Fri, 10 Jul 2020

Package ypr updated to version 0.5.1 with previous version 0.5.0 dated 2020-03-18

Title: Yield Per Recruit
Description: An implementation of equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield for a fish population as described by Walters and Martell (2004) <isbn:0-691-11544-3>. The yield can be based on the number of fish caught (or harvested) or biomass caught for all fish or just large (trophy) individuals.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between ypr versions 0.5.0 dated 2020-03-18 and 0.5.1 dated 2020-07-10

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Package yesno updated to version 0.1.2 with previous version 0.1.1 dated 2020-03-04

Title: Ask Yes-No Questions
Description: Asks Yes-No questions with variable or custom responses.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package SwimmeR updated to version 0.3.0 with previous version 0.2.0 dated 2020-04-10

Title: Data Import, Cleaning, and Conversions for Swimming Results
Description: There are two goals for 'SwimmeR' as presently constructed. The first is reading in swimming results from html or pdf sources and returning tidy dataframes. The second is working with the resulting data. To this end 'SwimmeR' converts swimming times (performances) between the computationally useful format of seconds, reported to the 100ths place (eg 95.37), and the conventional reporting format (1:35.37) used in the swimming community, as well as providing tools for assigning team names etc. Additionally 'SwimmeR' has functions for drawing single-elimination brackets and also converts times between the various pool sizes used in competitive swimming, namely 50m length (LCM), 25m length (SCM) and 25y length (SCY).
Author: Greg Pilgrim [aut, cre] (<https://orcid.org/0000-0001-7831-442X>), Caitlin Baldwin [ctb]
Maintainer: Greg Pilgrim <gpilgrim2670@gmail.com>

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Package pins updated to version 0.4.3 with previous version 0.4.2 dated 2020-07-05

Title: Pin, Discover and Share Resources
Description: Pin remote resources into a local cache to work offline, improve speed and avoid recomputing; discover and share resources in local folders, 'GitHub', 'Kaggle' or 'RStudio Connect'. Resources can be anything from 'CSV', 'JSON', or image files to arbitrary R objects.
Author: Javier Luraschi [aut, cre], RStudio [cph]
Maintainer: Javier Luraschi <javier@rstudio.com>

Diff between pins versions 0.4.2 dated 2020-07-05 and 0.4.3 dated 2020-07-10

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Package pillar updated to version 1.4.6 with previous version 1.4.5 dated 2020-07-09

Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed for formatting columns of data using the full range of colours provided by modern terminals.
Author: Kirill Müller [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

Diff between pillar versions 1.4.5 dated 2020-07-09 and 1.4.6 dated 2020-07-10

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Package phonfieldwork updated to version 0.0.7 with previous version 0.0.6 dated 2020-06-20

Title: Linguistic Phonetic Fieldwork Tools
Description: There are a lot of different typical tasks that have to be solved during phonetic research and experiments. This includes creating a presentation that will contain all stimuli, renaming and concatenating multiple sound files recorded during a session, automatic annotation in 'Praat' TextGrids (this is one of the sound annotation standards provided by 'Praat' software, see Boersma & Weenink 2018 <http://www.fon.hum.uva.nl/praat/>), creating an html table with annotations and spectrograms, and converting multiple formats ('Praat' TextGrid, 'ELAN', 'EXMARaLDA', 'Audacity', subtitles '.srt', and 'FLEx' flextext). All of these tasks can be solved by a mixture of different tools (any programming language has programs for automatic renaming, and Praat contains scripts for concatenating and renaming files, etc.). 'phonfieldwork' provides a functionality that will make it easier to solve those tasks independently of any additional tools. You can also compare the functionality with other packages: 'rPraat' <https://CRAN.R-project.org/package=rPraat>, 'textgRid' <https://CRAN.R-project.org/package=textgRid>.
Author: George Moroz [aut, cre] (<https://orcid.org/0000-0003-1990-6083>)
Maintainer: George Moroz <agricolamz@gmail.com>

Diff between phonfieldwork versions 0.0.6 dated 2020-06-20 and 0.0.7 dated 2020-07-10

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Package bubblyr updated to version 0.1.1 with previous version 0.1.0 dated 2020-06-29

Title: Beautiful Bubbles for 'shiny' and 'rmarkdown' Backgrounds
Description: Creates bubbles within 'shiny' and 'rmarkdown' backgrounds using the 'bubbly-bg' 'JavaScript' library.
Author: Mohamed El Fodil Ihaddaden [aut, cre], David Åse [cph] (bubbly-bg library)
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>

Diff between bubblyr versions 0.1.0 dated 2020-06-29 and 0.1.1 dated 2020-07-10

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New package gen3sis with initial version 1.0
Package: gen3sis
Type: Package
Title: General Engine for Eco-Evolutionary Simulations
Version: 1.0
Authors@R: c( person("ETH Zürich", role=c("cph")), person("Oskar", "Hagen", email = "oskar@hagen.bio", role = c("aut", "cre"), comment = "Landscape Ecology, WSL and ETH Zürich, Switzerland"), person("Benjamin", "Flueck", email="benjamin.flueck@alumni.ethz.ch", role = c("aut"), comment = "Landscape Ecology, WSL and ETH Zürich, Switzerland"), person("Fabian", "Fopp", email="fabian.fopp@usys.ethz.ch", role = c("aut"), comment = "Landscape Ecology, WSL and ETH Zürich, Switzerland"), person(c("Juliano","S."), "Cabral", email = "juliano.sarmento_cabral@uni-wuerzburg.de", role = c("aut"), comment = "Ecosystem Modeling, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany"), person("Florian", "Hartig", email = "florian.hartig@biologie.uni-regensburg.de", role = c("aut"), comment = "Theoretical Ecology, University of Regensburg, Regensburg, Germany"), person("Mikael", "Pontarp", email = "mikael.pontarp@biol.lu.se", role = c("aut"), comment = "Department of Biology, Lund University, Lund, Sweden"), person("Charles", "Novaes de Santana ", email = "charles.novaes@usys.ethz.ch", role = c("ctb"), comment = "Landscape Ecology, WSL and ETH Zürich, Switzerland"), person(c("Thiago", "F."), "Rangel", email = "rangel.tf@gmail.com", role = c("aut"), comment = "Department of Ecology, Universidade Federal de Goiás, Goiás, Brazil"), person("Theo", "Gaboriau", email = "theo.gaboriau@unil.ch", role = c("ctb"), comment = "Depatment of Computational Biology, Lausanne University, Switzerland"), person("Loïc", "Pellissier", email = "loic.pellissier@usys.ethz.ch", role = c("aut","ths"), comment = "Landscape Ecology, WSL and ETH Zürich, Switzerland"))
Description: Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 0.12.16), Matrix, methods, utils, raster, gdistance, sp, stringr, tools, grDevices
Suggests: knitr, testthat (>= 2.1.0), rmarkdown
LinkingTo: Rcpp, BH
URL: https://github.com/project-Gen3sis/R-package
BugReports: https://github.com/project-Gen3sis/R-package/issues
RoxygenNote: 7.1.1
VignetteBuilder: knitr
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2020-07-09 12:43:57 UTC; ohagen
Author: ETH Zürich [cph], Oskar Hagen [aut, cre] (Landscape Ecology, WSL and ETH Zürich, Switzerland), Benjamin Flueck [aut] (Landscape Ecology, WSL and ETH Zürich, Switzerland), Fabian Fopp [aut] (Landscape Ecology, WSL and ETH Zürich, Switzerland), Juliano S. Cabral [aut] (Ecosystem Modeling, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany), Florian Hartig [aut] (Theoretical Ecology, University of Regensburg, Regensburg, Germany), Mikael Pontarp [aut] (Department of Biology, Lund University, Lund, Sweden), Charles Novaes de Santana [ctb] (Landscape Ecology, WSL and ETH Zürich, Switzerland), Thiago F. Rangel [aut] (Department of Ecology, Universidade Federal de Goiás, Goiás, Brazil), Theo Gaboriau [ctb] (Depatment of Computational Biology, Lausanne University, Switzerland), Loïc Pellissier [aut, ths] (Landscape Ecology, WSL and ETH Zürich, Switzerland)
Maintainer: Oskar Hagen <oskar@hagen.bio>
Repository: CRAN
Date/Publication: 2020-07-10 16:40:02 UTC

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Package TreeDist updated to version 1.1.1 with previous version 1.0.0 dated 2020-06-30

Title: Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith, 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Calculates the median of a set of trees under any distance metric.
Author: Martin R. Smith [aut, cre, cph, prg] (<https://orcid.org/0000-0001-5660-1727>), Roy Jonker [prg, cph], Yong Yang [ctb, cph], Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between TreeDist versions 1.0.0 dated 2020-06-30 and 1.1.1 dated 2020-07-10

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Package specmine updated to version 3.0.1 with previous version 3.0.0 dated 2020-07-10

Title: Metabolomics and Spectral Data Analysis and Mining
Description: Provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, feature selection and pathway analysis. Case studies can be found on the website: <http://bio.di.uminho.pt/metabolomicspackage/index.html>. This package suggests 'rcytoscapejs', a package not in mainstream repositories. If you need to install it, use: devtools::install_github('cytoscape/r-cytoscape.js@v0.0.7').
Author: Christopher Costa <chrisbcl@hotmail.com> [aut], Marcelo Maraschin <mtocsy@gmail.com> [aut], Miguel Rocha <mrocha@di.uminho.pt> [aut, cre], Sara Cardoso <saracardoso501@gmail.com> [aut], Telma Afonso <telma.afonso94@gmail.com> [aut], C. Beleites [cph], Jie Hao [cph]
Maintainer: Miguel Rocha <mrocha@di.uminho.pt>

Diff between specmine versions 3.0.0 dated 2020-07-10 and 3.0.1 dated 2020-07-10

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Package SLOPE updated to version 0.3.2 with previous version 0.3.0 dated 2020-07-02

Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation (SLOPE): generalized linear models regularized with the sorted L1-norm (Bogdan et al. (2015) <doi:10/gfgwzt>). Supported models include ordinary least-squares regression, binomial regression, multinomial regression, and Poisson regression. Both dense and sparse predictor matrices are supported. In addition, the package features predictor screening rules that enable fast and efficient solutions to high-dimensional problems.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>), Jonas Wallin [aut] (<https://orcid.org/0000-0003-0381-6593>), Malgorzata Bogdan [aut], Ewout van den Berg [aut], Chiara Sabatti [aut], Emmanuel Candes [aut], Evan Patterson [aut], Weijie Su [aut], Jerome Friedman [ctb] (code adapted from 'glmnet'), Trevor Hastie [ctb] (code adapted from 'glmnet'), Rob Tibshirani [ctb] (code adapted from 'glmnet'), Balasubramanian Narasimhan [ctb] (code adapted from 'glmnet'), Noah Simon [ctb] (code adapted from 'glmnet'), Junyang Qian [ctb] (code adapted from 'glmnet'), Akarsh Goyal [ctb]
Maintainer: Johan Larsson <johan.larsson@stat.lu.se>

Diff between SLOPE versions 0.3.0 dated 2020-07-02 and 0.3.2 dated 2020-07-10

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 16 files changed, 154 insertions(+), 75 deletions(-)

More information about SLOPE at CRAN
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Package qtl2 updated to version 0.22-11 with previous version 0.22-8 dated 2020-06-26

Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>

Diff between qtl2 versions 0.22-8 dated 2020-06-26 and 0.22-11 dated 2020-07-10

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More information about qtl2 at CRAN
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Package partykit updated to version 1.2-9 with previous version 1.2-8 dated 2020-06-10

Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from different sources ('rpart', 'RWeka', 'PMML') yielding objects that share functionality for print()/plot()/predict() methods. Furthermore, new and improved reimplementations of conditional inference trees (ctree()) and model-based recursive partitioning (mob()) from the 'party' package are provided based on the new infrastructure. A description of this package was published by Hothorn and Zeileis (2015) <http://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>), Heidi Seibold [ctb] (<https://orcid.org/0000-0002-8960-9642>), Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between partykit versions 1.2-8 dated 2020-06-10 and 1.2-9 dated 2020-07-10

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More information about partykit at CRAN
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Package mixl updated to version 1.2.0 with previous version 1.1.2 dated 2020-03-21

Title: Simulated Maximum Likelihood Estimation of Mixed Logit Models for Large Datasets
Description: Specification and estimation of multinomial logit models. Large datasets and complex models are supported, with an intuitive syntax. Multinomial Logit Models, Mixed models, random coefficients and Hybrid Choice are all supported. For more information, see Molloy et al. (2019) <doi:10.3929/ethz-b-000334289>.
Author: Joseph Molloy [aut, cre]
Maintainer: Joseph Molloy <joseph.molloy@ivt.baug.ethz.ch>

Diff between mixl versions 1.1.2 dated 2020-03-21 and 1.2.0 dated 2020-07-10

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Package miceFast updated to version 0.6.2 with previous version 0.6.1 dated 2020-07-06

Title: Fast Imputations Using 'Rcpp' and 'Armadillo'
Description: Fast imputations under the object-oriented programming paradigm. Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'. The biggest improvement in time performance could be achieve for a calculation where a grouping variable have to be used. A single evaluation of a quantitative model for the multiple imputations is another major enhancement. A new major improvement is one of the fastest predictive mean matching in the R world because of presorting and binary search.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>

Diff between miceFast versions 0.6.1 dated 2020-07-06 and 0.6.2 dated 2020-07-10

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Package EPX updated to version 1.0.1 with previous version 1.0.0 dated 2020-07-03

Title: Ensemble of Phalanxes
Description: An ensemble method for the statistical detection of a rare class in two-class classification problems. The method uses an ensemble of classifiers where the constituent models of the ensemble use disjoint subsets (phalanxes) of explanatory variables. We provide an implementation of the phalanx-formation algorithm. Please see Tomal et al. (2015) <doi:10.1214/14-AOAS778>, Tomal et al. (2016) <doi:10.1021/acs.jcim.5b00663>, and Tomal et al. (2019) <arXiv:1706.06971> for more details.
Author: Jabed Tomal [aut, cre], Grace Hsu [aut], William Welch [aut], Marcia Wang [ctb]
Maintainer: Jabed Tomal <jtomal@tru.ca>

Diff between EPX versions 1.0.0 dated 2020-07-03 and 1.0.1 dated 2020-07-10

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Package emdi updated to version 2.0.1 with previous version 2.0.0 dated 2020-07-07

Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional disaggregated indicators. So far, estimation methods comprise direct estimation, the model-based unit-level approach Empirical Best Prediction (see "Small area estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), the area-level model (see "Estimates of income for small places: An application of James-Stein procedures to Census Data" by (Fay and Herriot 1979) <doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance estimation methods, log and arcsin transformation, spatial, robust and measurement error models), as well as their precision estimates. The assessment of the used model is supported by a summary and diagnostic plots. For a suitable presentation of estimates, map plots can be easily created. Furthermore, results can easily be exported to excel. For a detailed description of the package and the methods used see "The {R} Package {emdi} for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07>.
Author: Sylvia Harmening [aut], Ann-Kristin Kreutzmann [aut], Soeren Pannier [aut, cre], Natalia Rojas-Perilla [aut], Nicola Salvati [aut], Timo Schmid [aut], Matthias Templ [aut], Nikos Tzavidis [aut], Nora Würz [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>

Diff between emdi versions 2.0.0 dated 2020-07-07 and 2.0.1 dated 2020-07-10

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More information about emdi at CRAN
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Package DescTools updated to version 0.99.37 with previous version 0.99.36 dated 2020-05-23

Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell [aut, cre], Ken Aho [ctb], Andreas Alfons [ctb], Nanina Anderegg [ctb], Tomas Aragon [ctb], Antti Arppe [ctb], Adrian Baddeley [ctb], Kamil Barton [ctb], Ben Bolker [ctb], Hans W. Borchers [ctb], Frederico Caeiro [ctb], Stephane Champely [ctb], Daniel Chessel [ctb], Leanne Chhay [ctb], Clint Cummins [ctb], Michael Dewey [ctb], Harold C. Doran [ctb], Stephane Dray [ctb], Charles Dupont [ctb], Dirk Eddelbuettel [ctb], Jeff Enos [ctb], Claus Ekstrom [ctb], Martin Elff [ctb], Richard W. Farebrother [ctb], John Fox [ctb], Romain Francois [ctb], Michael Friendly [ctb], Tal Galili [ctb], Matthias Gamer [ctb], Joseph L. Gastwirth [ctb], Yulia R. Gel [ctb], Vilmantas Gegzna [ctb], Juergen Gross [ctb], Gabor Grothendieck [ctb], Frank E. Harrell Jr [ctb], Richard Heiberger [ctb], Michael Hoehle [ctb], Christian W. Hoffmann [ctb], Soeren Hojsgaard [ctb], Torsten Hothorn [ctb], Markus Huerzeler [ctb], Wallace W. Hui [ctb], Pete Hurd [ctb], Rob J. Hyndman [ctb], Pablo J. Villacorta Iglesias [ctb], Christopher Jackson [ctb], Matthias Kohl [ctb], Mikko Korpela [ctb], Max Kuhn [ctb], Detlew Labes [ctb], Duncan Temple Lang [ctb], Friederich Leisch [ctb], Jim Lemon [ctb], Dong Li [ctb], Martin Maechler [ctb], Arni Magnusson [ctb], Ben Mainwaring [ctb], Daniel Malter [ctb], George Marsaglia [ctb], John Marsaglia [ctb], Alina Matei [ctb], David Meyer [ctb], Weiwen Miao [ctb], Giovanni Millo [ctb], Yongyi Min [ctb], David Mitchell [ctb], Franziska Mueller [ctb], Markus Naepflin [ctb], Daniel Navarro [ctb], Henric Nilsson [ctb], Klaus Nordhausen [ctb], Derek Ogle [ctb], Hong Ooi [ctb], Nick Parsons [ctb], Sandrine Pavoine [ctb], Tony Plate [ctb], Roland Rapold [ctb], William Revelle [ctb], Tyler Rinker [ctb], Brian D. Ripley [ctb], Caroline Rodriguez [ctb], Nathan Russell [ctb], Nick Sabbe [ctb], Venkatraman E. Seshan [ctb], Greg Snow [ctb], Michael Smithson [ctb], Karline Soetaert [ctb], Werner A. Stahel [ctb], Alec Stephenson [ctb], Mark Stevenson [ctb], Ralf Stubner [ctb], Matthias Templ [ctb], Terry Therneau [ctb], Yves Tille [ctb], Luis Torgo [ctb], Adrian Trapletti [ctb], Joshua Ulrich [ctb], Kevin Ushey [ctb], Jeremy VanDerWal [ctb], Bill Venables [ctb], John Verzani [ctb], Gregory R. Warnes [ctb], Stefan Wellek [ctb], Hadley Wickham [ctb], Rand R. Wilcox [ctb], Peter Wolf [ctb], Daniel Wollschlaeger [ctb], Joseph Wood [ctb], Ying Wu [ctb], Thomas Yee [ctb], Achim Zeileis [ctb]
Maintainer: Andri Signorell <andri@signorell.net>

