Tue, 01 Oct 2019

Package blogdown updated to version 0.16 with previous version 0.15 dated 2019-08-21

Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<http://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Beilei Bian [ctb], Forest Fang [ctb], Garrick Aden-Buie [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], JJ Allaire [ctb], Kevin Ushey [ctb], Leonardo Collado-Torres [ctb], Xianying Tan [ctb], Raniere Silva [ctb], Jozef Hajnala [ctb], RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between blogdown versions 0.15 dated 2019-08-21 and 0.16 dated 2019-10-01

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Package testit updated to version 0.10 with previous version 0.9 dated 2018-12-05

Title: A Simple Package for Testing R Packages
Description: Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Steven Mortimer [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between testit versions 0.9 dated 2018-12-05 and 0.10 dated 2019-10-01

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Package SplitSoftening updated to version 2.0-0 with previous version 1.0-0 dated 2018-09-19

Title: Softening Splits in Decision Trees
Description: Allows to produce and use classification trees with soft (probability) splits, as described in: Dvořák, J. (2019), <doi:10.1007/s00180-019-00867-1>.
Author: Jakub Dvorak
Maintainer: Jakub Dvorak <JakubDvorak@email.cz>

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Package simode updated to version 1.1.6 with previous version 1.1.5 dated 2019-09-29

Title: Statistical Inference for Systems of Ordinary Differential Equations using Separable Integral-Matching
Description: Implements statistical inference for systems of ordinary differential equations, that uses the integral-matching criterion and takes advantage of the separability of parameters, in order to obtain initial parameter estimates for nonlinear least squares optimization. Dattner & Yaari (2018) <arXiv:1807.04202>. Dattner et al. (2017) <doi:10.1098/rsif.2016.0525>. Dattner & Klaassen (2015) <doi:10.1214/15-EJS1053>.
Author: Itai Dattner [aut], Rami Yaari [aut, cre]
Maintainer: Rami Yaari <ramiyaari@gmail.com>

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Package rticles updated to version 0.11 with previous version 0.10 dated 2019-08-21

Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), R Foundation [aut, cph], Hadley Wickham [aut], Journal of Statistical Software [aut, cph], RStudio [cph], Ramnath Vaidyanathan [aut, cph], Association for Computing Machinery [aut, cph], Carl Boettiger [aut, cph], Elsevier [aut, cph], Karl Broman [aut, cph], Kirill Mueller [aut, cph], Bastiaan Quast [aut, cph], Randall Pruim [aut, cph], Ben Marwick [aut, cph], Charlotte Wickham [aut, cph], Oliver Keyes [aut, cph], Miao Yu [aut, cph], Daniel Emaasit [aut, cph], Thierry Onkelinx [aut, cph], Alessandro Gasparini [aut, cph] (<https://orcid.org/0000-0002-8319-7624>), Marc-Andre Desautels [aut, cph], Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>), MDPI [aut, cph], Taylor and Francis [aut, cph], Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>), Dalton Hance [aut], Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>), Petter Uvesten [aut, cph], Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>), John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>)
Maintainer: Yihui Xie <xie@yihui.name>

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Package rmarkdown updated to version 1.16 with previous version 1.15 dated 2019-08-21

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Barret Schloerke [ctb], Christophe Dervieux [ctb], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Jeff Allen [ctb], Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak lua filter), Albert Krewinkel [ctb, cph] (pagebreak lua filter)
Maintainer: Yihui Xie <xie@yihui.name>

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Package rgdal updated to version 1.4-6 with previous version 1.4-4 dated 2019-05-29

Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. From 'rgdal' 1.4.1, provision is made for 'PROJ6' accommodation, with 'PROJ6' functionality to follow; from 1.4.1 'rgdal' will build and function when 'PROJ' >= 6. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Tim Keitt [aut], Barry Rowlingson [aut, ctb], Edzer Pebesma [ctb], Michael Sumner [ctb], Robert Hijmans [ctb], Even Rouault [cph, ctb], Frank Warmerdam [cph, ctb], Jeroen Ooms [ctb], Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package chicane updated to version 0.1.1 with previous version 0.1.0 dated 2018-08-30

Title: Capture Hi-C Analysis Engine
Description: Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
Author: Erle Holgersen [aut, cre], Olivia Leavy [aut], Olivia Fletcher [aut], Frank Dudbridge [aut], Syed Haider [aut]
Maintainer: Erle Holgersen <erle.holgersen@gmail.com>

