/
BugReports: https://github.com/coatless/rcppensmallen/issues
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
RoxygenNote: 6.1.0
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2018-10-21 22:38:41 UTC; jjb
Author: James Balamuta [aut, cre, cph] (<https://orcid.org/0000-0003-2826-8458>), Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Balamuta <balamut2@illinois.edu>
Repository: CRAN
Date/Publication: 2018-10-30 15:50:25 UTC

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Package freetypeharfbuzz updated to version 0.2.5 with previous version 0.2.4 dated 2018-10-21

Title: Deterministic Computation of Text Box Metrics
Description: Unlike other tools that dynamically link to the 'Cairo' stack, 'freetypeharfbuzz' is statically linked to specific versions of the 'FreeType' and 'harfbuzz' libraries (2.9 and 1.7.6 respectively). This ensures deterministic computation of text box extents for situations where reproducible results are crucial (for instance unit tests of graphics).
Author: Lionel Henry [aut, cre], RStudio [cph], David Turner [aut] (FreeType library), Robert Wilhelm [aut] (FreeType library), Werner Wilhelm [aut] (FreeType library), Behdad Esfahbod [aut] (Harfbuzz library), Simon Hausmann [aut] (Harfbuzz library), Martin Hosken [aut] (Harfbuzz library), Jonathan Kew [aut] (Harfbuzz library), Lars Knoll [aut] (Harfbuzz library), Werner Lemberg [aut] (Harfbuzz library), Roozbeh Pournader [aut] (Harfbuzz library), Owen Taylor [aut] (Harfbuzz library), David Turner [aut] (Harfbuzz library), Red Hat [cph] (Harfbuzz library)
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between freetypeharfbuzz versions 0.2.4 dated 2018-10-21 and 0.2.5 dated 2018-10-30

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New package distreg.vis with initial version 1.0.1
Package: distreg.vis
Type: Package
Title: Framework for the Visualization of Distributional Regression Models
Version: 1.0.1
Authors@R: c(person("Stanislaus", "Stadlmann", email = "stadlmann@uni-goettingen.de", role = c("cre", "aut"), comment = c(ORCID = "0000-0001-6542-6342")))
Maintainer: Stanislaus Stadlmann <stadlmann@uni-goettingen.de>
Depends: R (>= 3.3.0)
Imports: stats, utils, methods, shiny (>= 1.0.3), bamlss (>= 0.1-2), gamlss (>= 5.0-6), gamlss.dist (>= 5.1-0), ggplot2 (>= 2.2.1), rhandsontable (>= 0.3.4), magrittr (>= 1.5), mvtnorm (>= 1.0-6), viridis (>= 0.4.0), RColorBrewer (>= 1.1-2), formatR (>= 1.5)
Suggests: testthat, gridExtra, glogis
Description: Functions for visualizing distributional regression models fitted using the 'gamlss' or 'bamlss' R package. The core of the package consists of a 'shiny' application, where the model results can be interactively explored and visualized.
License: GPL-3
LazyData: TRUE
URL: https://github.com/Stan125/distreg.vis
BugReports: https://github.com/Stan125/distreg.vis/issues
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-22 08:43:00 UTC; stani
Author: Stanislaus Stadlmann [cre, aut] (<https://orcid.org/0000-0001-6542-6342>)
Repository: CRAN
Date/Publication: 2018-10-30 15:50:17 UTC

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Package dbx updated to version 0.2.3 with previous version 0.2.2 dated 2018-09-15

Title: A Fast, Easy-to-Use Database Interface
Description: Provides select, insert, update, upsert, and delete database operations. Supports 'PostgreSQL', 'MySQL', 'SQLite', and more, and plays nicely with the 'DBI' package.
Author: Andrew Kane [aut, cre]
Maintainer: Andrew Kane <andrew@chartkick.com>

Diff between dbx versions 0.2.2 dated 2018-09-15 and 0.2.3 dated 2018-10-30

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Package BCRA updated to version 2.1 with previous version 2.0 dated 2018-04-25

Title: Breast Cancer Risk Assessment
Description: Functions provide risk projections of invasive breast cancer based on Gail model according to National Cancer Institute's Breast Cancer Risk Assessment Tool algorithm for specified race/ethnic groups and age intervals.
Author: Fanni Zhang
Maintainer: Fanni Zhang <zhangf@imsweb.com>

Diff between BCRA versions 2.0 dated 2018-04-25 and 2.1 dated 2018-10-30

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Package ratematrix updated to version 1.1 with previous version 1.0 dated 2018-06-10

Title: Bayesian Estimation of the Evolutionary Rate Matrix
Description: Estimates the evolutionary rate matrix (R) using Markov chain Monte Carlo (MCMC) as described in Caetano and Harmon (2017) <doi:10.1111/2041-210X.12826>. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.
Author: Daniel Caetano [aut, cre], Luke Harmon [aut]
Maintainer: Daniel Caetano <caetanods1@gmail.com>

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Package scriptexec updated to version 0.3.0 with previous version 0.2.3 dated 2018-10-13

Title: Execute Native Scripts
Description: Run complex native scripts with a single command, similar to system commands.
Author: Sagie Gur-Ari [aut, cre]
Maintainer: Sagie Gur-Ari <sagiegurari@gmail.com>

Diff between scriptexec versions 0.2.3 dated 2018-10-13 and 0.3.0 dated 2018-10-30

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Package tm1r updated to version 1.1.1 with previous version 1.1.0 dated 2018-10-23