Diff between DescTools versions 0.99.36 dated 2020-05-23 and 0.99.37 dated 2020-07-10

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Package BCRA updated to version 2.1.2 with previous version 2.1.1 dated 2020-06-18

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. Gail MH, Brinton LA, et al (1989) <doi:10.1093/jnci/81.24.1879>. Marthew PB, Gail MH, et al (2016) <doi:10.1093/jnci/djw215>.
Author: Fanni Zhang
Maintainer: Fanni Zhang <rstatpackages@gmail.com>

Diff between BCRA versions 2.1.1 dated 2020-06-18 and 2.1.2 dated 2020-07-10

 DESCRIPTION         |   14 ++++++++------
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Package GenBinomApps updated to version 1.1 with previous version 1.0-2 dated 2014-06-30

Title: Clopper-Pearson Confidence Interval and Generalized Binomial Distribution
Description: Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution. Functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Enhanced model for burn-in studies, where failures are tackled by countermeasures.
Author: Horst Lewitschnig, David Lenzi
Maintainer: Horst Lewitschnig <Horst.Lewitschnig@infineon.com>

Diff between GenBinomApps versions 1.0-2 dated 2014-06-30 and 1.1 dated 2020-07-10

 DESCRIPTION |    8 ++++----
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New package newFocus with initial version 1.0
Package: newFocus
Type: Package
Title: True Discovery Guarantee by the New Focus Level Procedure
Version: 1.0
Date: 2020-07-09
Author: Ningning Xu
Maintainer: Ningning Xu <n.xu@lumc.nl>
Description: A new focus level procedure is developed based on the old focus level procedure of Goeman and Mansmann (2008) <doi:10.1093/bioinformatics/btm628> and the closed testing procedure with globaltest of Xu and Goeman (2020) <arXiv:2001.01541>. It produces the lower bound for the number of true discoveries in any gene set or GO (Gene Ontology) term. It is more powerful for the focus level GO terms chosen by user before seeing the data than the non-focus level GO terms or gene sets chosen after seeing the data.
License: GPL (>= 2)
Depends: ctgt
NeedsCompilation: no
Packaged: 2020-07-10 09:50:32 UTC; nxu
Repository: CRAN
Date/Publication: 2020-07-10 13:40:03 UTC

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Package KeyboardSimulator updated to version 2.5.1 with previous version 2.5.0 dated 2020-04-14

Title: Keyboard and Mouse Input Simulation for Windows OS
Description: Control your keyboard and mouse with R code by simulating key presses and mouse clicks. The input simulation is implemented with the Windows API.
Author: Jim Chen [aut, cre], Jeff Keller [aut, ctb], Garry Hopwood [ctb], Chieh Hsu [ctb]
Maintainer: Jim Chen <jim71183@gmail.com>

Diff between KeyboardSimulator versions 2.5.0 dated 2020-04-14 and 2.5.1 dated 2020-07-10

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Package sweep updated to version 0.2.3 with previous version 0.2.2 dated 2019-10-08

Title: Tidy Tools for Forecasting
Description: Tidies up the forecasting modeling and prediction work flow, extends the 'broom' package with 'sw_tidy', 'sw_glance', 'sw_augment', and 'sw_tidy_decomp' functions for various forecasting models, and enables converting 'forecast' objects to "tidy" data frames with 'sw_sweep'.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

Diff between sweep versions 0.2.2 dated 2019-10-08 and 0.2.3 dated 2020-07-10

 DESCRIPTION                                       |   15 
 MD5                                               |   74 +--
 NAMESPACE                                         |    3 
 NEWS.md                                           |   10 
 R/global_vars.R                                   |    2 
 R/sw_augment.R                                    |    2 
 R/sw_sweep.R                                      |    6 
 R/sweep-package.R                                 |    4 
 R/tidiers_arima.R                                 |    2 
 R/tidiers_ets.R                                   |    2 
 R/tidiers_robets.R                                |    2 
 R/tidiers_stl.R                                   |   83 +++
 R/utils-broom.R                                   |   21 
 README.md                                         |    6 
 build/vignette.rds                                |binary
 inst/doc/SW00_Introduction_to_sweep.R             |   40 -
 inst/doc/SW00_Introduction_to_sweep.html          |  385 +++++++++--------
 inst/doc/SW01_Forecasting_Time_Series_Groups.R    |   34 -
 inst/doc/SW01_Forecasting_Time_Series_Groups.html |  485 +++++++++++-----------
 inst/doc/SW02_Forecasting_Multiple_Models.R       |   46 +-
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 man/arima_string.Rd                               |    2 
 man/bats_string.Rd                                |    2 
 man/bike_sales.Rd                                 |    6 
 man/sw_augment.Rd                                 |    2 
 man/sw_sweep.Rd                                   |    3 
 man/sweep_package.Rd                              |    6 
 man/tbats_string.Rd                               |    2 
 man/tidiers_HoltWinters.Rd                        |    6 
 man/tidiers_StructTS.Rd                           |    3 
 man/tidiers_arima.Rd                              |   16 
 man/tidiers_bats.Rd                               |    6 
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 man/tidiers_ets.Rd                                |    6 
 man/tidiers_nnetar.Rd                             |    3 
 man/tidiers_robets.Rd                             |    6 
 man/tidiers_stl.Rd                                |   43 +
 tests/testthat/test_tidiers_lm.R                  |    4 
 38 files changed, 992 insertions(+), 760 deletions(-)

More information about sweep at CRAN
Permanent link

Package strvalidator updated to version 2.3.0 with previous version 2.2.0 dated 2019-03-22

Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control. Tools to analyze data from internal validation of forensic short tandem repeat (STR) kits are provided. The tools are developed to provide the necessary data to conform with guidelines for internal validation issued by the European Network of Forensic Science Institutes (ENFSI) DNA Working Group, and the Scientific Working Group on DNA Analysis Methods (SWGDAM). A front-end graphical user interface is provided. More information about each function can be found in the respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>

Diff between strvalidator versions 2.2.0 dated 2019-03-22 and 2.3.0 dated 2020-07-10

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More information about strvalidator at CRAN
Permanent link

Package tbl2xts updated to version 1.0.0 with previous version 0.1.3 dated 2019-08-01

Title: Convert Tibbles or Data Frames to Xts Easily
Description: Facilitate the movement between data frames to 'xts'. Particularly useful when moving from 'tidyverse' to the widely used 'xts' package, which is the input format of choice to various other packages. It also allows the user to use a 'spread_by' argument for a character column 'xts' conversion.
Author: Nico Katzke [aut, cre]
Maintainer: Nico Katzke <nfkatzke@gmail.com>

Diff between tbl2xts versions 0.1.3 dated 2019-08-01 and 1.0.0 dated 2020-07-10

 DESCRIPTION                    |   16 +++---
 MD5                            |   46 ++++++++++++-----
 NAMESPACE                      |    4 +
 R/data.R                       |    3 -
 R/tbl_xts.R                    |   47 +++++++----------
 R/xts_tbl.R                    |    5 +
 README.md                      |  108 +++++++++++++++++++++++++----------------
 build/vignette.rds             |binary
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Package metacart updated to version 2.0-3 with previous version 2.0-2 dated 2019-12-06

Title: Meta-CART: A Flexible Approach to Identify Moderators in Meta-Analysis
Description: Meta-CART integrates classification and regression trees (CART) into meta-analysis. Meta-CART is a flexible approach to identify interaction effects between moderators in meta-analysis. The method is described in Dusseldorp et al. (2014) <doi:10.1037/hea0000018> and Li et al. (2017) <doi:10.1111/bmsp.12088>.
Author: Xinru Li [aut, cre], Elise Dusseldorp [aut, cph], Kaihua Liu [ctb] (supported with the plot function), Juan Claramunt [ctb], Jacqueline Meulman [ctb]
Maintainer: Juan Claramunt <j.claramunt.gonzalez@fsw.leidenuniv.nl>

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Package bootImpute updated to version 1.1.0 with previous version 1.0.0 dated 2019-07-18

Title: Bootstrap Inference for Multiple Imputation
Description: Bootstraps and imputes incomplete datasets. Then performs inference on estimates obtained from analysing the imputed datasets as proposed by von Hippel and Bartlett (2019) <arXiv:1210.0870v10>.
Author: Jonathan Bartlett
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>

Diff between bootImpute versions 1.0.0 dated 2019-07-18 and 1.1.0 dated 2020-07-10

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Package VALERIE updated to version 1.1.0 with previous version 1.0.0 dated 2020-02-11

Title: Visualising Splicing at Single-Cell Resolution
Description: Alternative splicing produces a variety of different protein products from a given gene. 'VALERIE' enables visualisation of alternative splicing events from high-throughput single-cell RNA-sequencing experiments. 'VALERIE' computes percent spliced-in (PSI) values for user-specified genomic coordinates corresponding to alternative splicing events. PSI is the proportion of sequencing reads supporting the included exon/intron as defined by Shiozawa (2018) <doi:10.1038/s41467-018-06063-x>. PSI are inferred from sequencing reads data based on specialised infrastructures for representing and computing annotated genomic ranges by Lawrence (2013) <doi:10.1371/journal.pcbi.1003118>. Computed PSI for each single cell are subsequently presented in the form of a heatmap implemented using the 'pheatmap' package by Kolde (2010) <https://CRAN.R-project.org/package=pheatmap>. Board overview of the mean PSI difference and associated p-values across different user-defined groups of single cells are presented in the form of a line graph using the 'ggplot2' package by Wickham (2007) <https://CRAN.R-project.org/package=ggplot2>.
Author: Sean Wen
Maintainer: Sean Wen <sean.wenwx@gmail.com>

Diff between VALERIE versions 1.0.0 dated 2020-02-11 and 1.1.0 dated 2020-07-10

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New package specmine with initial version 3.0.0
Package: specmine
Type: Package
Title: Metabolomics and Spectral Data Analysis and Mining
Version: 3.0.0
Date: 2020-07-10
Author: Christopher Costa <chrisbcl@hotmail.com> [aut], Marcelo Maraschin <mtocsy@gmail.com> [aut], Miguel Rocha <mrocha@di.uminho.pt> [aut, cre], Sara Cardoso <saracardoso501@gmail.com> [aut], Telma Afonso <telma.afonso94@gmail.com> [aut], C. Beleites [cph], Jie Hao [cph]
Maintainer: Miguel Rocha <mrocha@di.uminho.pt>
Depends: R (>= 4.0.0)
SystemRequirements: Python (>=3.5.2) and the following python module: nmrglue.
Imports: hyperSpec, caret, ggplot2, impute, ellipse, GGally, pcaPP, compare, baseline, MASS, pls, readJDX, speaq, gdata, genefilter, RColorBrewer, grDevices, graphics, methods, stats, utils, Metrics
Suggests: ggdendro, reticulate, qdap, scatterplot3d, MAIT, xcms, KEGGgraph, KEGGREST, rcytoscapejs, rgl, grid, curl, RCurl
LazyData: true
Description: Provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, feature selection and pathway analysis. Case studies can be found on the website: <http://bio.di.uminho.pt/metabolomicspackage/index.html>. This package suggests 'rcytoscapejs', a package not in mainstream repositories. If you need to install it, use: devtools::install_github('cytoscape/r-cytoscape.js@v0.0.7').
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2020-07-10 08:52:05 UTC; saracardoso
Repository: CRAN
Date/Publication: 2020-07-10 10:10:02 UTC

More information about specmine at CRAN
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Package SmartEDA updated to version 0.3.6 with previous version 0.3.5 dated 2020-04-25

Title: Summarize and Explore the Data
Description: Exploratory analysis on any input data describing the structure and the relationships present in the data. The package automatically select the variable and does related descriptive statistics. Analyzing information value, weight of evidence, custom tables, summary statistics, graphical techniques will be performed for both numeric and categorical predictors.
Author: Dayanand Ubrangala [aut, cre], Kiran R [aut, ctb], Ravi Prasad Kondapalli [aut, ctb], Sayan Putatunda [aut, ctb]
Maintainer: Dayanand Ubrangala <daya6489@gmail.com>

Diff between SmartEDA versions 0.3.5 dated 2020-04-25 and 0.3.6 dated 2020-07-10

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Package rtide updated to version 0.0.8 with previous version 0.0.7 dated 2020-03-18

Title: Tide Heights
Description: Calculates tide heights based on tide station harmonics. It includes the harmonics data for 637 US stations. The harmonics data was converted from <https://github.com/poissonconsulting/rtide/blob/master/data-raw/harmonics-dwf-20151227-free.tar.bz2>, NOAA web site data processed by David Flater for 'XTide'. The code to calculate tide heights from the harmonics is based on 'XTide'.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Luke Miller [aut], Abram Fleishman [aut], Poisson Consulting [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package readODS updated to version 1.7.0 with previous version 1.6.7 dated 2018-11-26

Title: Read and Write ODS Files
Description: Import ODS (OpenDocument Spreadsheet) into R as a data frame. Also support writing data frame into ODS file.
Author: Gerrit-Jan Schutten, Chung-hong Chan, Thomas J. Leeper, John Foster, and other contributors
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>

Diff between readODS versions 1.6.7 dated 2018-11-26 and 1.7.0 dated 2020-07-10

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Package PreciseSums updated to version 0.4 with previous version 0.3 dated 2018-04-12

Title: Accurate Floating Point Sums and Products
Description: Most of the time floating point arithmetic does approximately the right thing. When adding sums or having products of numbers that greatly differ in magnitude, the floating point arithmetic may be incorrect. This package implements the Kahan (1965) sum <doi:10.1145/363707.363723>, Neumaier (1974) sum <doi:10.1002/zamm.19740540106>, pairwise-sum (adapted from 'NumPy', See Castaldo (2008) <doi:10.1137/070679946> for a discussion of accuracy), and arbitrary precision sum (adapted from the fsum in 'Python' ; Shewchuk (1997) <http://www.cs.berkeley.edu/~jrs/papers/robustr.pdf>). In addition, products are changed to long double precision for accuracy, or changed into a log-sum for accuracy.
Author: Matthew Fidler [aut, cre, cph], Raymond Hettinger [cph, aut], Jonathan Shewchuk [cph, aut], Julian Taylor [cph, aut], Nathaniel Smith [cph, aut], NumPy Team [cph], Python Team [cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>

Diff between PreciseSums versions 0.3 dated 2018-04-12 and 0.4 dated 2020-07-10

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Package parSim updated to version 0.1.4 with previous version 0.1.1 dated 2019-06-21

Title: Parallel Simulation Studies
Description: Perform flexible simulation studies using one or multiple computer cores. The package is set up to be usable on high-performance clusters in addition to being run locally, see examples on <https://github.com/SachaEpskamp/parSim>.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

Diff between parSim versions 0.1.1 dated 2019-06-21 and 0.1.4 dated 2020-07-10

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Package faoutlier updated to version 0.7.4 with previous version 0.7.2 dated 2017-07-22

Title: Influential Case Detection Methods for Factor Analysis and Structural Equation Models
Description: Tools for detecting and summarize influential cases that can affect exploratory and confirmatory factor analysis models as well as structural equation models more generally (Chalmers, 2015, <doi:10.1177/0146621615597894>; Flora, D. B., LaBrish, C. & Chalmers, R. P., 2012, <10.3389/fpsyg.2012.00055>).
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

Diff between faoutlier versions 0.7.2 dated 2017-07-22 and 0.7.4 dated 2020-07-10

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Package EBPRS updated to version 2.0.4 with previous version 2.0.3 dated 2020-02-12

Title: Derive Polygenic Risk Score Based on Emprical Bayes Theory
Description: EB-PRS is a novel method that leverages information for effect sizes across all the markers to improve the prediction accuracy. No parameter tuning is needed in the method, and no external information is needed. This R-package provides the calculation of polygenic risk scores from the given training summary statistics and testing data. We can use EB-PRS to extract main information, estimate Empirical Bayes parameters, derive polygenic risk scores for each individual in testing data, and evaluate the PRS according to AUC and predictive r2. See Song et al. (2020) <doi:10.1371/journal.pcbi.1007565> for a detailed presentation of the method.
Author: Shuang Song [aut, cre], Wei Jiang [aut], Lin Hou [aut] and Hongyu Zhao [aut]
Maintainer: Shuang Song <song-s19@mails.tsinghua.edu.cn>

Diff between EBPRS versions 2.0.3 dated 2020-02-12 and 2.0.4 dated 2020-07-10

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Package dttr2 updated to version 0.3.0 with previous version 0.2.0 dated 2020-05-01

Title: Manipulate Date, POSIXct and hms Vectors
Description: Manipulates date ('Date'), date time ('POSIXct') and time ('hms') vectors. Date/times are considered discrete and are floored whenever encountered. Times are wrapped and time zones are maintained unless explicitly altered by the user.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between dttr2 versions 0.2.0 dated 2020-05-01 and 0.3.0 dated 2020-07-10

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Package shipunov updated to version 1.10 with previous version 1.9 dated 2020-07-01

Title: Miscellaneous Functions from Alexey Shipunov
Description: A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2020) <http://ashipunov.info/shipunov/software/r/r-en.htm>. Most useful functions: Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode() which does multiple recoding in a fast, simple and flexible way; Misclass() which outputs confusion matrix even if classes are not concerted; Overlap() which measures group separation on any projection; Biarrows() which converts any scatterplot into biplot; and Pleiad() which is fast and flexible correlogram.
Author: Alexey Shipunov [aut, cre], Paul Murrell [ctb], Marcello D'Orazio [ctb], Stephen Turner [ctb], Eugeny Altshuler [ctb], Roland Rau [ctb], Marcus W Beck [ctb], Sebastian Gibb [ctb], Weiliang Qiu [ctb], Emmanuel Paradis [ctb], Roger Koenker [ctb], R Core Team [ctb]
Maintainer: Alexey Shipunov <dactylorhiza@gmail.com>