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Package xfun updated to version 0.10 with previous version 0.9 dated 2019-08-21

Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package vtreat updated to version 1.4.7 with previous version 1.4.6 dated 2019-09-23

Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner. 'vtreat' prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new categorical levels (levels seen during application, but not during training). Reference: "'vtreat': a data.frame Processor for Predictive Modeling", Zumel, Mount, 2016, <DOI:10.5281/zenodo.1173313>.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package traitdataform updated to version 0.5.6 with previous version 0.5.5 dated 2019-06-05

Title: Formatting and Harmonizing Ecological Trait-Data
Description: Assistance for handling ecological trait data and applying the Ecological Trait-Data Standard terminology (Schneider et al. 2019 <doi:10.1111/2041-210X.13288>). There are two major use cases: (1) preparation of own trait datasets for upload into public data bases, and (2) harmonizing trait datasets from different sources by re-formatting them into a unified format. See 'traitdataform' website for full documentation.
Author: Florian D. Schneider [aut, cre] (<https://orcid.org/0000-0002-1494-5684>), Caterina Penone [ctb] (<https://orcid.org/0000-0002-8170-6659>), Andreas Ostrowski [ctb] (<https://orcid.org/0000-0002-2033-779X>), Dennis Heimann [ctb], Felix Neff [ctb], Markus J. Ankenbrand [ctb]
Maintainer: Florian D. Schneider <florian.dirk.schneider@gmail.com>

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Package TPMplt updated to version 0.1.3 with previous version 0.1.2 dated 2018-12-14

Title: Tool-Kit for Dynamic Materials Model and Thermal Processing Maps
Description: Provides a simple approach for constructing dynamic materials modeling suggested by Prasad and Gegel <doi:10.1007/BF02664902>. It can easily generate various processing-maps based on this model as well. The calculation result in this package contains full materials constants, information about power dissipation efficiency factor, and rheological properties, can be exported completely also, through which further analysis and customized plots will be applicable as well.
Author: Chen ZHANG [aut, com, cre, cph], Rui LUO [ctb], Lingxiao OUYANG [ctb], Huakang BIAN [ctb], Kenta YAMANAKA [ctb], Akihiko CHIBA [ctb]
Maintainer: Chen ZHANG <447974102@qq.com>

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Package runner updated to version 0.2.1 with previous version 0.2.0 dated 2019-03-08

Title: Running Operations for Vectors
Description: Calculates running functions (a.k.a. windowed, rolling, cumulative) with varying window size and missing handling options. Package brings also running streak and running which, what extends beyond range of functions already implemented in R packages. Calculating on windows depending on date also available.
Author: Dawid Kałędkowski [aut, cre]
Maintainer: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>

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Package praznik updated to version 7.0.0 with previous version 6.0.0 dated 2019-06-21

Title: Tools for Information-Based Feature Selection
Description: A toolbox of fast, native and parallel implementations of various information-based importance criteria estimators and feature selection filters based on them, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <http://www.jmlr.org/papers/v13/brown12a.html>. Contains, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <http://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre] (<https://orcid.org/0000-0001-7672-648X>)
Maintainer: Miron B. Kursa <m@mbq.me>

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Package lintr updated to version 2.0.0 with previous version 1.0.3 dated 2018-11-08

Title: A 'Linter' for R Code
Description: Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text' and 'Atom'.
Author: Jim Hester [aut, cre], Florent Angly [aut]
Maintainer: Jim Hester <james.f.hester@gmail.com>

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New package KTensorGraphs with initial version 0.2
Package: KTensorGraphs
Type: Package
Title: Co-Tucker3 Analysis of Two Sequences of Matrices
Version: 0.2
Date: 2019-10-01
Author: Miguel Rodriguez-Rosa <miguel_rosa90@usal.es> [aut, cre]
Maintainer: Miguel Rodriguez-Rosa <miguel_rosa90@usal.es>
Description: Provides a function called COTUCKER3() (Co-Inertia Analysis + Tucker3 method) which performs a Co-Tucker3 analysis of two sequences of matrices, as well as other functions called PCA() (Principal Component Analysis) and BGA() (Between-Groups Analysis), which perform analysis of one matrix, COIA() (Co-Inertia Analysis), which performs analysis of two matrices, PTA() (Partial Triadic Analysis) and TUCKER3(), which perform analysis of a sequence of matrices, and BGCOIA() (Between-Groups Co-Inertia Analysis), STATICO() (STATIS method + Co-Inertia Analysis), COSTATIS() (Co-Inertia Analysis + STATIS method), which also perform analysis of two sequences of matrices.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2019-10-01 07:23:50 UTC; Magnet
Repository: CRAN
Date/Publication: 2019-10-01 18:40:09 UTC