Title: The Integration Between 'IBM COGNOS TM1' and R
Description: Useful functions to connect to 'TM1' <https://www.ibm.com/uk-en/marketplace/planning-and-analytics> instance from R via REST API. With the functions in the package, data can be imported from 'TM1' via mdx view or native view, data can be sent to 'TM1', processes and chores can be executed, and cube and dimension metadata information can be taken.
Author: Muhammed Ali Onder
Maintainer: Muhammed Ali Onder <muhammedalionder@gmail.com>

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Package sdStaf updated to version 1.0.2 with previous version 1.0.0 dated 2018-10-03

Title: Species Distribution and Stability Future Models
Description: Functions for post processing the outcomes of ecological niche models. It further include methods to build stability maps based on species distribution models under climate change projections and to reduce environmental data.
Author: P. Joser Atauchi [aut, cre]
Maintainer: P. Joser Atauchi <patauchi@gmail.com>

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Package sdols updated to version 1.7 with previous version 1.6 dated 2018-06-29

Title: Summarizing Distributions of Latent Structures
Description: Summaries of distributions on clusterings and feature allocations are provided. Specifically, point estimates are obtained by the sequentially-allocated latent structure optimization (SALSO) algorithm to minimize squared error loss, absolute error loss, Binder loss, or the lower bound of the variation of information loss. Clustering uncertainty can be assessed with the confidence calculations and the associated plot.
Author: David B. Dahl [aut, cre], Peter Müller [aut]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between sdols versions 1.6 dated 2018-06-29 and 1.7 dated 2018-10-30

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Package remotes updated to version 2.0.2 with previous version 2.0.1 dated 2018-10-19

Title: R Package Installation from Remote Repositories, Including 'GitHub'
Description: Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package is a lightweight replacement of the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Author: Gábor Csárdi [aut, cre], Hadley Wickham [aut], Winston Chang [aut], Jim Hester [aut], RStudio [cph], Martin Morgan [aut], Dan Tenenbaum [aut], Mango Solutions [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package politeness updated to version 0.2.6 with previous version 0.2.5 dated 2018-10-26

Title: Detecting Politeness Features in Text
Description: Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness (Brown & Levinson, 1987 <http://psycnet.apa.org/record/1987-97641-000>; Danescu-Niculescu-Mizil et al., 2013 <arXiv:1306.6078>; Voigt et al., 2017 <doi:10.1073/pnas.1702413114>). We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.
Author: Mike Yeomans, Alejandro Kantor, Dustin Tingley
Maintainer: Mike Yeomans <yeomans@fas.harvard.edu>

Diff between politeness versions 0.2.5 dated 2018-10-26 and 0.2.6 dated 2018-10-30

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Package dexter updated to version 0.8.2 with previous version 0.8.1 dated 2018-08-20

Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests. Developed at Cito, The Netherlands, with subsidy from the Dutch Ministry of Education, Culture, and Science.
Author: Gunter Maris, Timo Bechger, Jesse Koops, Ivailo Partchev
Maintainer: Ivailo Partchev <partchev@gmail.com>

Diff between dexter versions 0.8.1 dated 2018-08-20 and 0.8.2 dated 2018-10-30

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Package BAS updated to version 1.5.3 with previous version 1.5.2 dated 2018-10-25

Title: Bayesian Variable Selection and Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Variable Selection and Model Averaging in linear models and generalized linear models using stochastic or deterministic sampling without replacement from posterior distributions. Prior distributions on coefficients are from Zellner's g-prior or mixtures of g-priors corresponding to the Zellner-Siow Cauchy Priors or the mixture of g-priors from Liang et al (2008) <DOI:10.1198/016214507000001337> for linear models or mixtures of g-priors in GLMs of Li and Clyde (2018) <arXiv:1503.06913>. Other model selection criteria include AIC, BIC and Empirical Bayes estimates of g. Sampling probabilities may be updated based on the sampled models using Sampling w/out Replacement or an efficient MCMC algorithm samples models using the BAS tree structure as an efficient hash table. Uniform priors over all models or beta-binomial prior distributions on model size are allowed, and for large p truncated priors on the model space may be used. The user may force variables to always be included. Details behind the sampling algorithm are provided in Clyde, Ghosh and Littman (2010) <DOI:10.1198/jcgs.2010.09049>. This material is based upon work supported by the National Science Foundation under Grant DMS-1106891. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Author: Merlise Clyde [aut, cre, cph] (<https://orcid.org/-5469>), Michael Littman [ctb], Quanli Wang [ctb], Joyee Ghosh [ctb], Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@duke.edu>

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Package greta updated to version 0.3.0 with previous version 0.2.3 dated 2018-01-22

Title: Simple and Scalable Statistical Modelling in R
Description: Write statistical models in R and fit them by MCMC on CPUs and GPUs, using Google TensorFlow (see <https://greta-dev.github.io/greta> for more information).
Author: Nick Golding [aut, cre] (<https://orcid.org/0000-0001-8916-5570>), Simon Dirmeier [ctb], Adam Fleischhacker [ctb], Shirin Glander [ctb], Martin Ingram [ctb], Lee Hazel [ctb], Tiphaine Martin [ctb], Matt Mulvahill [ctb], Michael Quinn [ctb], David Smith [ctb], Paul Teetor [ctb], Jian Yen [ctb]
Maintainer: Nick Golding <nick.golding.research@gmail.com>

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