Diff between shipunov versions 1.9 dated 2020-07-01 and 1.10 dated 2020-07-10

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New package GSA.UN with initial version 1.0.0
Package: GSA.UN
Type: Package
Title: Global Sensitivity Analysis Tool
Version: 1.0.0
Authors@R: c(person("Camila", "Garcia-Echeverri", email = "cagarciae@unal.edu.co", comment = c(ORCID = "0000-0001-8227-7684"),role = c("aut", "cre")), person("Maria", "Arenas-Bautista", email = "mcarenasb@unal.edu.co", comment = c(ORCID = "0000-0003-1578-5157"), role = c("cot")), person("Leonardo", "Donado", email = "lddonadog@unal.edu.co", comment=c(ORCID = "0000-0002-5479-3419" ), role = c("cot")))
Maintainer: Camila Garcia-Echeverri <cagarciae@unal.edu.co>
Description: A tool to sensitivity analysis using SOBOL (Sobol, 1993) and AMA (Dell'Oca et al. 2017 <doi:10.5194/hess-21-6219-2017>) indices. It allows to identify the most sensitive parameter or parameters of a model.
Depends: R (>= 3.4)
Imports: stats, e1071, utils
Suggests: knitr, rmarkdown
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-07-09 20:41:30 UTC; camil
Author: Camila Garcia-Echeverri [aut, cre] (<https://orcid.org/0000-0001-8227-7684>), Maria Arenas-Bautista [cot] (<https://orcid.org/0000-0003-1578-5157>), Leonardo Donado [cot] (<https://orcid.org/0000-0002-5479-3419>)
Repository: CRAN
Date/Publication: 2020-07-10 09:40:03 UTC

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New package fastquant with initial version 0.1.2
Package: fastquant
Title: Backtest Investment Strategies with 3 Lines of Code
Version: 0.1.2
Authors@R: c(person(given = "Jose", family = "Endrinal", role = c("aut", "cre"), email = "francis.endrinal@gmail.com"), person(given = "Lorenzo", family = "Ampil", role = c("aut", "cph"), email = "lorenzo.ampil@gmail.com"), person(given = "Jerome", family = "de Leon", role = c("aut"), email = "jpdeleon.bsap@gmail.com"))
Maintainer: Jose Endrinal <francis.endrinal@gmail.com>
Description: Easily backtest investment strategies with as few as 3 lines of 'Python' or 'R' code. Its goal is to promote data driven investing in finance accessible to everyone. This version only contains functionality for pulling Philippine Stock Exchange and Yahoo Finance stock data.
License: MIT + file LICENSE
Imports: dplyr, httr, magrittr, purrr, tidyr, lubridate, assertthat, quantmod, tibble, stringr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: testthat, spelling
Language: en-US
NeedsCompilation: no
Packaged: 2020-07-09 12:49:26 UTC; jgendrinal
Author: Jose Endrinal [aut, cre], Lorenzo Ampil [aut, cph], Jerome de Leon [aut]
Repository: CRAN
Date/Publication: 2020-07-10 09:10:09 UTC

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New package plotmm with initial version 0.1.0
Package: plotmm
Type: Package
Title: Tidy Tools for Visualizing Mixture Models
Version: 0.1.0
BugReports: https://github.com/pdwaggoner/plotmm/issues
Authors@R: c(person("Philip", "Waggoner", role = c("aut", "cre"), email = "philip.waggoner@gmail.com"), person("Fong", "Chan", role = c("aut", "ctb")), person("Lu", "Zhang", role = c("aut", "ctb")))
Maintainer: Philip Waggoner <philip.waggoner@gmail.com>
Description: The main function, plot_mm(), is used for plotting output from mixture models, including both densities and overlaying mixture weight component curves from the fit models. In line with the tidyverse, the package also includes the plot_cut_point() function to visualize the cutpoint (mu) from the model over a histogram of the data density with several color options. Finally, the package includes the plot_mix_comps() helper function, which is used for both added customization as well as in the plot_mm() function. Supported model objects include: 'mixtools', 'EMCluster', and 'flexmix', with more from each forthcoming. Supported mixture model specifications include mixtures of univariate Gaussians, multivariate Gaussians, Gammas, logistic regressions, linear regressions, and Poisson regressions.
Imports: methods, wesanderson, amerika, ggplot2, dplyr, patchwork
Suggests: mixtools, EMCluster, flexmix, testthat, graphics
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2020-07-08 14:40:38 UTC; philipwaggoner
Author: Philip Waggoner [aut, cre], Fong Chan [aut, ctb], Lu Zhang [aut, ctb]
Repository: CRAN
Date/Publication: 2020-07-10 08:40:02 UTC

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New package fhircrackr with initial version 0.1.0
Package: fhircrackr
Type: Package
Title: Handling HL7 FHIR Resources in R
Version: 0.1.0
Date: 2020-07-01
Authors@R: c( person( given = "Thomas", family = "Peschel", email = "tpeschel@imise.uni-leipzig.de", role = c("aut","cre")), person( given = "Julia", family = "Gantner", email = "julia.gantner@med.uni-jena.de", role = "aut", comment=c(ORCID = "0000-0003-1568-5893")), person( given = "Jens", family = "Przybilla", email = "jprzybilla@imise.uni-leipzig.de", role = "aut"), person( given = "Frank", family = "Meineke", email = "frank.meineke@imise.uni-leipzig.de", role = "aut", comment=c(ORCID = "0000-0002-9256-7543")))
Description: Useful tools for conveniently downloading FHIR resources in xml format and converting them to R data frames. The package uses FHIR-search to download bundles from a FHIR server, provides functions to save and read xml-files containing such bundles and allows flattening the bundles to data.frames using XPath expressions.
BugReports: https://github.com/POLAR-fhiR/fhircrackr/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Imports: xml2, stringr, httr, utils, dplyr
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2020-07-08 13:07:01 UTC; tpeschel
Author: Thomas Peschel [aut, cre], Julia Gantner [aut] (<https://orcid.org/0000-0003-1568-5893>), Jens Przybilla [aut], Frank Meineke [aut] (<https://orcid.org/0000-0002-9256-7543>)
Maintainer: Thomas Peschel <tpeschel@imise.uni-leipzig.de>
Repository: CRAN
Date/Publication: 2020-07-10 08:30:03 UTC

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New package fddm with initial version 0.1-1
Package: fddm
Type: Package
Title: Fast Implementation of the Diffusion Decision Model
Version: 0.1-1
Authors@R: c(person(given="Kendal B.", family="Foster", role=c("aut")), person(given="Henrik", family="Singmann", role=c("ctb", "cre"), email="singmann@gmail.com", comment=c(ORCID="0000-0002-4842-3657")))
Description: Provides the probability density function (PDF) of the diffusion decision model (DDM; e.g., Ratcliff & McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) with across-trial variability in the drift rate. Because the PDF of the DDM contains an infinite sum, it needs to be approximated. 'fddm' implements all published approximations (Navarro & Fuss, 2009, <doi:10.1016/j.jmp.2009.02.003>; Gondan, Blurton, & Kesselmeier, 2014, <doi:10.1016/j.jmp.2014.05.002>) plus new approximations. All approximations are implemented purely in 'C++' providing faster speed than existing packages.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.1)
LinkingTo: Rcpp
Depends: R (>= 3.5.0)
Suggests: rtdists, RWiener, ggplot2, reshape2, testthat, knitr, rmarkdown, microbenchmark, ggnewscale
SystemRequirements: C++11
RoxygenNote: 7.1.1
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2020-07-08 14:14:38 UTC; singm
Author: Kendal B. Foster [aut], Henrik Singmann [ctb, cre] (<https://orcid.org/0000-0002-4842-3657>)
Maintainer: Henrik Singmann <singmann@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-10 08:40:05 UTC

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New package cpp11 with initial version 0.1.0
Package: cpp11
Title: A C++11 Interface for R's C Interface
Version: 0.1.0
Authors@R: c(person(given = "Jim", family = "Hester", role = c("aut", "cre"), email = "jim.hester@rstudio.com", comment = c(ORCID = "0000-0002-2739-7082")), person(given = "RStudio", role = c("cph", "fnd")))
Description: Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
SystemRequirements: C++11
RoxygenNote: 7.1.1
Suggests: bench, brio, cli, callr, covr, decor, desc, glue, ggplot2, knitr, lobstr, mockery, scales, testthat, tibble, utils, vctrs, withr, xml2, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/r-lib/cpp11
BugReports: https://github.com/r-lib/cpp11/issues
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2020-07-08 20:34:04 UTC; jhester
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>), RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Repository: CRAN
Date/Publication: 2020-07-10 09:00:02 UTC

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Package ggstar updated to version 0.0.9 with previous version 0.0.6 dated 2020-05-15

Title: Star Layer for 'ggplot2'
Description: To create the regular polygon layer for easily discernible shapes, we developed the package, it can be easily used if you know the 'ggplot2'.
Author: Shuangbin Xu [aut, cre] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Shuangbin Xu <xshuangbin@163.com>

Diff between ggstar versions 0.0.6 dated 2020-05-15 and 0.0.9 dated 2020-07-10

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Package dialr updated to version 0.3.2 with previous version 0.3.1 dated 2020-04-04

Title: Parse, Format, and Validate International Phone Numbers
Description: Parse, format, and validate international phone numbers using Google's 'libphonenumber' java library, <https://github.com/google/libphonenumber>.
Author: Danny Smith [aut, cre], The Social Research Centre [cph]
Maintainer: Danny Smith <danny@gorcha.org>

Diff between dialr versions 0.3.1 dated 2020-04-04 and 0.3.2 dated 2020-07-10

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Package sarsop (with last version 0.6.2) was removed from CRAN

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

2020-06-26 0.6.2
2020-06-26 0.6.3

Permanent link
Package RcmdrPlugin.BiclustGUI (with last version 1.1.1) was removed from CRAN

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

2017-07-03 1.1.1
2017-01-26 1.1.0
2016-08-08 1.0.6
2016-06-28 1.0.4

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Package SparkR (with last version 2.4.6) was removed from CRAN

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

2020-06-06 2.4.6
2020-02-07 2.4.5
2019-09-02 2.4.4
2019-05-09 2.4.3
2019-04-25 2.4.2
2019-04-04 2.4.1

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Package HDoutliers updated to version 1.0.2 with previous version 1.0.1 dated 2020-04-01

Title: Leland Wilkinson's Algorithm for Detecting Multidimensional Outliers
Description: An implementation of an algorithm for outlier detection that can handle a) data with a mixed categorical and continuous variables, b) many columns of data, c) many rows of data, d) outliers that mask other outliers, and e) both unidimensional and multidimensional datasets. Unlike ad hoc methods found in many machine learning papers, HDoutliers is based on a distributional model that uses probabilities to determine outliers.
Author: Chris Fraley [aut, cre], Leland Wilkinson [ctb]
Maintainer: Chris Fraley <cfraley@tableau.com>

Diff between HDoutliers versions 1.0.1 dated 2020-04-01 and 1.0.2 dated 2020-07-10

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Package DysPIA updated to version 1.3 with previous version 1.2 dated 2020-06-24

Title: Dysregulated Pathway Identification Analysis
Description: It is used to identify dysregulated pathways based on a pre-ranked gene pair list. A fast algorithm is used to make the computation really fast. The data in package 'DysPIAData' is needed.
Author: Limei Wang [aut, cre], Jin Li [aut, ctb]
Maintainer: Limei Wang <lemon619@gmail.com>

Diff between DysPIA versions 1.2 dated 2020-06-24 and 1.3 dated 2020-07-10

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Package tilemaps updated to version 0.2.0 with previous version 0.1.0 dated 2020-06-19

Title: Generate Tile Maps
Description: Implements an algorithm for generating maps, known as tile maps, in which each region is represented by a single tile of the same shape and size. The algorithm was first proposed in "Generating Tile Maps" by Graham McNeill and Scott Hale (2017) <doi:10.1111/cgf.13200>. Functions allow users to generate, plot, and compare square or hexagon tile maps.
Author: Kaelyn Rosenberg [aut, cre]
Maintainer: Kaelyn Rosenberg <kaerosenberg@gmail.com>

Diff between tilemaps versions 0.1.0 dated 2020-06-19 and 0.2.0 dated 2020-07-10

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Package tidytuesdayR updated to version 1.0.1 with previous version 1.0.0 dated 2020-06-26

Title: Access the Weekly 'TidyTuesday' Project Dataset
Description: 'TidyTuesday' is a project by the 'R4DS Online Learning Community' in which they post a weekly dataset onto post a weekly dataset in a public data repository (<https://github.com/rfordatascience/tidytuesday>) for people to analyze and visualize. This package provides the tools to easily download this data and the description of the source.
Author: Ellis Hughes [aut, cre], Jon Harmon [ctb], Thomas Mock [ctb], R4DS Online Learning Community [dtc]
Maintainer: Ellis Hughes <ellishughes@live.com>

Diff between tidytuesdayR versions 1.0.0 dated 2020-06-26 and 1.0.1 dated 2020-07-10

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Package mirtCAT updated to version 1.10 with previous version 1.9.3 dated 2019-06-28

Title: Computerized Adaptive Testing with Multidimensional Item Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive and non-adaptive educational and psychological tests using the shiny package (Chalmers (2016) <doi:10.18637/jss.v071.i05>). Suitable for applying unidimensional and multidimensional computerized adaptive tests (CAT) using item response theory methodology and for creating simple questionnaires forms to collect response data directly in R. Additionally, optimal test designs (e.g., "shadow testing") are supported for tests which contain a large number of item selection constraints. Finally, package contains tools useful for performing Monte Carlo simulations for studying the behavior of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre] (<https://orcid.org/0000-0001-5332-2810>)
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

Diff between mirtCAT versions 1.9.3 dated 2019-06-28 and 1.10 dated 2020-07-10

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Thu, 09 Jul 2020

Package tfer updated to version 1.2 with previous version 1.1 dated 2010-11-08

Title: Forensic Glass Transfer Probabilities
Description: Statistical interpretation of forensic glass transfer (Simulation of the probability distribution of recovered glass fragments).
Author: James Curran and TingYu Huang
Maintainer: James Curran <j.curran@auckland.ac.nz>

Diff between tfer versions 1.1 dated 2010-11-08 and 1.2 dated 2020-07-09

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Package SUMMER updated to version 1.0.0 with previous version 0.3.0 dated 2019-10-23

Title: Spatio-Temporal Under-Five Mortality Methods for Estimation
Description: Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872> and Li et al. (2019) <doi:10.1371/journal.pone.0210645>.
Author: Zehang R Li [cre, aut], Bryan D Martin [aut], Yuan Hsiao [aut], Jessica Godwin [aut], Jon Wakefield [aut], Samuel J Clark [aut], Geir-Arne Fuglstad [aut], Andrea Riebler [aut]
Maintainer: Zehang R Li <lizehang@gmail.com>

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Package ssdtools updated to version 0.3.0 with previous version 0.2.0 dated 2020-04-15

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

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Package spant updated to version 1.7.0 with previous version 1.6.0 dated 2020-06-05

Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. <https://martin3141.github.io/spant/>.
Author: Martin Wilson [cre, aut], Yong Wang [ctb], John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

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Package rpdo updated to version 0.3.1 with previous version 0.3.0 dated 2020-03-04

Title: Pacific Decadal Oscillation Index Data
Description: Monthly Pacific Decadal Oscillation (PDO) index values from January 1900 to September 2018. Superseded by 'rsoi' package which includes the historical and most recent monthly PDO index values together with related climate indices.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Nathan Mantua [aut, dtc], Steven R. Hare [aut, dtc]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package rlang updated to version 0.4.7 with previous version 0.4.6 dated 2020-05-02

Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between rlang versions 0.4.6 dated 2020-05-02 and 0.4.7 dated 2020-07-09

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More information about rlang at CRAN
Permanent link

Package Pareto updated to version 2.1.0 with previous version 2.0.0 dated 2020-05-02

Title: The Pareto, Piecewise Pareto and Generalized Pareto Distribution
Description: Utilities for the Pareto, piecewise Pareto and generalized Pareto distribution that are useful for reinsurance pricing. In particular, the package provides a non-trivial algorithm that can be used to match the expected losses of a tower of reinsurance layers with a layer-independent collective risk model. The theoretical background of the matching algorithm and most other methods are described in Ulrich Riegel (2018) <doi:10.1007/s13385-018-0177-3>.
Author: Ulrich Riegel [aut, cre]
Maintainer: Ulrich Riegel <ulrich.riegel@gmx.de>

Diff between Pareto versions 2.0.0 dated 2020-05-02 and 2.1.0 dated 2020-07-09

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More information about Pareto at CRAN
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Package apsimx updated to version 1.946 with previous version 1.941 dated 2020-07-01

Title: Inspect, Read, Edit and Run 'APSIM' "Next Generation" and 'APSIM' Classic
Description: The functions in this package inspect, read, edit and run files for 'APSIM' "Next Generation" ('JSON') and 'APSIM' "Classic" ('XML'). The files with an 'apsim' extension correspond to 'APSIM' Classic (7.x) - Windows only - and the ones with an 'apsimx' extension correspond to 'APSIM' "Next Generation". For more information about 'APSIM' see (<https://www.apsim.info/>) and for 'APSIM' next generation (<https://apsimnextgeneration.netlify.com/>).
Author: Fernando Miguez [aut, cre] (<https://orcid.org/0000-0002-4627-8329>)
Maintainer: Fernando Miguez <femiguez@iastate.edu>

Diff between apsimx versions 1.941 dated 2020-07-01 and 1.946 dated 2020-07-09

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More information about apsimx at CRAN
Permanent link

Package pillar updated to version 1.4.5 with previous version 1.4.4 dated 2020-05-05

Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed for formatting columns of data using the full range of colours provided by modern terminals.
Author: Kirill Müller [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

Diff between pillar versions 1.4.4 dated 2020-05-05 and 1.4.5 dated 2020-07-09

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Package ncvreg updated to version 3.12.0 with previous version 3.11.2 dated 2020-02-13