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Package glasso updated to version 1.11 with previous version 1.10 dated 2018-07-13

Title: Graphical Lasso: Estimation of Gaussian Graphical Models
Description: Estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.
Author: Jerome Friedman, Trevor Hastie and Rob Tibshirani
Maintainer: Rob Tibshirani <tibs@stat.stanford.edu>

Diff between glasso versions 1.10 dated 2018-07-13 and 1.11 dated 2019-10-01

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Package GetTDData updated to version 1.4.2 with previous version 1.4.1 dated 2019-07-15

Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <http://www.tesouro.fazenda.gov.br/tesouro-direto-balanco-e-estatisticas>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between GetTDData versions 1.4.1 dated 2019-07-15 and 1.4.2 dated 2019-10-01

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Package bookdown updated to version 0.14 with previous version 0.13 dated 2019-08-21

Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), JJ Allaire [ctb], Albert Kim [ctb], Alessandro Samuel-Rosa [ctb], Andrzej Oles [ctb], Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Aust Frederik [ctb] (<https://orcid.org/0000-0003-4900-788X>), Bastiaan Quast [ctb], Ben Marwick [ctb], Chester Ismay [ctb], Christophe Dervieux [ctb], Clifton Franklund [ctb], Daniel Emaasit [ctb], David Shuman [ctb], Dean Attali [ctb], Drew Tyre [ctb], Ellis Valentiner [ctb], Frans van Dunne [ctb], Hadley Wickham [ctb], Jeff Allen [ctb], Jennifer Bryan [ctb], Jonathan McPhers [ctb], JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>), Junwen Huang [ctb], Kevin Cheung [ctb], Kevin Ushey [ctb], Kim Seonghyun [ctb], Kirill Muller [ctb], Luciano Selzer [ctb], Matthew Lincoln [ctb], Maximilian Held [ctb], Michael Sachs [ctb], Michal Bojanowski [ctb], Noam Ross [ctb], Peter Hickey [ctb], Romain Lesur [ctb] (<https://orcid.org/0000-0002-0721-5595>), Sahir Bhatnagar [ctb], Steve Simpson [ctb], Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>), Vincent Fulco [ctb], Yixuan Qiu [ctb], Zhuoer Dong [ctb], RStudio Inc [cph], Bartek Szopka [ctb] (The jQuery Highlight plugin), Zeno Rocha [cph] (clipboard.js library), jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/resources/AUTHORS), MathQuill contributors [ctb] (The MathQuill library; authors listed in inst/resources/AUTHORS), FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between bookdown versions 0.13 dated 2019-08-21 and 0.14 dated 2019-10-01

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Package BMTME updated to version 1.0.11 with previous version 1.0.10 dated 2019-09-26

Title: Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis
Description: Genomic selection and prediction models with the capacity to use multiple traits and environments, through ready-to-use Bayesian models. It consists a group of functions that help to create regression models for some genomic models proposed by Montesinos-López, et al. (2016) <doi:10.1534/g3.116.032359> also in Montesinos-López et al. (2018) <doi:10.1534/g3.118.200728> and Montesinos-López et al. (2018) <doi:10.2134/agronj2018.06.0362>.
Author: Francisco Javier Luna-Vazquez [aut, cre] (<https://orcid.org/0000-0002-5370-7152>), Fernando H. Toledo [aut], Osval Antonio Montesinos-Lopez [aut] (<https://orcid.org/0000-0002-3973-6547>), Abelardo Montesinos-Lopez [aut], Jose Crossa [aut] (<https://orcid.org/0000-0001-9429-5855>)
Maintainer: Francisco Javier Luna-Vazquez <frahik@gmail.com>

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Package rscorecard updated to version 0.13.0 with previous version 0.12.0 dated 2019-05-21