Title: Regularization Paths for SCAD and MCP Penalized Regression Models
Description: Fits regularization paths for linear regression, GLM, and Cox regression models using lasso or nonconvex penalties, in particular the minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) penalty, with options for additional L2 penalties (the "elastic net" idea). Utilities for carrying out cross-validation as well as post-fitting visualization, summarization, inference, and prediction are also provided.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/0000-0002-0650-1119>)
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>

Diff between ncvreg versions 3.11.2 dated 2020-02-13 and 3.12.0 dated 2020-07-09

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Package sparklyr updated to version 1.3.1 with previous version 1.3.0 dated 2020-06-27

Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data processing, see <http://spark.apache.org>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut], Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), Kevin Ushey [aut], JJ Allaire [aut], Samuel Macedo [ctb], Hossein Falaki [aut], Lu Wang [aut], Andy Zhang [aut], Yitao Li [aut, cre], RStudio [cph], The Apache Software Foundation [aut, cph]
Maintainer: Yitao Li <yitao@rstudio.com>

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Package hmstimer updated to version 0.1.0 with previous version 0.0.2 dated 2019-07-24

Title: 'hms' Based Timer
Description: Tracks elapsed clock time using a `hms::hms()` scalar, which if running has an attribute named start that specifies the system time when the timer was started. The elapsed time is the value of the scalar plus the difference between the current system time and the system time when the timer was started.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package blocksdesign updated to version 4.3 with previous version 4.2 dated 2020-06-11

Title: Nested and Crossed Block Designs for Factorial and Unstructured Treatment Sets
Description: Constructs D-optimal or near D-optimal treatment and block designs for linear treatment models with crossed or nested block factors. The treatment design can be any arbitrary linear model defined by a treatment model formula and the block design can be any feasible combination of crossed or nested block factors. The block design factors are optimized sequentially and the levels of each successive block factor are optimized within the levels of each preceding block factor. Crossed block designs with non-singular interaction effects are optimized using a weighting scheme that allows for differential weighting of first and second-order block effects. Outputs include a table showing the allocation of treatments to blocks and tables showing the achieved D-efficiency factors for each block and treatment design.
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>

Diff between blocksdesign versions 4.2 dated 2020-06-11 and 4.3 dated 2020-07-09

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New package dnapath with initial version 0.6.4
Package: dnapath
Type: Package
Title: Differential Network Analysis using Gene Pathways
Version: 0.6.4
Author: Tyler Grimes and Somnath Datta
Maintainer: Tyler Grimes <tyler.grimes@ufl.edu>
Description: Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.
Depends: R (>= 3.6.0)
License: GPL-2 | GPL-3
LazyData: true
Imports: Rcpp (>= 1.0.1), biomaRt, reactome.db, corpcor, igraph, ggplot2, SeqNet, Rdpack, dplyr, tibble, stats, methods, curl, graphics, grDevices, utils
RdMacros: Rdpack
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
RoxygenNote: 7.1.0
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, readr, bc3net, DWLasso, GENIE3, huge, minet
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2020-07-09 14:05:22 UTC; Grimes
Repository: CRAN
Date/Publication: 2020-07-09 17:30:03 UTC

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Package dae updated to version 3.1-27 with previous version 3.1-23 dated 2020-03-16

Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii) Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions, (vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions. There is a vignette describing how to use the design functions for randomizing and assessing designs available as a vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of information when the 'Error' function has been used in the call to 'aov'. The package 'dae' can also be installed from <http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre] (<https://orcid.org/0000-0003-0581-1817>)
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>

Diff between dae versions 3.1-23 dated 2020-03-16 and 3.1-27 dated 2020-07-09

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New package ActivePathways with initial version 1.0.2
Package: ActivePathways
Title: Integrative Pathway Enrichment Analysis of Multivariate Omics Data
Version: 1.0.2
Authors@R: c(person("Juri", "Reimand", email = "juri.reimand@utoronto.ca", role = c("aut", "cre")), person("Jonathan", "Barenboim", email = "jon.barenboim@gmail.com", role = "aut"))
Description: Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The package is part of the following publication: Integrative Pathway Enrichment Analysis of Multivariate Omics Data. Paczkowska M^, Barenboim J^, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group; Reimand J, PCAWG Consortium. Nature Communications (2020) <doi:10.1038/s41467-019-13983-9>.
Depends: R (>= 3.6)
Imports: data.table, ggplot2
License: GPL-3
URL:
BugReports: https://github.com/reimandlab/ActivePathways/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Suggests: testthat, knitr, rmarkdown, metap, EmpiricalBrownsMethod
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-07-09 15:28:05 UTC; jreimand
Author: Juri Reimand [aut, cre], Jonathan Barenboim [aut]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>
Repository: CRAN
Date/Publication: 2020-07-09 17:20:02 UTC

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Package R.rsp updated to version 0.44.0 with previous version 0.43.2 dated 2019-10-17

Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package PublicationBias updated to version 2.1.0 with previous version 2.0.0 dated 2020-03-30

Title: Sensitivity Analysis for Publication Bias in Meta-Analyses
Description: Performs sensitivity analysis for publication bias in meta-analyses (per Mathur & VanderWeele, 2020 [<https://osf.io/s9dp6>]). These analyses enable statements such as: "For publication bias to shift the observed point estimate to the null, 'significant' results would need to be at least 30-fold more likely to be published than negative or 'nonsignificant' results." Comparable statements can be made regarding shifting to a chosen non-null value or shifting the confidence interval. Provides a worst-case meta-analytic point estimate under maximal publication bias obtained simply by conducting a standard meta-analysis of only the negative and "nonsignificant" studies.
Author: Maya B. Mathur, Tyler J. VanderWeele
Maintainer: Maya B. Mathur <mmathur@stanford.edu>

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Package gsbm updated to version 0.1.1 with previous version 0.1.0 dated 2020-02-28

Title: Estimate Parameters in the Generalized SBM
Description: Given an adjacency matrix drawn from a Generalized Stochastic Block Model with missing observations, this package robustly estimates the probabilities of connection between nodes and detects outliers nodes, as describes in Gaucher, Klopp and Robin (2019) <arXiv:1911.13122>.
Author: Genevieve Robin [aut], Solenne Gaucher [aut, cre]
Maintainer: Solenne Gaucher <solenne.gaucher@math.u-psud.fr>

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Package tmap updated to version 3.1 with previous version 3.0 dated 2020-04-09

Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre], Jakub Nowosad [ctb], Joel Gombin [ctb], Sebastian Jeworutzki [ctb], Kent Russell [ctb], Richard Zijdeman [ctb], John Clouse [ctb], Robin Lovelace [ctb], Jannes Muenchow [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>

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Package splines2 updated to version 0.3.0 with previous version 0.2.8 dated 2018-06-14

Title: Regression Spline Functions and Classes
Description: Constructs B-splines and its integral, M-splines and its integral (I-splines), convex splines (C-splines), generalized Bernstein polynomials, and their derivatives. It also contains a C++ head-only library integrated with Rcpp. See De Boor (1978) <doi:10.1002/zamm.19800600129>, Ramsay (1988) <doi:10.1214/ss/1177012761>, and Meyer (2008) <doi:10.1214/08-AOAS167> for more information about the spline basis.
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>), Jun Yan [aut] (<https://orcid.org/0000-0003-4401-7296>)
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>

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Package sos4R updated to version 0.4.2 with previous version 0.4.1 dated 2020-06-10

Title: Client for OGC Sensor Observation Services
Description: A client for Sensor Observation Services (SOS, see <https://www.opengeospatial.org/standards/sos>) as specified by the Open Geospatial Consortium (OGC). With the package users can retrieve (meta)data from SOS instances and interactively create requests for near real-time observation data based on the available sensors, phenomena, observations etc. using thematic, temporal, and spatial filtering.
Author: Daniel Nuest [cre, aut] (<https://orcid.org/0000-0002-0024-5046>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>), Ben Graeler [aut] (<https://orcid.org/0000-0001-5443-4304>), Benjamin Pross [aut], Eike Hinderk Juerrens [aut], 52°North Initiative for Geospatial Open Source Software GmbH [cph]
Maintainer: Daniel Nuest <daniel.nuest@uni-muenster.de>

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Package politeness updated to version 0.6.1 with previous version 0.6.0 dated 2020-04-18

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 <mk.yeomans@gmail.com>

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New package NRejections with initial version 1.2.0
Package: NRejections
Type: Package
Title: Metrics for Multiple Testing with Correlated Outcomes
Version: 1.2.0
Author: Maya B. Mathur, Tyler J. VanderWeele
Maintainer: Maya B. Mathur <mmathur@stanford.edu>
Description: Implements methods in Mathur and VanderWeele (in preparation) to characterize global evidence strength across W correlated ordinary least squares (OLS) hypothesis tests. Specifically, uses resampling to estimate a null interval for the total number of rejections in, for example, 95% of samples generated with no associations (the global null), the excess hits (the difference between the observed number of rejections and the upper limit of the null interval), and a test of the global null based on the number of rejections.
LazyData: true
License: GPL-2
Imports: stats, doParallel, matrixcalc, StepwiseTest, foreach, mvtnorm
RoxygenNote: 7.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-07-09 12:58:21 UTC; mmathur
Repository: CRAN
Date/Publication: 2020-07-09 13:50:02 UTC

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Package TreeSearch updated to version 0.4.3 with previous version 0.4.2 dated 2020-07-07

Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Description: Searches for phylogenetic trees that are optimal using a user-defined criterion. Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>. Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Martin Brazeau [cph] (<https://orcid.org/0000-0002-0650-1282>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

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Package todor updated to version 0.1.1 with previous version 0.1.0 dated 2020-03-03

Title: Find All TODO Comments and More
Description: This is a simple addin to 'RStudio' that finds all 'TODO', 'FIX ME', 'CHANGED' etc. comments in your project and shows them as a markers list.
Author: Dominik Krzemiński [aut, cre]
Maintainer: Dominik Krzemiński <raymon92@gmail.com>

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Package stringfish updated to version 0.13.3 with previous version 0.13.2 dated 2020-07-08

Title: Alt String Implementation
Description: Provides an extendable and performant 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph], Phillip Hazel [ctb] (Bundled PCRE2 code), Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code), University of Cambridge [cph] (Bundled PCRE2 code), Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with PCRE2), Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash code)
Maintainer: Travers Ching <traversc@gmail.com>

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Package stratvns updated to version 1.1 with previous version 1.0 dated 2017-05-27

Title: Optimal Stratification in Stratified Sampling
Description: An Optimization Algorithm Applied to Stratification Problem.This function aims at constructing optimal strata with an optimization algorithm based on a global optimisation technique called vns.
Author: Leonardo de Lima, Jose Brito, Pedro Gonzalez and Breno Oliveira
Maintainer: Jose Brito <jambrito@gmail.com>

Diff between stratvns versions 1.0 dated 2017-05-27 and 1.1 dated 2020-07-09

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Package RobustGaSP updated to version 0.6.0 with previous version 0.5.7 dated 2019-06-05

Title: Robust Gaussian Stochastic Process Emulation
Description: Robust parameter estimation and prediction of Gaussian stochastic process emulators. It allows for robust parameter estimation and prediction using Gaussian stochastic process emulator. It also implements the parallel partial Gaussian stochastic process emulator for computer model with massive outputs See the reference: Mengyang Gu and Jim Berger, 2016, Annals of Applied Statistics; Mengyang Gu, Xiaojing Wang and Jim Berger, 2018, Annals of Statistics.
Author: Mengyang Gu [aut, cre], Jesus Palomo [aut], James Berger [aut]
Maintainer: Mengyang Gu <mengyang@pstat.ucsb.edu>

Diff between RobustGaSP versions 0.5.7 dated 2019-06-05 and 0.6.0 dated 2020-07-09

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Package quantreg updated to version 5.61 with previous version 5.55 dated 2020-04-01

Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included.
Author: Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Blaise Melly [ctb] (Contributions to preprocessing code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>

Diff between quantreg versions 5.55 dated 2020-04-01 and 5.61 dated 2020-07-09

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Package IRISMustangMetrics updated to version 2.4.0 with previous version 2.3.0 dated 2019-11-15

Title: Statistics and Metrics for Seismic Data
Description: Classes and functions for metrics calculation as part of the 'IRIS DMC MUSTANG' project. The functionality in this package builds upon the base classes of the 'IRISSeismic' package. Metrics include basic statistics as well as higher level 'health' metrics that can help identify problematic seismometers.
Author: Jonathan Callahan [aut], Rob Casey [aut], Mary Templeton [aut], Gillian Sharer [aut, cre]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>

Diff between IRISMustangMetrics versions 2.3.0 dated 2019-11-15 and 2.4.0 dated 2020-07-09

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Package growthPheno updated to version 1.0-26 with previous version 1.0-22 dated 2020-03-18

Title: Plotting, Smoothing and Growth Trait Extraction for Longitudinal Data
Description: Assists in producing longitudinal or profile plots of measured traits. These allow checks to be made for anomalous data and growth patterns in the data to be explored. Smoothing of growth trends for individual plants using smoothing splines is available for removing transient effects. There are tools for diagnosing the adequacy of trait smoothing, either using this package or other packages, such as those that fit nonlinear growth models. A range of per-unit (pot, plant, plot) growth traits can be extracted from longitudinal data, including single time-point smoothed trait values and their growth rates, interval growth rates and other growth statistics, such as maximum growth. The package is particularly suited to preparing data from high-throughput phenotyping facilities, such as imaging data from a Lemna-Tec Scananalyzer 3D (see <https://www.youtube.com/watch?v=MRAF_mAEa7E/> for more information). The package 'growthPheno' can also be installed from <http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre] (<https://orcid.org/0000-0003-0581-1817>)
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>

Diff between growthPheno versions 1.0-22 dated 2020-03-18 and 1.0-26 dated 2020-07-09

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New package cwbtools with initial version 0.3.0
Package: cwbtools
Type: Package
Title: Tools to Create, Modify and Manage 'CWB' Corpora
Version: 0.3.0
Date: 2020-06-24
Authors@R: c(person("Andreas", "Blaette", role = c("aut", "cre"), email = "andreas.blaette@uni-due.de"), person("Christoph", "Leonhardt", role = "ctb", email = "christoph.leonhardt@uni-due.de") )
Description: The 'Corpus Workbench' ('CWB', <http://cwb.sourceforge.net/>) offers a classic and mature approach for working with large, linguistically and structurally annotated corpora. The 'CWB' is memory efficient and its design makes running queries fast (Evert and Hardie 2011, <http://www.stefan-evert.de/PUB/EvertHardie2011.pdf>). The 'cwbtools' package offers pure R tools to create indexed corpus files as well as high-level wrappers for the original C implementation of CWB as exposed by the 'RcppCWB' package <https://CRAN.R-project.org/package=RcppCWB>. Additional functionality to add and modify annotations of corpora from within R makes working with CWB indexed corpora much more flexible and convenient. The 'cwbtools' package in combination with the R packages 'RcppCWB' (<https://CRAN.R-project.org/package=RcppCWB>) and 'polmineR' (<https://CRAN.R-project.org/package=polmineR>) offers a lightweight infrastructure to support the combination of quantitative and qualitative approaches for working with textual data.
Imports: data.table, R6, xml2, stringi, curl, RcppCWB (>= 0.2.8), pbapply, methods, cli, jsonlite, RCurl, rstudioapi, zen4R
Suggests: tm (>= 0.7.3), knitr, tokenizers (>= 0.2.1), tidytext, SnowballC, janeaustenr, devtools, polmineR, NLP, testthat, usethis, rmarkdown
VignetteBuilder: knitr
LazyData: yes
License: GPL-3
Language: en-US
Encoding: UTF-8
URL: https://www.github.com/PolMine/cwbtools
BugReports: https://github.com/PolMine/cwbtools/issues
Collate: 'CorpusData.R' 'corpus.R' 'cwb.R' 'cwbtools.R' 'directories.R' 'encoding.R' 'ner.R' 'p_attribute.R' 'pkg.R' 'registry_file.R' 's_attribute.R'
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-07-09 08:08:32 UTC; andreasblaette
Author: Andreas Blaette [aut, cre], Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Repository: CRAN
Date/Publication: 2020-07-09 12:20:03 UTC

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New package corclass with initial version 0.2
Package: corclass
Type: Package
Title: Correlational Class Analysis
Version: 0.2
Date: 2020-07-08
Author: Andrei Boutyline
Maintainer: Andrei Boutyline <aboutyl@umich.edu>
Description: Perform a correlational class analysis of the data, resulting in a partition of the data into separate modules.
License: GPL-2
Depends: igraph, methods
Suggests: Cairo
NeedsCompilation: no
Packaged: 2020-07-09 00:06:39 UTC; aboutyl
Repository: CRAN
Date/Publication: 2020-07-09 13:00:13 UTC

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Package broom updated to version 0.7.0 with previous version 0.5.6 dated 2020-04-20

Title: Convert Statistical 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>), Simon Couch [aut], Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>), Derek Chiu [ctb], 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], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (<https://orcid.org/0000-0003-0523-7309>), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (<https://orcid.org/0000-0002-3207-0375>), Jasper Cooper [ctb] (<https://orcid.org/0000-0002-8639-3188>), E Auden Krauska [ctb] (<https://orcid.org/0000-0002-1466-5850>), Alex Wang [ctb], Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>), Charles Gray [ctb] (<https://orcid.org/0000-0002-9978-011X>), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (<https://orcid.org/0000-0002-9500-5167>), Eduard Szoecs [ctb], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (<https://orcid.org/0000-0002-3421-6665>), Bruna Wundervald [ctb] (<https://orcid.org/0000-0001-8163-220X>), Joyce Cahoon [ctb] (<https://orcid.org/0000-0001-7217-4702>), Grant McDermott [ctb] (<https://orcid.org/0000-0001-7883-8573>), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (<https://orcid.org/0000-0002-5687-2647>), Lukas Wallrich [ctb] (<https://orcid.org/0000-0003-2121-5177>), James Martherus [ctb] (<https://orcid.org/0000-0002-8285-3300>), Chuliang Xiao [ctb] (<https://orcid.org/0000-0002-8466-9398>), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Cory Brunson [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (<https://orcid.org/0000-0001-9190-6032>), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb]
Maintainer: Alex Hayes <alexpghayes@gmail.com>

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Package pubmedR updated to version 0.0.3 with previous version 0.0.2 dated 2020-04-03

Title: Gathering Metadata About Publications, Grants, Clinical Trials from 'PubMed' Database
Description: A set of tools to extract bibliographic content from 'PubMed' database using 'NCBI' REST API <https://www.ncbi.nlm.nih.gov/home/develop/api/>.
Author: Massimo Aria [aut, cre] (<https://orcid.org/0000-0002-8517-9411>)
Maintainer: Massimo Aria <massimo.aria@gmail.com>

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Package wrGraph updated to version 1.0.2 with previous version 1.0.1 dated 2020-06-02

Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here. This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots, automatic checking for optimal location of legends in plots, small histograms to insert as legends, histograms re-transforming axis labels to linear when plotting log2-transformed data, a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats, principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples, generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>, staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>

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Package weatherr updated to version 0.1.3 with previous version 0.1.2 dated 2015-09-08

Title: Tools for Handling and Scraping Instant Weather Forecast Feeds
Description: Handle instant weather forecasts and geographical information. It combines multiple sources of information to obtain instant weather forecasts.
Author: Stan Yip [aut, cre]
Maintainer: Stan Yip <stanyip101@gmail.com>

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Package jsmodule updated to version 1.1.0 with previous version 1.0.8 dated 2020-06-04

Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>), Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package glmmfields updated to version 0.1.4 with previous version 0.1.3 dated 2019-05-18

Title: Generalized Linear Mixed Models with Robust Random Fields for Spatiotemporal Modeling
Description: Implements Bayesian spatial and spatiotemporal models that optionally allow for extreme spatial deviations through time. 'glmmfields' uses a predictive process approach with random fields implemented through a multivariate-t distribution instead of the usual multivariate normal. Sampling is conducted with 'Stan'. References: Anderson and Ward (2019) <doi:10.1002/ecy.2403>.
Author: Sean C. Anderson [aut, cre], Eric J. Ward [aut], Trustees of Columbia University [cph]
Maintainer: Sean C. Anderson <sean@seananderson.ca>

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Package future updated to version 1.18.0 with previous version 1.17.0 dated 2020-04-18

Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. The simplest way to evaluate an expression in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers etc. Because of its unified API, there is no need to modify any code in order switch from sequential on the local machine to, say, distributed processing on a remote compute cluster. Another strength of this package is that global variables and functions are automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package chest updated to version 0.3.2 with previous version 0.3.1 dated 2020-01-29

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

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Package allestimates updated to version 0.1.7 with previous version 0.1.6 dated 2020-02-05

Title: Effect Estimates from All Models
Description: Estimates and plots effect estimates from models with all possible combinations of a list of variables. It can be used for assessing treatment effects in clinical trials or risk factors in bio-medical and epidemiological research. Like Stata command 'confall' (Wang Z (2007) <doi:10.1177/1536867X0700700203> ), 'allestimates' calculates and stores all effect estimates, and plots them against p values or Akaike information criterion (AIC) values. It currently has functions for linear regression: all_lm(), logistic and Poisson regression: all_glm() and all_speedglm(), and Cox proportional hazards regression: all_cox().
Author: Zhiqiang Wang [aut, cre]
Maintainer: Zhiqiang Wang <zhiqiang.wang@menzies.edu.au>

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Package modgetxl updated to version 0.4 with previous version 0.3 dated 2020-06-28

Title: A 'shiny' Module for Reading Excel Sheets
Description: This is a shiny module that presents a file picker user interface to get an Excel file name, and reads the Excel sheets using 'readxl' package and returns the resulting sheet(s) as a vector and data in dataframe(s).
Author: Yadu Balehosur <yadu@vizualytics.com>
Maintainer: Yadu Balehosur <yadu@vizualytics.com>

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Package causact updated to version 0.3.2 with previous version 0.3.1 dated 2020-06-24

Title: Accelerated Bayesian Analytics with DAGs
Description: Accelerate Bayesian analytics workflows in 'R' through interactive modelling, visualization, and inference. Define probabilistic graphical models using directed acyclic graphs (DAGs) as a unifying language for business stakeholders, statisticians, and programmers. This package relies on the sleek and elegant 'greta' package for Bayesian inference. 'greta', in turn, is an interface into 'TensorFlow' from 'R'. Install 'greta' using instructions available here: <http://causact.com/install-greta.html>. See <http://github.com/flyaflya/causact> or <http://causact.com> for more documentation.
Author: Adam Fleischhacker [aut, cre, cph], Daniela Dapena [ctb], Rose Nguyen [ctb], Jared Sharpe [ctb]
Maintainer: Adam Fleischhacker <ajf@udel.edu>

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Package dnapath (with last version 0.6.3) was removed from CRAN

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

2020-06-25 0.6.3

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Package TestCor (with last version 0.0.2.0) was removed from CRAN

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

2020-06-25 0.0.2.0
2020-01-17 0.0.1.1
2019-07-06 0.0.1.0
2019-02-08 0.0.0.9

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Wed, 08 Jul 2020

Package statebins updated to version 1.4.0 with previous version 1.2.2 dated 2015-12-21

Title: Create United States Uniform Cartogram Heatmaps
Description: The 'cartogram' heatmaps generated by the included methods are an alternative to choropleth maps for the United States and are based on work by the Washington Post graphics department in their report on "The states most threatened by trade" (<http://www.washingtonpost.com/wp-srv/special/business/states-most-threatened-by-trade/>). "State bins" preserve as much of the geographic placement of the states as possible but have the look and feel of a traditional heatmap. Functions are provided that allow for use of a binned, discrete scale, a continuous scale or manually specified colors depending on what is needed for the underlying data.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>), Harold Gil [ctb] (fix for show.guide), Brian Adams [ctb] (theme testing & feedback), Thomas Wood [ctb] (Significant suggestions & testing that made new features possible), Mathew Kiang [ctb] (Minor fix for NA handling)
Maintainer: Bob Rudis <bob@rud.is>

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Package fishflux updated to version 0.0.1.1 with previous version 0.0.1 dated 2020-07-03

Title: Model Elemental Fluxes in Fishes
Description: Model fluxes of carbon, nitrogen, and phosphorus with the use of a coupled bioenergetics and stoichiometric model that incorporates flexible elemental limitation. Additional functions to help the user to find parameters are included. Finally, functions to extract and visualize results are available as well. For an introduction, see vignette. For more information on the theoretical background of this model, see Schiettekatte et al. (2020) <doi:10.1111/1365-2435.13618>.
Author: Nina M. D. Schiettekatte [aut, cre], Diego Barneche [aut]
Maintainer: Nina M. D. Schiettekatte <nina.schiettekatte@gmail.com>

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Package emld updated to version 0.5.0 with previous version 0.4.0 dated 2020-02-05

Title: Ecological Metadata as Linked Data
Description: This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Matthew B. Jones [aut, cph] (<https://orcid.org/0000-0003-0077-4738>), Bryce Mecum [aut, cph] (<https://orcid.org/0000-0002-0381-3766>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package corHMM updated to version 2.2 with previous version 2.1 dated 2020-07-07

Title: Hidden Markov Models of Character Evolution
Description: Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
Author: Jeremy Beaulieu [aut, cre], Brian O'Meara [aut], Jeffrey Oliver [aut], James Boyko [aut]
Maintainer: Jeremy Beaulieu <jmbeauli@uark.edu>

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Package textrecipes updated to version 0.3.0 with previous version 0.2.3 dated 2020-05-22

Title: Extra 'Recipes' for Text Processing
Description: Converting text to numerical features requires specifically created procedures, which are implemented as steps according to the 'recipes' package. These steps allows for tokenization, filtering, counting (tf and tfidf) and feature hashing.
Author: Emil Hvitfeldt [aut, cre] (<https://orcid.org/0000-0002-0679-1945>)
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>

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Package IsoplotR updated to version 3.4 with previous version 3.3 dated 2020-03-19

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

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Package Qtools updated to version 1.5.2 with previous version 1.5.1 dated 2019-12-13

Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These include methods for transformation-based quantile regression, quantile-based measures of location, scale and shape, methods for quantiles of discrete variables, quantile-based multiple imputation, restricted quantile regression, and directional quantile classification. A vignette is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>), Alessio Farcomeni [ctb] (Contributions to midrq code, <https://orcid.org/0000-0002-7104-5826>)
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>

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Package mexhaz updated to version 1.8 with previous version 1.7 dated 2019-12-10

Title: Mixed Effect Excess Hazard Models
Description: Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a random effect at the cluster level (corresponding to a shared frailty).
Author: Hadrien Charvat, Aurelien Belot
Maintainer: Hadrien Charvat <chadrien@ncc.go.jp>

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Package RcppCWB updated to version 0.3.0 with previous version 0.2.9 dated 2020-06-25

Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query engine to efficiently analyze large corpora (<http://cwb.sourceforge.net>). 'RcppCWB' is licensed under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>). The 'CWB' relies on 'pcre' (BSD license, see <http://www.pcre.org/licence.txt>) and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>). See the file LICENSE.note for further information. The package includes modified code of the 'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre], Bernard Desgraupes [aut], Sylvain Loiseau [aut], Oliver Christ [ctb], Bruno Maximilian Schulze [ctb], Stefan Evert [ctb], Arne Fitschen [ctb], Jeroen Ooms [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>

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More information about RcppCWB at CRAN
Permanent link

Package tune updated to version 0.1.1 with previous version 0.1.0 dated 2020-04-02

Title: Tidy Tuning Tools
Description: The ability to tune models is important. 'tune' contains functions and classes to be used in conjunction with other 'tidymodels' packages for finding reasonable values of hyper-parameters in models, pre-processing methods, and post-processing steps.
Author: Max Kuhn [aut, cre], RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>

Diff between tune versions 0.1.0 dated 2020-04-02 and 0.1.1 dated 2020-07-08

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Package dials updated to version 0.0.8 with previous version 0.0.7 dated 2020-06-10

Title: Tools for Creating Tuning Parameter Values
Description: Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.
Author: Max Kuhn [aut, cre], RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>

Diff between dials versions 0.0.7 dated 2020-06-10 and 0.0.8 dated 2020-07-08

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Package bbsBayes updated to version 2.3.3.2020 with previous version 2.3.2.2020 dated 2020-06-27

Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running program that seeks to monitor the status and trends of the breeding birds in North America. Since its start in 1966, the BBS has accumulated over 50 years of data for over 500 species of North American Birds. Given the temporal and spatial structure of the data, hierarchical Bayesian models are used to assess the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform hierarchical Bayesian analysis of BBS data. You can run a full model analysis for one or more species that you choose, or you can take more control and specify how the data should be stratified, prepared for 'JAGS', or modelled. The functions provided here allow you to replicate analyses performed by the United State Geological Survey (USGS, see Link and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service (CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre], Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <edwardsb@uoguelph.ca>

Diff between bbsBayes versions 2.3.2.2020 dated 2020-06-27 and 2.3.3.2020 dated 2020-07-08

 DESCRIPTION           |    8 ++++----
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More information about bbsBayes at CRAN
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Package seismicRoll updated to version 1.1.4 with previous version 1.1.3 dated 2018-12-04

Title: Fast Rolling Functions for Seismology using 'Rcpp'
Description: Fast versions of seismic analysis functions that 'roll' over a vector of values. See the 'RcppRoll' package for alternative versions of basic statistical functions such as rolling mean, median, etc.
Author: Jonathan Callahan [aut], Rob Casey [aut], Mary Templeton [aut], Gillian Sharer [aut, cre]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>

Diff between seismicRoll versions 1.1.3 dated 2018-12-04 and 1.1.4 dated 2020-07-08

 DESCRIPTION          |    8 ++++----
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Package AQuadtree updated to version 1.0.1 with previous version 1.0.0 dated 2020-03-13

Title: Confidentiality of Spatial Point Data
Description: Provides an automatic aggregation tool to manage point data privacy, intended to be helpful for the production of official spatial data and for researchers. The package pursues the data accuracy at the smallest possible areas preventing individual information disclosure. The methodology, based on hierarchical geographic data structures performs aggregation and local suppression of point data to ensure privacy as described in Lagonigro, R., Oller, R., Martori J.C. (2017) <doi:10.2436/20.8080.02.55>. The data structures are created following the guidelines for grid datasets from the European Forum for Geography and Statistics.
Author: Raymond Lagonigro [aut, cre] (<https://orcid.org/0000-0002-8091-4296>), Ramon Oller [aut] (<https://orcid.org/0000-0002-4333-0021>), Joan Carles Martori [aut] (<https://orcid.org/0000-0002-8400-5487>)
Maintainer: Raymond Lagonigro <raymond.lagonigro@uvic.cat>

Diff between AQuadtree versions 1.0.0 dated 2020-03-13 and 1.0.1 dated 2020-07-08

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Package rstan updated to version 2.21.1 with previous version 2.19.3 dated 2020-02-11

Title: R Interface to Stan
Description: User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via 'variational' approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut], Jonah Gabry [aut], Ben Goodrich [cre, aut], Sebastian Weber [aut], Daniel Lee [ctb], Krzysztof Sakrejda [ctb], Modrak Martin [ctb], Trustees of Columbia University [cph], Oleg Sklyar [cph] (R/cxxfunplus.R), The R Core Team [cph] (R/pairs.R, R/dynGet.R), Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R), John Maddock [cph] (gamma.hpp), Paul Bristow [cph] (gamma.hpp), Nikhar Agrawal [cph] (gamma.hpp), Christopher Kormanyos [cph] (gamma.hpp)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

Diff between rstan versions 2.19.3 dated 2020-02-11 and 2.21.1 dated 2020-07-08

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Package landscapemetrics updated to version 1.4.5 with previous version 1.4.4 dated 2020-05-15

Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>) and new ones from the current literature on landscape metrics. This package supports 'raster' spatial objects and takes RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the 'raster' package as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre] (<https://orcid.org/0000-0003-1125-9918>), Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>), Laura J. Graham [ctb] (Input on package structure), Jeffrey Hollister [ctb] (Input on package structure), Kimberly A. With [ctb] (Input on package structure), Florian Privé [ctb] (Original author of underlying C++ code for get_nearestneighbour() function), Project Nayuki [ctb] (Original author of underlying C++ code for get_circumscribingcircle and lsm_p_circle), Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>

Diff between landscapemetrics versions 1.4.4 dated 2020-05-15 and 1.4.5 dated 2020-07-08

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Package googleVis updated to version 0.6.6 with previous version 0.6.5 dated 2020-06-08

Title: R Interface to Google Charts
Description: R interface to Google's chart tools, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required and for some charts a Flash player. The data remains local and is not uploaded to Google.
Author: Markus Gesmann [aut, cre], Diego de Castillo [aut], Joe Cheng [ctb], Ashley Baldry [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>

Diff between googleVis versions 0.6.5 dated 2020-06-08 and 0.6.6 dated 2020-07-08

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Package WaterML updated to version 1.9.5 with previous version 1.9.0 dated 2020-02-12

Title: Fetch and Analyze Data from 'WaterML' and 'WaterOneFlow' Web Services
Description: Lets you connect to any of the 'Consortium of Universities for the Advancement of Hydrological Science, Inc.' ('CUAHSI') Water Data Center 'WaterOneFlow' web services and read any 'WaterML' time series data file. To see list of available web services, see <http://hiscentral.cuahsi.org>. All versions of 'WaterML' (1.0, 1.1 and 2.0) and both types of the web service protocol ('SOAP' and 'REST') are supported. The package has six data download functions: GetServices(): show all public web services from the HIS Central Catalog. HISCentral_GetSites() and HISCentral_GetSeriesCatalog(): search for sites or time series from the HIS Central catalog based on geographic bounding box, server, or keyword. GetVariables(): Show a data.frame with all variables on the server. GetSites(): Show a data.frame with all sites on the server. GetSiteInfo(): Show what variables, methods and quality control levels are available at the specific site. GetValues(): Given a site code, variable code, start time and end time, fetch a data.frame of all the observation time series data values. The GetValues() function can also parse 'WaterML' data from a custom URL or from a local file. The package also has five data upload functions: AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues(). These functions can be used for uploading data to a 'HydroServer Lite' Observations Data Model ('ODM') database via the 'JSON' data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>

Diff between WaterML versions 1.9.0 dated 2020-02-12 and 1.9.5 dated 2020-07-08

 DESCRIPTION                     |   13 
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 R/GetServices.R                 |  156 ++---
 R/GetSiteInfo.R                 | 1164 +++++++++++++++++++-------------------
 R/GetSites.R                    |  630 ++++++++++-----------
 R/GetValues.R                   | 1195 ++++++++++++++++++++--------------------
 R/GetVariables.R                |  454 +++++++--------
 R/HISCentral_GetSeriesCatalog.R |  306 +++++-----
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New package rbscCI with initial version 0.1.0
Package: rbscCI
Type: Package
Title: Blyth-Still-Casella Confidence Interval
Version: 0.1.0
Date: 2020-07-05
Authors@R: c(person("Shimeng", "Huang", role = c("aut", "cre"), email = "dora.huang.sunshine@gmail.com"), person("Keith", "Winstein", role = "aut", email = "keithw@cs.stanford.edu"))
Description: Provides a fast calculation of the Blyth-Still-Casella confidence interval. The implementation follows the 'StatXact' 9 manual (Cytel 2010) and "Refining Binomial Confidence Intervals" by George Casella (1986) <doi:10.2307/3314658>.
License: GPL (>= 3)
Imports: Rcpp
LinkingTo: Rcpp, BH
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2020-07-08 11:43:44 UTC; shimenghuang
Author: Shimeng Huang [aut, cre], Keith Winstein [aut]
Maintainer: Shimeng Huang <dora.huang.sunshine@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-08 13:00:02 UTC

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New package doebioresearch with initial version 0.1.0
Package: doebioresearch
Type: Package
Title: Analysis of Design of Experiments for Biological Research
Version: 0.1.0
Authors@R: c(person("Raj", "Popat", email = "popatrajc@gmail.com", role = c("aut", "cre")), person("Kanthesh", "Banakara", email = "kantheshbanakara@gmail.com ", role = "aut"))
Description: Performs analysis of popular experimental designs used in the field of biological research. The designs covered are completely randomized design, randomized complete block design, factorial completely randomized design, factorial randomized complete block design, split plot design, strip plot design and latin square design. The analysis include analysis of variance, coefficient of determination, normality test of residuals, standard error of mean, standard error of difference and multiple comparison test of means. The package has functions for transformation of data and yield data conversion. Some datasets are also added in order to facilitate examples.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Imports: agricolae (>= 1.3.3), stats (>= 4.0.2)
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-07-08 11:19:58 UTC; Asus
Author: Raj Popat [aut, cre], Kanthesh Banakara [aut]
Maintainer: Raj Popat <popatrajc@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-08 12:20:03 UTC