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

Diff between rscorecard versions 0.12.0 dated 2019-05-21 and 0.13.0 dated 2019-10-01

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Package pls updated to version 2.7-2 with previous version 2.7-1 dated 2019-03-23

Title: Partial Least Squares and Principal Component Regression
Description: Multivariate regression methods Partial Least Squares Regression (PLSR), Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).
Author: Bjørn-Helge Mevik [aut, cre], Ron Wehrens [aut], Kristian Hovde Liland [aut], Paul Hiemstra [ctb]
Maintainer: Bjørn-Helge Mevik <b-h@mevik.net>

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Package mlflow updated to version 1.3.0 with previous version 1.2.0 dated 2019-08-19

Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre], Javier Luraschi [aut], Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>

Diff between mlflow versions 1.2.0 dated 2019-08-19 and 1.3.0 dated 2019-10-01

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Package devEMF updated to version 3.7 with previous version 3.6-3 dated 2019-06-24

Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>

Diff between devEMF versions 3.6-3 dated 2019-06-24 and 3.7 dated 2019-10-01

 DESCRIPTION    |    8 +++----
 MD5            |   12 +++++------
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 configure      |    1 
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Package calibrate updated to version 1.7.5 with previous version 1.7.2 dated 2013-09-10

Title: Calibration of Scatterplot and Biplot Axes
Description: Package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots. Also provides some functions for multivariate analysis such principal coordinate analysis.
Author: Jan Graffelman <jan.graffelman@upc.edu>
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>

Diff between calibrate versions 1.7.2 dated 2013-09-10 and 1.7.5 dated 2019-10-01

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Package gradeR updated to version 1.0.2 with previous version 1.0.1 dated 2019-07-29

Title: Helps Grade Assignment Submissions that are R Scripts
Description: After being given the location of your students' submissions and a test file, the function runs each .R file, and evaluates the results from all the given tests. Results are neatly returned in a data frame that has a row for each student, and a column for each test.
Author: Taylor Brown [aut, cre]
Maintainer: Taylor Brown <trb5me@virginia.edu>

Diff between gradeR versions 1.0.1 dated 2019-07-29 and 1.0.2 dated 2019-10-01

 DESCRIPTION                      |    6 ++---
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 tests/testthat/test_calcGrades.r |    8 +++----
 6 files changed, 70 insertions(+), 34 deletions(-)

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New package baycn with initial version 1.0.0
Package: baycn
Type: Package
Title: Bayesian Inference for Causal Networks
Version: 1.0.0
Author: Evan A Martin [aut, cre], Audrey Qiuyan Fu [aut]
Maintainer: Evan A Martin <evanamartin@gmail.com>
Description: A Bayesian hybrid approach for inferring Directed Acyclic Graphs (DAGs) for continuous, discrete, and mixed data. The algorithm can use the graph inferred by another more efficient graph inference method as input; the input graph may contain false edges or undirected edges but can help reduce the search space to a more manageable size. A Bayesian Markov chain Monte Carlo algorithm is then used to infer the probability of direction and absence for the edges in the network. References: Martin and Fu (2019) <arXiv:1909.10678>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: egg, ggplot2, MASS, methods
RoxygenNote: 6.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2019-09-25 17:33:01 UTC; Evatar
Repository: CRAN
Date/Publication: 2019-10-01 15:30:02 UTC

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New package KbMvtSkew with initial version 1.0.1
Package: KbMvtSkew
Type: Package
Title: Khattree-Bahuguna's Univariate and Multivariate Skewness
Version: 1.0.1
Authors@R: c( person("Zhixin", "Lun", email = "zlun@oakland.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8980-1554")), person("Ravindra", "Khattree", email = "khattree@oakland.edu", role = "aut", comment = c(ORCID = "0000-0002-9305-2365")))
Maintainer: Zhixin Lun <zlun@oakland.edu>
Description: Computes Khattree-Bahuguna's univariate and multivariate skewness, principal-component-based Khattree-Bahuguna's multivariate skewness. It also provides several measures of univariate or multivariate skewnesses including, Pearson’s coefficient of skewness, Bowley’s univariate skewness and Mardia's multivariate skewness. See Khattree, R. and Bahuguna, M. (2019) <doi: 10.1007/s41060-018-0106-1>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: stats
Depends: R (>= 3.5.0)
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-09-24 21:35:46 UTC; Zhixin Lun
Author: Zhixin Lun [aut, cre] (<https://orcid.org/0000-0002-8980-1554>), Ravindra Khattree [aut] (<https://orcid.org/0000-0002-9305-2365>)
Repository: CRAN
Date/Publication: 2019-10-01 14:40:08 UTC

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New package hilldiv with initial version 1.5.1
Package: hilldiv
Title: Integral Analysis of Diversity Based on Hill Numbers
Version: 1.5.1
Author: Antton Alberdi [aut, cre]
Maintainer: Antton Alberdi <antton.alberdi@bio.ku.dk>
Description: Tools for analysing, comparing, visualising and partitioning diversity based on Hill numbers. 'hilldiv' is an R package that provides a set of functions to assist analysis of diversity for diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses based on Hill numbers, using OTU/ASV tables and associated phylogenetic trees as inputs. The package includes functions for (phylo)diversity measurement, (phylo)diversity profile plotting, (phylo)diversity comparison between samples and groups, (phylo)diversity partitioning and (dis)similarity measurement. All of these grounded in abundance-based and incidence-based Hill numbers. The statistical framework developed around Hill numbers encompasses many of the most broadly employed diversity (e.g. richness, Shannon index, Simpson index), phylogenetic diversity (e.g. Faith's PD, Allen's H, Rao's quadratic entropy) and dissimilarity (e.g. Sorensen index, Unifrac distances) metrics. This enables the most common analyses of diversity to be performed while grounded in a single statistical framework. The methods are described in Jost et al. (2007) <DOI:10.1890/06-1736.1>, Chao et al. (2010) <DOI:10.1098/rstb.2010.0272> and Chiu et al. (2014) <DOI:10.1890/12-0960.1>; and reviewed in the framework of molecularly characterised biological systems in Alberdi & Gilbert (2019) <DOI:10.1111/1755-0998.13014>.
License: GPL-3
LazyData: true
URL: https://github.com/anttonalberdi/hilldiv
BugReports: https://github.com/anttonalberdi/hilldiv/issues
Depends: R (>= 3.1.0)
Suggests:
Imports: stats, ggplot2, scales, ggpubr, RColorBrewer, data.table, ape, vegan, geiger, qgraph, FSA
Encoding: UTF-8
RoxygenNote: 6.1.1
Collate: 'index_div.R' 'hill_div.R' 'div_profile.R' 'div_profile_plot.R' 'div_test.R' 'div_test_plot.R' 'depth_cov.R' 'div_part.R' 'alpha_div.R' 'gamma_div.R' 'beta_dis.R' 'pair_dis.R' 'pair_dis_plot.R' 'UqN.R' 'CqN.R' 'VqN.R' 'SqN.R' 'match_data.R' 'depth_filt.R' 'copy_filt.R' 'to.incidence.R' 'tss.R' 'is.nested.R' 'tree_depth.R' 'data.R'
NeedsCompilation: no
Packaged: 2019-10-01 13:32:38 UTC; jpl786
Repository: CRAN
Date/Publication: 2019-10-01 14:40:02 UTC

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New package factorEx with initial version 1.0.0
Package: factorEx
Type: Package
Title: Design and Analysis for Factorial Experiments
Version: 1.0.0
Author: Naoki Egami, Brandon de la Cuesta, Kosuke Imai
Maintainer: Naoki Egami <naoki.egami5@gmail.com>
Description: Provides design-based and model-based estimators for the population average marginal component effects in general factorial experiments, including conjoint analysis. The package also implements a series of recommendations offered in de la Cuesta, Egami, and Imai (2019+), and Egami and Imai (2019) <doi:10.1080/01621459.2018.1476246>.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 3.5.0), arm, genlasso
Imports: prodlim, sandwich, igraph, pbmcapply, pbapply, mvtnorm, stringr, doParallel, foreach, estimatr
URL: https://github.com/naoki-egami/factorEx
BugReports: https://github.com/naoki-egami/factorEx/issues
NeedsCompilation: no
Packaged: 2019-10-01 13:03:08 UTC; negami
Repository: CRAN
Date/Publication: 2019-10-01 14:40:05 UTC