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Package stars updated to version 0.4-3 with previous version 0.4-2 dated 2020-07-01

Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Michael Sumner [ctb] (<https://orcid.org/0000-0002-2471-7511>), Etienne Racine [ctb], Adriano Fantini [ctb], David Blodgett [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between stars versions 0.4-2 dated 2020-07-01 and 0.4-3 dated 2020-07-08

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Package ForestFit updated to version 0.6.1 with previous version 0.6.0 dated 2020-06-27

Title: Statistical Modelling for Plant Size Distributions
Description: Developed for the following tasks. 1 ) Computing the probability density function, cumulative distribution function, random generation, and estimating the parameters of the eleven mixture models. 2 ) Point estimation of the parameters of two - parameter Weibull distribution using twelve methods and three - parameter Weibull distribution using nine methods. 3 ) The Bayesian inference for the three - parameter Weibull distribution. 4 ) Estimating parameters of the three - parameter Birnbaum - Saunders, generalized exponential, and Weibull distributions fitted to grouped data using three methods including approximated maximum likelihood, expectation maximization, and maximum likelihood. 5 ) Estimating the parameters of the gamma, log-normal, and Weibull mixture models fitted to the grouped data through the EM algorithm, 6 ) Estimating parameters of the nonlinear height curve fitted to the height - diameter observation, 7 ) Estimating parameters, computing probability density function, cumulative distribution function, and generating realizations from gamma shape mixture model introduced by Venturini et al. (2008) <doi:10.1214/07-AOAS156> , 8 ) The Bayesian inference, computing probability density function, cumulative distribution function, and generating realizations from four - parameter Johnson SB distribution, and 9 ) Robust multiple linear regression analysis when error term follows skewed t distribution.
Author: Mahdi Teimouri
Maintainer: Mahdi Teimouri <teimouri@aut.ac.ir>

Diff between ForestFit versions 0.6.0 dated 2020-06-27 and 0.6.1 dated 2020-07-08

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Package pspline.inference updated to version 0.24 with previous version 0.23 dated 2020-07-01

Title: Estimation of Characteristics of Seasonal and Sporadic Infectious Disease Outbreaks Using Generalized Additive Modeling with Penalized Basis Splines
Description: Stochastic inference of infectious disease outcomes using generalized additive (mixed) models.
Author: Ben Artin [aut, cre, cph]
Maintainer: Ben Artin <ben@artins.org>

Diff between pspline.inference versions 0.23 dated 2020-07-01 and 0.24 dated 2020-07-08

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New package StrathE2E2 with initial version 3.1.0
Package: StrathE2E2
Version: 3.1.0
Title: End-to-End Marine Food Web Model
Author: Michael Heath [aut], Ian Thurlbeck [ctb]
Maintainer: Michael Heath <m.heath@strath.ac.uk>
Depends: R (>= 3.6.0),
Imports: deSolve, methods, NetIndices
Description: A dynamic model of the big-picture, whole ecosystem effects of hydrodynamics, temperature, nutrients, and fishing on continental shelf marine food webs. The package has been developed from a prototype described in: Heath, M.R. (2012) <doi:10.1016/j.pocean.2012.03.004> Ecosystem limits to food web fluxes and fisheries yields in the North Sea simulated with an end-to-end food web model. Progress in Oceanography (Special issue: End-to-end modelling: Towards Comparative Analysis of Marine Ecosystem Organisation) 102, 42-66.
License: GPL (>= 2)
LazyData: yes
NeedsCompilation: yes
Date: 2020-06-11
URL: https://gitlab.com/MarineResourceModelling/StrathE2E/StrathE2E2, https://marineresourcemodelling.gitlab.io/
Suggests: knitr, StrathE2E2examples, testthat (>= 2.1.0)
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.1.1
Additional_repositories: https://marineresourcemodelling.gitlab.io/sran
Packaged: 2020-07-07 21:57:14 UTC; ais04103
Repository: CRAN
Date/Publication: 2020-07-08 09:40:02 UTC

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Package IsoSpecR updated to version 2.1.1 with previous version 2.1.0 dated 2020-05-27

Title: The IsoSpec Algorithm
Description: IsoSpec is a fine structure calculator used for obtaining the most probable masses of a chemical compound given the frequencies of the composing isotopes and their masses. It finds the smallest set of isotopologues with a given probability. The probability is assumed to be that of the product of multinomial distributions, each corresponding to one particular element and parametrized by the frequencies of finding these elements in nature. These numbers are supplied by IUPAC - the International Union of Pure and Applied Chemistry.
Author: Mateusz Krzysztof Lacki and Michal Startek
Maintainer: Matteo Lacki <matteo.lacki@gmail.com>

Diff between IsoSpecR versions 2.1.0 dated 2020-05-27 and 2.1.1 dated 2020-07-08

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New package BrasilMF with initial version 1.0.0
Package: BrasilMF
Title: Best Brazilian Financial Market Package
Description: Focuses on unifying the main data of the Brazilian financial market in one package this will help the user to make the best investment decisions, for more information <https://brasilmf.herokuapp.com>.
Version: 1.0.0
Authors@R: c(person(given = "Davi", family = "Rufino", role = c("aut", "cre"), email = "davirufino@gmail.com"), person(given = "Bernardo", family = "Volker", role = "aut"), person(given = "BrasilMF", role = c("cph", "fnd")))
Maintainer: Davi Rufino <davirufino@gmail.com>
License: MIT + file LICENSE
URL: https://github.com/SrMercado/BrasilMF
BugReports: https://github.com/SrMercado/BrasilMF/issues
Depends: R (>= 3.6.0)
Imports: bizdays, dplyr, rvest, RCurl, xml2
Suggests: ipeadatar, highcharter
Encoding: UTF-8
LazyData: yes
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-07-07 12:27:23 UTC; davir
Author: Davi Rufino [aut, cre], Bernardo Volker [aut], BrasilMF [cph, fnd]
Repository: CRAN
Date/Publication: 2020-07-08 09:30:02 UTC

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New package UnifiedDoseFinding with initial version 0.1.7
Package: UnifiedDoseFinding
Type: Package
Title: Dose-Finding Methods for Non-Binary Outcomes
Version: 0.1.7
Author: Chia-Wei Hsu, Haitao Pan, Rongji Mu
Maintainer: Chia-Wei Hsu <Chia-Wei.Hsu@stjude.org>
Description: In many phase I trials, the design goal is to find the dose associated with a certain target toxicity rate. In some trials, the goal can be to find the dose with a certain weighted sum of rates of various toxicity grades. For others, the goal is to find the dose with a certain mean value of a continuous response. This package provides the setup and calculations needed to run a dose-finding trial with non-binary endpoints and performs simulations to assess design’s operating characteristics under various scenarios. Three dose finding designs are included in this package: unified phase I design (Ivanova et al. (2009) <doi:10.1111/j.1541-0420.2008.01045.x>), Quasi-CRM/Robust-Quasi-CRM (Yuan et al. (2007) <doi:10.1111/j.1541-0420.2006.00666.x>, Pan et al. (2014) <doi:10.1371/journal.pone.0098147>) and generalized BOIN design (Mu et al. (2018) <doi:10.1111/rssc.12263>). The toxicity endpoints can be handled with these functions including equivalent toxicity score (ETS), total toxicity burden (TTB), general continuous toxicity endpoints, with incorporating ordinal grade toxicity information into dose-finding procedure. These functions allow customization of design characteristics to vary sample size, cohort sizes, target dose-limiting toxicity (DLT) rates, discrete or continuous toxicity score, and incorporate safety and/or stopping rules.
License: GPL-2
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2020-07-07 18:48:28 UTC; chsu1
Repository: CRAN
Date/Publication: 2020-07-08 08:30:13 UTC

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New package timedeppar with initial version 1.0
Package: timedeppar
Type: Package
Title: Infer Constant and Stochastic, Time-Dependent Model Parameters
Version: 1.0
Date: 2020-07-07
Author: Peter Reichert <peter.reichert@eawag.ch>
Maintainer: Peter Reichert <peter.reichert@eawag.ch>
Description: Infer constant and stochastic, time-dependent parameters to consider intrinsic stochasticity of a dynamic model and/or to analyze model structure modifications that could reduce model deficits. The concept is based on inferring time-dependent parameters as stochastic processes in the form of Ornstein-Uhlenbeck processes jointly with inferring constant model parameters and parameters of the Ornstein-Uhlenbeck processes. The package also contains functions to sample from and calculate densities of Ornstein-Uhlenbeck processes. References: Tomassini, L., Reichert, P., Kuensch, H.-R. Buser, C., Knutti, R. and Borsuk, M.E. (2009) "A smoothing algorithm for estimating stochastic, continuous-time model parameters and its application to a simple climate model." Journal of the Royal Statistical Society: Series C (Applied Statistics) 58, 679-704, <doi:10.1111/j.1467-9876.2009.00678.x>; Reichert, P., and Mieleitner, J. (2009) "Analyzing input and structural uncertainty of nonlinear dynamic models with stochastic, time-dependent parameters." Water Resources Research, 45, W10402, <doi:10.1029/2009WR007814>; Reichert, P., Ammann, L. and Fenicia, F. (2020) "Potential and challenges of investigating intrinsic uncertainty of hydrological models with stochastic, time-dependent parameters", in preparation; Reichert, P. (2020) "timedeppar: An R package for inferring stochastic, time-dependent model parameters", in preparation.
License: GPL-3
Depends: mvtnorm
URL: https://gitlab.com/p.reichert/timedeppar
BugReports: https://gitlab.com/p.reichert/timedeppar/issues
Encoding: UTF-8
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-07-07 19:23:30 UTC; reichert
Repository: CRAN
Date/Publication: 2020-07-08 08:40:02 UTC

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New package supreme with initial version 1.1.0
Package: supreme
Title: Modeling Tool for 'Shiny' Applications Developed with Modules
Version: 1.1.0
Authors@R: person("Metin", "Yazici", email = "stradivariusboul+r@gmail.com", role = c("aut", "cre", "cph"))
Description: A modeling tool helping users better structure 'Shiny' applications developed with 'Shiny' modules. Users are able to: 1. Visualize relationship of modules in existing applications 2. Design new applications from scratch.
License: MIT + file LICENSE
URL: https://strboul.github.io/supreme/
BugReports: https://github.com/strboul/supreme/issues
Depends: R (>= 3.6.0)
Imports: stats, utils, yaml (>= 2.2.0), nomnoml, shiny (>= 1.5.0)
Suggests: testthat (>= 2.1.0), covr, knitr, rmarkdown, digest (>= 0.6.23)
Language: en-US
LazyData: true
Encoding: UTF-8
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-07-07 18:14:06 UTC; metin
Author: Metin Yazici [aut, cre, cph]
Maintainer: Metin Yazici <stradivariusboul+r@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-08 08:30:02 UTC

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Package stringfish updated to version 0.13.2 with previous version 0.12.1 dated 2020-06-05

Title: Alt String Implementation
Description: Provides an extendable and performant 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph], Phillip Hazel [ctb] (Bundled PCRE2 code), Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code), University of Cambridge [cph] (Bundled PCRE2 code), Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with PCRE2), Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash code)
Maintainer: Travers Ching <traversc@gmail.com>

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New package npregderiv with initial version 1.0
Package: npregderiv
Title: Nonparametric Estimation of the Derivatives of a Regression Function
Version: 1.0
Authors@R: c(person("Olga", "Savchuk", role = c("aut", "cre"), email = "olga.y.savchuk@gmail.com"), person("Alex", "Volinsky", role = "aut", email = "volinsky@usf.edu"))
Depends: R (>= 3.1.0)
Description: Estimating the first and second derivatives of a regression function by the method of Wang and Lin (2015) <http://www.jmlr.org/papers/v16/wang15b.html>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-07-07 18:29:11 UTC; olgay
Author: Olga Savchuk [aut, cre], Alex Volinsky [aut]
Maintainer: Olga Savchuk <olga.y.savchuk@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-08 08:30:10 UTC

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New package libgeos with initial version 3.8.1-0
Package: libgeos
Title: Open Source Geometry Engine ('GEOS') C API
Version: 3.8.1-0
Authors@R: c( person(given = "Dewey", family = "Dunnington", role = c("aut", "cre"), email = "dewey@fishandwhistle.net", comment = c(ORCID = "0000-0002-9415-4582")), person("GEOS authors", role = "aut"), person("Martin", "Davis", role = c("ctb", "cph")), person("Benjamin", "Campbell", role = c("ctb", "cph")), person("Tomasz", "Sowa", role = c("ctb", "cph")), person("Christian", "Kaiser", role = c("ctb", "cph")), person("David", "Skea", role = c("ctb", "cph")), person("Daniel", "Baston", role = c("ctb", "cph")), person("Sandro", "Santilli", role = c("ctb", "cph")), person("Mateusz", "Loskot", role = c("ctb", "cph")), person("Paul", "Ramsey", role = c("ctb", "cph")), person("Olivier", "Devillers", role = c("ctb", "cph")), person("Sean", "Gillies", role = c("ctb", "cph")), person("Mika", "Heiskanen", role = c("ctb", "cph")), person("Safe Software Inc.", role = "cph"), person("Refractions Research Inc.", role = "cph"), person("Vivid Solutions Inc.", role = "cph") )
Description: Provides the Open Source Geometry Engine ('GEOS') as a C API that can be used to write high-performance C and C++ geometry operations using R as an interface. Headers are provided to make linking to and using these functions from C++ code as easy and as safe as possible.
License: LGPL (>= 2.1)
Copyright: file COPYRIGHTS
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://paleolimbot.github.io/libgeos, https://github.com/paleolimbot/libgeos
BugReports: https://github.com/paleolimbot/libgeos/issues
Suggests: Rcpp, testthat
NeedsCompilation: yes
Packaged: 2020-07-07 19:34:56 UTC; dewey
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>), GEOS authors [aut], Martin Davis [ctb, cph], Benjamin Campbell [ctb, cph], Tomasz Sowa [ctb, cph], Christian Kaiser [ctb, cph], David Skea [ctb, cph], Daniel Baston [ctb, cph], Sandro Santilli [ctb, cph], Mateusz Loskot [ctb, cph], Paul Ramsey [ctb, cph], Olivier Devillers [ctb, cph], Sean Gillies [ctb, cph], Mika Heiskanen [ctb, cph], Safe Software Inc. [cph], Refractions Research Inc. [cph], Vivid Solutions Inc. [cph]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Repository: CRAN
Date/Publication: 2020-07-08 08:40:05 UTC

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New package ARCokrig with initial version 0.1.1
Package: ARCokrig
Type: Package
Title: Autoregressive Cokriging Models for Multifidelity Codes
Version: 0.1.1
Date: 2020-07-03
Authors@R: c(person("Pulong", "Ma", role=c("aut", "cre"), email="mpulong@gmail.com"))
Maintainer: Pulong Ma <mpulong@gmail.com>
Description: For emulating multifidelity computer models. The major methods include univariate autoregressive cokriging and multivariate autoregressive cokriging. The autoregressive cokriging methods are implemented for both hierarchically nested design and non-nested design. For hierarchically nested design, the model parameters are estimated via standard optimization algorithms; For non-nested design, the model parameters are estimated via Monte Carlo expectation-maximization (MCEM) algorithms. In both cases, the priors are chosen such that the posterior distributions are proper. Notice that the uniform priors on range parameters in the correlation function lead to improper posteriors. This should be avoided when Bayesian analysis is adopted. The development of objective priors for autoregressive cokriging models can be found in Pulong Ma (2019) <arXiv:1910.10225>. The development of the multivariate autoregressive cokriging models with possibly non-nested design can be found in Pulong Ma, Georgios Karagiannis, Bledar A Konomi, Taylor G Asher, Gabriel R Toro, and Andrew T Cox (2019) <arXiv:1909.01836>.
License: GPL (>= 2)
Encoding: UTF-8
URL: https://github.com/pulongma/ARCokrig/issues
Depends: R (>= 3.5.0)
Imports: Rcpp, mvtnorm (>= 1.0-10), stats, methods, ggplot2
LinkingTo: Rcpp, RcppArmadillo, RcppEigen
Suggests: testthat
RoxygenNote: 7.1.0
NeedsCompilation: yes
Packaged: 2020-07-06 16:59:51 UTC; mapulong
Author: Pulong Ma [aut, cre]
Repository: CRAN
Date/Publication: 2020-07-08 08:30:16 UTC

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Package gganimate updated to version 1.0.6 with previous version 1.0.5 dated 2020-02-09

Title: A Grammar of Animated Graphics
Description: The grammar of graphics as implemented in the 'ggplot2' package has been successful in providing a powerful API for creating static visualisation. In order to extend the API for animated graphics this package provides a completely new set of grammar, fully compatible with 'ggplot2' for specifying transitions and animations in a flexible and extensible way.
Author: Thomas Lin Pedersen [aut, cre] (<https://orcid.org/0000-0002-5147-4711>), David Robinson [aut], RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

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Package worrms updated to version 0.4.2 with previous version 0.4.0 dated 2019-06-28

Title: World Register of Marine Species (WoRMS) Client
Description: Client for World Register of Marine Species (<http://www.marinespecies.org/>). Includes functions for each of the API methods, including searching for names by name, date and common names, searching using external identifiers, fetching synonyms, as well as fetching taxonomic children and taxonomic classification.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package universals updated to version 0.0.3 with previous version 0.0.2 dated 2020-06-11

Title: S3 Generics for Bayesian Analyses
Description: Provides S3 generic methods and some default implementations for Bayesian analyses that generate Markov Chain Monte Carlo (MCMC) samples. The purpose of 'universals' is to reduce package dependencies and conflicts. The 'nlist' package implements many of the methods for its 'nlist' class.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Kirill Müller [ctb] (<https://orcid.org/0000-0002-1416-3412>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package stplanr updated to version 0.6.2 with previous version 0.6.1 dated 2020-06-23

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

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Package rnoaa updated to version 1.1.0 with previous version 1.0.0 dated 2020-06-13

Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for each of the 'API' 'endpoints': data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Brooke Anderson [ctb], Maëlle Salmon [ctb], Adam Erickson [ctb], Nicholas Potter [ctb], Joseph Stachelek [ctb], Alex Simmons [ctb], Karthik Ram [ctb], Hart Edmund [ctb], rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package reda updated to version 0.5.2 with previous version 0.5.1 dated 2020-06-27

Title: Recurrent Event Data Analysis
Description: Contains implementations of recurrent event data analysis routines including (1) survival and recurrent event data simulation from stochastic process point of view by the thinning method proposed by Lewis and Shedler (1979) <doi:10.1002/nav.3800260304> and the inversion method introduced in Cinlar (1975, ISBN:978-0486497976), (2) the mean cumulative function (MCF) estimation by the Nelson-Aalen estimator of the cumulative hazard rate function, (3) two-sample recurrent event responses comparison with the pseudo-score tests proposed by Lawless and Nadeau (1995) <doi:10.2307/1269617>, (4) gamma frailty model with spline rate function following Fu, et al. (2016) <doi:10.1080/10543406.2014.992524>.
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>), Haoda Fu [aut], Jun Yan [ctb] (<https://orcid.org/0000-0003-4401-7296>)
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>

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Package proftools updated to version 0.99-3 with previous version 0.99-2 dated 2016-01-13

Title: Profile Output Processing Tools for R
Description: Tools for examining Rprof profile output.
Author: Luke Tierney and Riad Jarjour
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>

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Package memisc updated to version 0.99.25.6 with previous version 0.99.25.5 dated 2020-06-30

Title: Management of Survey Data and Presentation of Analysis Results
Description: An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.
Author: Martin Elff (with contributions from Christopher N. Lawrence, Dave Atkins, Jason W. Morgan, Achim Zeileis)
Maintainer: Martin Elff <memisc@elff.eu>

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Package lfe updated to version 2.8-5.1 with previous version 2.8-5 dated 2019-12-17

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors with many levels as pure control variables. Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>), Grant McDermott [ctb], Karl Dunkle Werner [ctb], Matthieu Stigler [ctb], Daniel Lüdecke [ctb]
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>

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Package doBy updated to version 4.6.7 with previous version 4.6.6 dated 2020-05-16

Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: Contains: 1) Facilities for working with grouped data: 'do' something to data stratified 'by' some variables. 2) LSmeans (least-squares means), general linear contrasts. 3) Miscellaneous other utilities.
Author: Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh <uhalekoh@health.sdu.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>

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Package BEDMatrix updated to version 2.0.3 with previous version 2.0.2 dated 2020-03-11

Title: Extract Genotypes from a PLINK .bed File
Description: A matrix-like data structure that allows for efficient, convenient, and scalable subsetting of binary genotype/phenotype files generated by PLINK (<https://www.cog-genomics.org/plink2>), the whole genome association analysis toolset, without loading the entire file into memory.
Author: Alexander Grueneberg [aut, cre], Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <cran@agrueneberg.info>

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Package skewlmm updated to version 0.2.2 with previous version 0.2.1 dated 2020-07-06

Title: Scale Mixture of Skew-Normal Linear Mixed Models
Description: It fits scale mixture of skew-normal linear mixed models using an expectation–maximization (EM) type algorithm, including some possibilities for modeling the within-subject dependence. Details can be found in Schumacher, Lachos and Matos (2020) <arXiv:2002.01040>.
Author: Fernanda L. Schumacher [aut, cre], Larissa A. Matos [aut], Victor H. Lachos [aut]
Maintainer: Fernanda L. Schumacher <fernandalschumacher@gmail.com>

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

Title: Ensemble Boolean Model Biomarker Analysis
Description: Analysis and visualization of an ensemble of boolean models for biomarker discovery in cancer cell networks. The package allows to easily load the simulation data results of the DrugLogics software pipeline which predicts synergistic drug combinations in cancer cell lines (developed by the DrugLogics research group in NTNU). It has generic functions that can be used to split a boolean model dataset to model groups with regards to the models predictive performance (number of true positive predictions/Matthews correlation coefficient score) or synergy prediction based on a given set of gold standard synergies and find the average activity difference per network node between all model group pairs. Thus, given user-specific thresholds, important nodes (biomarkers) can be accessed in the sense that they make the models predict specific synergies (synergy biomarkers) or have better performance in general (performance biomarkers). Lastly, if the boolean models have a specific equation form and differ only in their link operator, link operator biomarkers can also be found.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>

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Package fragilityindex (with last version 0.1.0) was removed from CRAN

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Package CorReg (with last version 1.2.17) was removed from CRAN

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Package sdwd (with last version 1.0.3) was removed from CRAN

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2020-02-17 1.0.3
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Package causalMGM (with last version 0.1.1) was removed from CRAN

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Tue, 07 Jul 2020

New package diceR with initial version 1.0.0
Type: Package
Package: diceR
Title: Diverse Cluster Ensemble in R
Version: 1.0.0
Authors@R: c(person(given = "Derek", family = "Chiu", role = c("aut", "cre"), email = "dchiu@bccrc.ca"), person(given = "Aline", family = "Talhouk", role = "aut", email = "atalhouk@bccrc.ca"), person(given = "Johnson", family = "Liu", role = c("ctb", "com"), email = "gliu@bccrc.ca"))
Description: Performs cluster analysis using an ensemble clustering framework, Chiu & Talhouk (2018) <doi:10.1186/s12859-017-1996-y>. Results from a diverse set of algorithms are pooled together using methods such as majority voting, K-Modes, LinkCluE, and CSPA. There are options to compare cluster assignments across algorithms using internal and external indices, visualizations such as heatmaps, and significance testing for the existence of clusters.
License: MIT + file LICENSE
URL: https://github.com/AlineTalhouk/diceR, https://alinetalhouk.github.io/diceR
BugReports: https://github.com/AlineTalhouk/diceR/issues
Depends: R (>= 3.5)
Imports: abind, assertthat, class, clue, clusterCrit, clValid, dplyr (>= 0.7.5), ggplot2, infotheo, klaR, magrittr, mclust, methods, NMF, purrr (>= 0.2.3), RankAggreg, Rcpp, stringr, tibble, tidyr, yardstick
Suggests: apcluster, blockcluster, cluster, covr, dbscan, e1071, kernlab, knitr, kohonen, pander, poLCA, progress, rmarkdown, Rtsne, sigclust, testthat
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-07-07 18:03:55 UTC; Derek
Author: Derek Chiu [aut, cre], Aline Talhouk [aut], Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Repository: CRAN
Date/Publication: 2020-07-07 22:30:02 UTC

More information about diceR at CRAN
Permanent link

New package corHMM with initial version 2.1
Package: corHMM
Version: 2.1
Date: 2020-07-6
Title: Hidden Markov Models of Character Evolution
Authors@R: c(person("Jeremy", "Beaulieu", role=c("aut", "cre"), email = "jmbeauli@uark.edu"), person("Brian", "O'Meara", role=c("aut")), person("Jeffrey", "Oliver", role=c("aut")), person("James", "Boyko", role=c("aut")))
Maintainer: Jeremy Beaulieu <jmbeauli@uark.edu>
Depends: ape, nloptr, GenSA
Suggests: testthat, knitr, markdown
Imports: expm, numDeriv, corpcor, MASS, nnet, phangorn, parallel, viridis, Rmpfr, igraph, phytools
Description: Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
License: GPL (>= 2)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-07-07 16:20:44 UTC; jmbeauli
Author: Jeremy Beaulieu [aut, cre], Brian O'Meara [aut], Jeffrey Oliver [aut], James Boyko [aut]
Repository: CRAN
Date/Publication: 2020-07-07 22:30:06 UTC

More information about corHMM at CRAN
Permanent link

Package varTestnlme updated to version 0.2.0 with previous version 0.1.0 dated 2020-01-10

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

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Package plotGMM updated to version 0.2.2 with previous version 0.2.1 dated 2019-06-28

Title: Tools for Visualizing Gaussian Mixture Models
Description: The main function, plot_GMM, is used for plotting output from Gaussian mixture models (GMMs), including both densities and overlaying mixture weight component curves from the fit GMM. The package also include the function, plot_cut_point, which plots the cutpoint (mu) from the GMM over a histogram of the distribution with several color options. Finally, the package includes the function, plot_mix_comps, which is used in the plot_GMM function, and can be used to create a custom plot for overlaying mixture component curves from GMMs. For the plot_mix_comps function, usage most often will be specifying the "fun" argument within "stat_function" in a ggplot2 object.
Author: Philip Waggoner [aut, cre], Fong Chan [aut]
Maintainer: Philip Waggoner <philip.waggoner@gmail.com>

Diff between plotGMM versions 0.2.1 dated 2019-06-28 and 0.2.2 dated 2020-07-07

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Package RcppSimdJson updated to version 0.1.0 with previous version 0.0.6 dated 2020-06-25

Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for 'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the 'simdjson' library written by Daniel Lemire (and many contributors) provides a high-performance parser for these files which by relying on parallel 'SIMD' instruction manages to parse these files as faster than disk speed. See the <arXiv:1902.08318> paper for more details about 'simdjson'. This package is at present still a fairly thin and not fully complete wrapper that does not aim to replace the existing and excellent 'JSON' packages for R.
Author: Dirk Eddelbuettel, Brendan Knapp
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppSimdJson versions 0.0.6 dated 2020-06-25 and 0.1.0 dated 2020-07-07

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Package thinkr updated to version 0.15 with previous version 0.13 dated 2018-06-21

Title: Tools for Cleaning Up Messy Files
Description: Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.
Author: Vincent Guyader [aut, cre] (<https://orcid.org/0000-0003-0671-9270>), Sébastien Rochette [aut] (<https://orcid.org/0000-0002-1565-9313>), ThinkR [cph]
Maintainer: Vincent Guyader <vincent@thinkr.fr>

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Package skmeans updated to version 0.2-12 with previous version 0.2-11 dated 2017-08-08

Title: Spherical k-Means Clustering
Description: Algorithms to compute spherical k-means partitions. Features several methods, including a genetic and a fixed-point algorithm and an interface to the CLUTO vcluster program.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), Ingo Feinerer [aut], Martin Kober [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between skmeans versions 0.2-11 dated 2017-08-08 and 0.2-12 dated 2020-07-07

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Package pkgcache updated to version 1.1.0 with previous version 1.0.7 dated 2020-04-18

Title: Cache 'CRAN'-Like Metadata and R Packages
Description: Metadata and package cache for CRAN-like repositories. This is a utility package to be used by package management tools that want to take advantage of caching.
Author: Gábor Csárdi [aut, cre]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package discrim updated to version 0.1.0 with previous version 0.0.2 dated 2020-04-09

Title: Model Wrappers for Discriminant Analysis
Description: Bindings for additional classification models for use with the 'parsnip' package. Models include flavors of discriminant analysis, such as linear (Fisher (1936) <doi:10.1111/j.1469-1809.1936.tb02137.x>), regularized (Friedman (1989) <doi:10.1080/01621459.1989.10478752>), and flexible (Hastie, Tibshirani, and Buja (1994) <doi:10.1080/01621459.1994.10476866>), as well as naive Bayes classifiers (Hand and Yu (2007) <doi:10.1111/j.1751-5823.2001.tb00465.x>).
Author: Max Kuhn [aut, cre] (<https://orcid.org/0000-0003-2402-136X>), RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>

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More information about discrim at CRAN
Permanent link

Package rcoreoa updated to version 0.4.0 with previous version 0.3.0 dated 2018-09-20

Title: Client for the CORE API
Description: Client for the CORE API (<https://core.ac.uk/docs/>). CORE (<https://core.ac.uk>) aggregates open access research outputs from repositories and journals worldwide and make them available to the public.
Author: Scott Chamberlain [aut, cre], Aristotelis Charalampous [ctb], Simon Goring [ctb]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

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Package PetfindeR updated to version 2.1.0 with previous version 2.0.0 dated 2019-08-23

Title: 'Petfinder' API Wrapper
Description: Wrapper of the 'Petfinder API' <https://www.petfinder.com/developers/v2/docs/> that implements methods for interacting with and extracting data from the 'Petfinder' database. The 'Petfinder REST API' allows access to the 'Petfinder' database, one of the largest online databases of adoptable animals and animal welfare organizations across North America.
Author: Aaron Schlegel
Maintainer: Aaron Schlegel <aaron@aaronschlegel.me>

Diff between PetfindeR versions 2.0.0 dated 2019-08-23 and 2.1.0 dated 2020-07-07

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

Title: Formal Concept Analysis
Description: Provides tools to perform fuzzy formal concept analysis, presented in Wille (1982) <doi:10.1007/978-3-642-01815-2_23> and in Ganter and Obiedkov (2016) <doi:10.1007/978-3-662-49291-8>. It provides functions to load and save a formal context, extract its concept lattice and implications. In addition, one can use the implications to compute semantic closures of fuzzy sets and, thus, build recommendation systems.
Author: Domingo Lopez Rodriguez [aut, cre] (<https://orcid.org/0000-0002-0172-1585>), Angel Mora [aut], Jesus Dominguez [aut], Ana Villalon [aut], Ian Johnson [ctb]
Maintainer: Domingo Lopez Rodriguez <dominlopez@uma.es>

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

Title: Rearrangement Distances Between Unrooted Phylogenetic Trees
Description: Fast calculation of the Subtree Prune and Regraft (SPR), Tree Bisection and Reconnection (TBR) and Replug distances between unrooted trees, using the algorithms of Whidden and Matsen (2017) <arxiv:1511.07529>.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Chris Whidden [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between TBRDist versions 1.0.0 dated 2020-07-01 and 1.0.1 dated 2020-07-07

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Package stratEst updated to version 1.0.1 with previous version 1.0.0 dated 2020-06-23

Title: Strategy Estimation
Description: Variants of strategy estimation (Dal Bo & Frechette, 2011, <doi:10.1257/aer.101.1.411>), including the model with parameters for the choice probabilities of the strategies (Breitmoser, 2015, <doi:10.1257/aer.20130675>), and the model with individual level covariates for the selection of strategies by individuals (Dvorak & Fehrler, 2018, <doi:10.2139/ssrn.2986445>).
Author: Fabian Dvorak
Maintainer: Fabian Dvorak <fabian.dvorak@uni.kn>

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Package grizbayr updated to version 1.2.3 with previous version 1.2.2 dated 2020-06-04

Title: Bayesian Inference for A|B and Bandit Marketing Tests
Description: Uses simple Bayesian conjugate prior update rules to calculate the win probability of each option, value remaining in the test, and percent lift over the baseline for various marketing objectives. References: Fink, Daniel (1997) "A Compendium of Conjugate Priors" <https://www.johndcook.com/CompendiumOfConjugatePriors.pdf>. Stucchio, Chris (2015) "Bayesian A/B Testing at VWO" <http://cdn2.hubspot.net/hubfs/310840/VWO_SmartStats_technical_whitepaper.pdf>.
Author: Ryan Angi
Maintainer: Ryan Angi <rangi@redventures.com>

Diff between grizbayr versions 1.2.2 dated 2020-06-04 and 1.2.3 dated 2020-07-07

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Package fbati updated to version 1.0-4 with previous version 1.0-3 dated 2018-04-23

Title: Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>

Diff between fbati versions 1.0-3 dated 2018-04-23 and 1.0-4 dated 2020-07-07

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New package ctsemOMX with initial version 1.0.2
Package: ctsemOMX
Type: Package
Title: Continuous Time SEM - 'OpenMx' Based Functions
Version: 1.0.2
Date: 2020-7-7
Authors@R: c(person("Charles", "Driver", role = c("aut","cre","cph"),email="driver@mpib-berlin.mpg.de"), person("Manuel", "Voelkle", role = c("aut","cph")), person("Han", "Oud", role = c("aut","cph") ))
Description: Original 'ctsem' (continuous time structural equation modelling) functionality, based on the 'OpenMx' software, as described in Driver, Oud, Voelkle (2017) <doi:10.18637/jss.v077.i05>, with updated details in vignette. Combines stochastic differential equations representing latent processes with structural equation measurement models. These functions were split off from the main package of 'ctsem', as the main package uses the 'rstan' package as a backend now -- offering estimation options from max likelihood to Bayesian. There are nevertheless use cases for the wide format SEM style approach as offered here, particularly when there are no individual differences in observation timing and the number of individuals is large. For the main 'ctsem' package, see <https://cran.r-project.org/package=ctsem>.
License: GPL-3
Depends: R (>= 3.5.0), ctsem (>= 3.3.2), OpenMx (>= 2.9.0)
URL: https://github.com/cdriveraus/ctsemOMX
Imports: graphics, grDevices, Matrix, methods, plyr, stats, utils
Encoding: UTF-8
LazyData: true
ByteCompile: true
Suggests: knitr, testthat
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-07-07 13:38:55 UTC; Driver
Author: Charles Driver [aut, cre, cph], Manuel Voelkle [aut, cph], Han Oud [aut, cph]
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Repository: CRAN
Date/Publication: 2020-07-07 15:40:02 UTC

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Package BIGL updated to version 1.5.1 with previous version 1.4.3 dated 2020-02-20

Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) <doi:10.1038/s41598-017-18068-5>.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>

Diff between BIGL versions 1.4.3 dated 2020-02-20 and 1.5.1 dated 2020-07-07

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Package TriadSim (with last version 0.1.1) was removed from CRAN

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

2017-05-24 0.1.1
2017-05-12 0.0.1

Permanent link
Package safedata updated to version 1.0.5 with previous version 1.0.1 dated 2020-06-02

Title: Interface to Data from the SAFE Project
Description: The SAFE Project (<https://www.safeproject.net/>) is a large scale ecological experiment in Malaysian Borneo that explores the impact of habitat fragmentation and conversion on ecosystem function and services. Data collected at the SAFE Project is made available under a common format through the Zenodo data repository and this package makes it easy to discover and load that data into R.
Author: Andy Aldersley [aut], David Orme [aut, cre] (<https://orcid.org/0000-0002-7005-1394>)
Maintainer: David Orme <d.orme@imperial.ac.uk>

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Package knitrdata updated to version 0.4.1 with previous version 0.3.1 dated 2020-06-23

Title: Data Language Engine for 'knitr' / 'rmarkdown'
Description: Implements a data language engine for incorporating data directly in 'rmarkdown' documents so that they can be made completely standalone.
Author: David M. Kaplan [aut, cre, cph] (<https://orcid.org/0000-0001-6087-359X>, dmkaplan2000)
Maintainer: David M. Kaplan <dmkaplan2000@gmail.com>

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Package hillR updated to version 0.5.0 with previous version 0.4.0 dated 2018-11-19

Title: Diversity Through Hill Numbers
Description: Calculate taxonomic, functional and phylogenetic diversity measures through Hill Numbers proposed by Chao, Chiu and Jost (2014) <doi:10.1146/annurev-ecolsys-120213-091540>.
Author: Daijiang Li
Maintainer: Daijiang Li <daijianglee@gmail.com>

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Package govdown updated to version 0.10.0 with previous version 0.9.1 dated 2020-05-13

Title: GOV.UK Style Templates for R Markdown
Description: A suite of custom R Markdown formats and templates for authoring web pages styled with the GOV.UK Design System.
Author: Crown Copyright 2019 [cph], Duncan Garmonsway [aut, cre]
Maintainer: Duncan Garmonsway <duncan.garmonsway@digital.cabinet-office.gov.uk>

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Package cmna updated to version 1.0.3 with previous version 1.0.2 dated 2019-07-23

Title: Computational Methods for Numerical Analysis
Description: Provides the source and examples for James P. Howard, II, "Computational Methods for Numerical Analysis with R," <https://jameshoward.us/cmna>, a book on numerical methods in R.
Author: James Howard [aut, cre] (<https://orcid.org/0000-0003-4530-1547>)
Maintainer: James Howard <jh@jameshoward.us>

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More information about cmna at CRAN
Permanent link

Package workflows updated to version 0.1.2 with previous version 0.1.1 dated 2020-03-17

Title: Modeling Workflows
Description: Managing both a 'parsnip' model and a preprocessor, such as a model formula or recipe from 'recipes', can often be challenging. The goal of 'workflows' is to streamline this process by bundling the model alongside the preprocessor, all within the same object.
Author: Davis Vaughan [aut, cre], RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>

Diff between workflows versions 0.1.1 dated 2020-03-17 and 0.1.2 dated 2020-07-07

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More information about workflows at CRAN
Permanent link

Package plinkQC updated to version 0.3.2 with previous version 0.3.0 dated 2019-10-19

Title: Genotype Quality Control with 'PLINK'
Description: Genotyping arrays enable the direct measurement of an individuals genotype at thousands of markers. 'plinkQC' facilitates genotype quality control for genetic association studies as described by Anderson and colleagues (2010) <doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic statistics (e.g. missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions accessible from 'R' and generates a per-individual and per-marker quality control report. Individuals and markers that fail the quality control can subsequently be removed to generate a new, clean dataset. Removal of individuals based on relationship status is optimised to retain as many individuals as possible in the study.
Author: Hannah Meyer [aut, cre] (<https://orcid.org/0000-0003-4564-0899>)
Maintainer: Hannah Meyer <hannah.v.meyer@gmail.com>

Diff between plinkQC versions 0.3.0 dated 2019-10-19 and 0.3.2 dated 2020-07-07

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More information about plinkQC at CRAN
Permanent link

New package epwshiftr with initial version 0.1.0
Package: epwshiftr
Title: Create Future 'EnergyPlus' Weather Files using 'CMIP6' Data
Version: 0.1.0
Authors@R: person(given = "Hongyuan", family = "Jia", role = c("aut", "cre"), email = "hongyuan.jia@bears-berkeley.sg", comment = c(ORCID = "0000-0002-0075-8183"))
Description: Query, download climate change projection data from the 'CMIP6' (Coupled Model Intercomparison Project Phase 6) project <https://pcmdi.llnl.gov/CMIP6> in the 'ESGF' (Earth System Grid Federation) platform <https://esgf.llnl.gov>, and create future 'EnergyPlus' <https://energyplus.net> Weather ('EPW') files adjusted from climate changes using data from Global Climate Models ('GCM').
Imports: checkmate, data.table (>= 1.12.4), eplusr, future.apply, fst, jsonlite, progressr, psychrolib, rappdirs, RNetCDF, units
Suggests: testthat, pingr, covr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/ideas-lab-nus/epwshiftr
BugReports: https://github.com/ideas-lab-nus/epwshiftr/issues
RoxygenNote: 7.0.2
Collate: 'coord.R' 'utils.R' 'epwshiftr-package.R' 'esgf.R' 'morph.R' 'netcdf.R'
NeedsCompilation: no
Packaged: 2020-07-07 13:38:42 UTC; hongyuanjia
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuan.jia@bears-berkeley.sg>
Repository: CRAN
Date/Publication: 2020-07-07 14:00:07 UTC

More information about epwshiftr at CRAN
Permanent link

Package disk.frame updated to version 0.3.7 with previous version 0.3.6 dated 2020-06-13

Title: Larger-than-RAM Disk-Based Data Manipulation Framework
Description: A disk-based data manipulation tool for working with large-than-RAM datasets. Aims to lower the barrier-to-entry for manipulating large datasets by adhering closely to popular and familiar data manipulation paradigms like 'dplyr' verbs and 'data.table' syntax.
Author: Dai ZJ [aut, cre], Jacky Poon [ctb]
Maintainer: Dai ZJ <zhuojia.dai@gmail.com>

Diff between disk.frame versions 0.3.6 dated 2020-06-13 and 0.3.7 dated 2020-07-07

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More information about disk.frame at CRAN
Permanent link

Package tibble updated to version 3.0.2 with previous version 3.0.1 dated 2020-04-20

Title: Simple Data Frames
Description: Provides a 'tbl_df' class (the 'tibble') that provides stricter checking and better formatting than the traditional data frame.
Author: Kirill Müller [aut, cre], Hadley Wickham [aut], Romain Francois [ctb], Jennifer Bryan [ctb], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

Diff between tibble versions 3.0.1 dated 2020-04-20 and 3.0.2 dated 2020-07-07

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More information about tibble at CRAN
Permanent link

New package parglm with initial version 0.1.5
Package: parglm
Type: Package
Title: Parallel GLM
Version: 0.1.5
Authors@R: c( person("Benjamin", "Christoffersen", email = "boennecd@gmail.com", role = c("cre", "aut")), person("Anthony", "Williams", role = c("cph")), person("Boost developers", role = c("cph")))
Description: Provides a parallel estimation method for generalized linear models without compiling with a multithreaded LAPACK or BLAS.
License: GPL-2
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, Matrix
SystemRequirements: C++11
Suggests: testthat, SuppDists, knitr, rmarkdown, speedglm, microbenchmark, R.rsp
RoxygenNote: 6.1.1
VignetteBuilder: R.rsp
NeedsCompilation: yes
Packaged: 2020-07-06 19:25:24 UTC; boennecd
Author: Benjamin Christoffersen [cre, aut], Anthony Williams [cph], Boost developers [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-07 12:50:02 UTC

More information about parglm at CRAN
Permanent link

Package loo updated to version 2.3.0 with previous version 2.2.0 dated 2019-12-19

Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
Description: Efficient approximate leave-one-out cross-validation (LOO) for Bayesian models fit using Markov chain Monte Carlo, as described in Vehtari, Gelman, and Gabry (2017) <doi:10.1007/s11222-016-9696-4>. The approximation uses Pareto smoothed importance sampling (PSIS), a new procedure for regularizing importance weights. As a byproduct of the calculations, we also obtain approximate standard errors for estimated predictive errors and for the comparison of predictive errors between models. The package also provides methods for using stacking and other model weighting techniques to average Bayesian predictive distributions.
Author: Aki Vehtari [aut], Jonah Gabry [cre, aut], Mans Magnusson [aut], Yuling Yao [aut], Paul-Christian Bürkner [aut], Topi Paananen [aut], Andrew Gelman [aut], Ben Goodrich [ctb], Juho Piironen [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>

Diff between loo versions 2.2.0 dated 2019-12-19 and 2.3.0 dated 2020-07-07

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 loo-2.3.0/loo/NEWS.md                                                       |   18 
 loo-2.3.0/loo/R/compare.R                                                   |    4 
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 loo-2.3.0/loo/man/loo.Rd                                                    |   37 
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Package logr updated to version 1.0.5 with previous version 1.0.4 dated 2020-07-05

Title: Creates Log Files
Description: Contains functions to help create log files. The package aims to overcome the difficulty of the base R sink() command. The log_print() function will print to both the console and the file log, without interfering in other write operations.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>

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Package emdi updated to version 2.0.0 with previous version 1.1.7 dated 2020-03-18

Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional disaggregated indicators. So far, estimation methods comprise direct estimation, the model-based unit-level approach Empirical Best Prediction (see "Small area estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), the area-level model (see "Estimates of income for small places: An application of James-Stein procedures to Census Data" by (Fay and Herriot 1979) <doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance estimation methods, log and arcsin transformation, spatial, robust and measurement error models), as well as their precision estimates. The assessment of the used model is supported by a summary and diagnostic plots. For a suitable presentation of estimates, map plots can be easily created. Furthermore, results can easily be exported to excel. For a detailed description of the package and the methods used see "The {R} Package {emdi} for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07>.
Author: Sylvia Harmening [aut], Ann-Kristin Kreutzmann [aut], Soeren Pannier [aut, cre], Natalia Rojas-Perilla [aut], Nicola Salvati [aut], Timo Schmid [aut], Matthias Templ [aut], Nikos Tzavidis [aut], Nora Würz [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>

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Package DNAtools updated to version 0.2-3 with previous version 0.2-2 dated 2020-03-03

Title: Tools for Analysing Forensic Genetic DNA Data
Description: Computationally efficient tools for comparing all pairs of profiles in a DNA database. The expectation and covariance of the summary statistic is implemented for fast computing. Routines for estimating proportions of close related individuals are available. The use of wildcards (also called F- designation) is implemented. Dedicated functions ease plotting the results. See Tvedebrink et al. (2012) <doi:10.1016/j.fsigen.2011.08.001>. Compute the distribution of the numbers of alleles in DNA mixtures. See Tvedebrink (2013) <doi:10.1016/j.fsigss.2013.10.142>.
Author: Torben Tvedebrink [aut], James Curran [aut], Mikkel Meyer Andersen [aut, cre]
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>

Diff between DNAtools versions 0.2-2 dated 2020-03-03 and 0.2-3 dated 2020-07-07

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New package climaemet with initial version 0.1.0
Package: climaemet
Title: Climate AEMET Tools
Version: 0.1.0
Author: Manuel Pizarro [aut, cre]
Maintainer: Manuel Pizarro <m.pizarro@csic.es>
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.).
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 3.6.0)
Imports: dplyr (>= 1.0.0), tidyr (>= 1.1.0), lubridate (>= 1.7.9), stringr (>= 1.4.0), scales (>= 1.1.1), ggplot2 (>= 3.3.2), ggpubr (>= 0.4.0), ggthemes (>= 4.2.0), gtable (>= 0.3.0), gganimate (>= 1.0.5), RColorBrewer (>= 1.1.2), jpeg (>= 0.1.8.1), httr (>= 1.4.1), jsonlite (>= 1.7.0), climatol (>= 3.1.2), rlang (>= 0.4.6), magrittr (>= 1.5)
Collate: 'aemet_tools.R' 'climaemet-package.R' 'plot_tools.R' 'climaemet_main.R' 'climaemet_news.R' 'utils-pipe.R'
Suggests: knitr, rmarkdown, learnr
NeedsCompilation: no
Repository: CRAN
URL: https://github.com/mpizarrotig/climaemet
BugReports: https://github.com/mpizarrotig/climaemet/issues
Packaged: 2020-07-07 12:03:06 UTC; BIODIVERSITYLAB
Date/Publication: 2020-07-07 12:50:16 UTC

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Package ariExtra updated to version 0.2.9 with previous version 0.2.7 dated 2020-07-03

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 lcmm updated to version 1.9.2 with previous version 1.9.1 dated 2020-06-03

Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method (Proust-Lima, Philipps, Liquet (2017) <doi:10.18637/jss.v078.i02>).
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>

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New package EFAtools with initial version 0.1.0
Package: EFAtools
Title: Fast and Flexible Implementations of Exploratory Factor Analysis Tools
Version: 0.1.0
Authors@R: c(person(given = "Markus", family = "Steiner", role = c("aut", "cre"), email = "markus.d.steiner@gmail.com"), person(given = "Silvia", family = "Grieder", role = "aut", email = "silvia.grieder@gmail.com"), person(given = "William", family = "Revelle", role = "ctb"), person(given = "Max", family = "Auerswald", role = "ctb"), person(given = "Morten", family = "Moshagen", role = "ctb"), person(given = "John", family = "Ruscio", role = "ctb"), person(given = "Brendan", family = "Roche", role = "ctb"), person(given = "Urbano", family = "Lorenzo-Seva", role = "ctb"), person(given = "David", family = "Navarro-Gonzalez", role = "ctb"))
Description: Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Depends: R (>= 3.6.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Imports: lavaan, psych, crayon, stringr, stats, ggplot2, plotly, tibble, magrittr, dplyr, cli, Rcpp, viridisLite, graphics, parallel, future.apply, future, GPArotation, checkmate, microbenchmark
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2020-07-07 09:59:28 UTC; msteiner
Author: Markus Steiner [aut, cre], Silvia Grieder [aut], William Revelle [ctb], Max Auerswald [ctb], Morten Moshagen [ctb], John Ruscio [ctb], Brendan Roche [ctb], Urbano Lorenzo-Seva [ctb], David Navarro-Gonzalez [ctb]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-07 11:10:02 UTC

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Package TreeSearch updated to version 0.4.2 with previous version 0.4.1 dated 2020-06-09

Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Description: Searches for phylogenetic trees that are optimal using a user-defined criterion. Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>. Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Martin Brazeau [cph] (<https://orcid.org/0000-0002-0650-1282>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between TreeSearch versions 0.4.1 dated 2020-06-09 and 0.4.2 dated 2020-07-07

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Package WeightIt updated to version 0.10.0 with previous version 0.9.0 dated 2020-02-11

Title: Weighting for Covariate Balance in Observational Studies
Description: Generates weights to form equivalent groups in observational studies with point or longitudinal treatments by easing and extending the functionality of the R packages 'twang' for generalized boosted modeling (McCaffrey, Ridgeway & Morral, 2004) <doi:10.1037/1082-989X.9.4.403>, 'CBPS' for covariate balancing propensity score weighting (Imai & Ratkovic, 2014) <doi:10.1111/rssb.12027>, 'ebal' for entropy balancing (Hainmueller, 2012) <doi:10.1093/pan/mpr025>, 'optweight' for optimization-based weights (Zubizarreta, 2015) <doi:10.1080/01621459.2015.1023805>, 'ATE' for empirical balancing calibration weighting (Chan, Yam, & Zhang, 2016) <doi:10.1111/rssb.12129>, and 'SuperLearner' for stacked machine learning-based propensity scores (Pirracchio, Petersen, & van der Laan, 2015) <doi:10.1093/aje/kwu253>. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt'.
Author: Noah Greifer [aut, cre] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>

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Package TreeTools updated to version 1.1.0 with previous version 1.0.0 dated 2020-06-08

Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; rooting of trees and extraction of subtrees; calculation and depiction of node support; calculation of ancestor-descendant relationships; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>), Klaus Schliep [cph] (<https://orcid.org/0000-0003-2941-0161>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

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 tests/testthat/test-tree_rearrange.R         |   54 ++++
 vignettes/load-trees.Rmd                     |    2 
 52 files changed, 847 insertions(+), 322 deletions(-)

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Package solitude updated to version 1.0.1 with previous version 1.0.0 dated 2020-07-05

Title: An Implementation of Isolation Forest
Description: Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detection (Liu, Ting and Zhou <doi:10.1145/2133360.2133363>).
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>

Diff between solitude versions 1.0.0 dated 2020-07-05 and 1.0.1 dated 2020-07-07

 DESCRIPTION            |   10 +-
 MD5                    |   10 +-
 NEWS.md                |   13 ++-
 R/isolationForest_r6.R |  157 +++++++++++++++++++++++++------------------
 README.md              |  176 +++++++++++++++++++++++++------------------------
 man/isolationForest.Rd |   46 ++++++------
 6 files changed, 221 insertions(+), 191 deletions(-)

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New package SiteAdapt with initial version 1.0.0
Package: SiteAdapt
Type: Package
Title: Site Adaptation of Solar Irradiance Modeled Series
Version: 1.0.0
Author: Carlos M. Fernandez-Peruchena
Maintainer: Carlos M. Fernandez-Peruchena <cfernandez@cener.com>
Description: The SiteAdapt procedure improves the accuracy of modeled solar irradiance series through site-adaptation with coincident ground-based measurements relying on the use of a regression preprocessing followed by an empirical quantile mapping (eQM) correction. Fernandez-Peruchena et al (2020) <doi:10.3390/rs12132127>.
Imports: glmulti, solaR, hyfo, hydroGOF, RColorBrewer, ggplot2, ggpubr, stats
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.2
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-07-07 08:20:41 UTC; cfernandez
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2020-07-07 09:40:07 UTC

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New package pubh with initial version 1.1.16
Package: pubh
Title: A Toolbox for Public Health and Epidemiology
Version: 1.1.16
Authors@R: c( person("Josie", "Athens", email = "josie.athens@otago.ac.nz", role = c("aut", "cre")), person("Frank", "Harell", email = "f.harrell@vanderbilt.edu", role = "ctb"), person("John", "Fox", email = "jfox@mcmaster.ca", role = "ctb"), person("R-Core", role="ctb"))
Maintainer: Josie Athens <josie.athens@otago.ac.nz>
Description: A toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand 'ggplot2' plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.
Depends: R (>= 4.0.0), emmeans, ggformula, magrittr, stats
Imports: car, dplyr, Epi, epiR, epitools, ggplot2, Hmisc, huxtable, lmtest, moonBook, sandwich, sjlabelled, sjmisc, sjPlot, survival, tibble, tidyselect
Suggests: broom, bookdown, GGally, ggeffects, ggfortify, ggpubr, ggsci, haven, ISwR, jtools, knitr, latex2exp, lme4, MASS, mosaic, nlme, nnet, ordinal, psych, reshape2, rmarkdown, rms, scales, tidyverse
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
URL: https://github.com/josie-athens/pubh
BugReports: https://github.com/josie-athens/pubh/issues
NeedsCompilation: no
Packaged: 2020-07-06 22:06:45 UTC; josie
Author: Josie Athens [aut, cre], Frank Harell [ctb], John Fox [ctb], R-Core [ctb]
Repository: CRAN
Date/Publication: 2020-07-07 09:10:02 UTC

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