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New package amber with initial version 0.1.5
Package: amber
Type: Package
Title: Automated Model Benchmarking Package for the Canadian Land Surface Scheme
Version: 0.1.5
Author: Christian Seiler [cre, aut]
Maintainer: Christian Seiler <christian.seiler@canada.ca>
Description: Functions that quantify how well the Canadian Land Surface Scheme Including Biogeochemical Cycles (CLASSIC) reproduces land surface processes when compared against reference data. To summarize model performance across different statistical metrics, this package employs a skill score system that was originally developed by Collier et. al., (2018) <doi:10.1029/2018MS001354> .
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0)
Imports: classInt, doParallel, foreach, latex2exp, ncdf4, parallel, raster, rgeos, scico, sp, spatial.tools, stats, utils, viridis, xtable
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-09-24 15:14:32 UTC; acrpcsr
Repository: CRAN
Date/Publication: 2019-10-01 14:20:02 UTC

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Package WhiteStripe updated to version 2.3.2 with previous version 2.3.1 dated 2018-04-18

Title: White Matter Normalization for Magnetic Resonance Images using WhiteStripe
Description: Shinohara (2014) <DOI:10.1016/j.nicl.2014.08.008> introduced 'WhiteStripe', an intensity-based normalization of T1 and T2 images, where normal appearing white matter performs well, but requires segmentation. This method performs white matter mean and standard deviation estimates on data that has been rigidly-registered to the 'MNI' template and uses histogram-based methods.
Author: R. Taki Shinohara, John Muschelli
Maintainer: John Muschelli <muschellij2@gmail.com>

Diff between WhiteStripe versions 2.3.1 dated 2018-04-18 and 2.3.2 dated 2019-10-01

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New package signs with initial version 0.1.0
Package: signs
Title: Insert Proper Minus Signs
Version: 0.1.0
Authors@R: person(given = c("Benjamin", "E."), family = "Wolfe", role = c("aut", "cre"), email = "benjamin.e.wolfe@gmail.com", comment = c(ORCID = "0000-0002-4339-9328"))
Description: Provides convenience functions to replace hyphen-minuses (ASCII 45) with proper minus signs (Unicode character 2212). The minus sign is wider and slightly nicer for display than the hyphen-minus we use for computation.
URL: https://benjaminwolfe.github.io/signs
BugReports: https://github.com/BenjaminWolfe/signs/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: scales, rlang (>= 0.4.0)
RoxygenNote: 6.1.1
Suggests: ggplot2, dplyr, ggrepel, testthat (>= 2.1.0), knitr, rmarkdown, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-09-24 04:57:02 UTC; Karin
Author: Benjamin E. Wolfe [aut, cre] (<https://orcid.org/0000-0002-4339-9328>)
Maintainer: Benjamin E. Wolfe <benjamin.e.wolfe@gmail.com>
Repository: CRAN
Date/Publication: 2019-10-01 12:40:02 UTC

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New package Rquefts with initial version 1.0-5
Package: Rquefts
Type: Package
Title: Quantitative Evaluation of the Native Fertility of Tropical Soils
Version: 1.0-5
Date: 2019-09-30
LinkingTo: Rcpp
SystemRequirements: C++11
Imports: meteor, methods, Rcpp (>= 0.12.4)
Authors@R: c( person("Robert J.", "Hijmans", role = c("cre", "aut"), email = "r.hijmans@gmail.com"), person("Joost", "Wolff", role = "ctb"))
Description: An implementation of the QUEFTS (Quantitative Evaluation of the Native Fertility of Tropical Soils) model. The model estimates nutrient requirements for crops to achieve a target yield given native soil fertility, as estimated from a few soil chemical properties. See Janssen et al. (1990) <doi:10.1016/0016-7061(90)90021-Z> for the technical details and Sattari et al. (2014) <doi:10.1016/j.fcr.2013.12.005> for a recent evaluation.
License: GPL (>= 3)
BugReports: https://github.com/cropmodels/Rquefts/issues
URL: https://github.com/cropmodels/Rquefts/
NeedsCompilation: yes
Packaged: 2019-10-01 02:55:13 UTC; rhijm
Author: Robert J. Hijmans [cre, aut], Joost Wolff [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Repository: CRAN
Date/Publication: 2019-10-01 12:00:14 UTC

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New package pedmut with initial version 0.1.0
Package: pedmut
Title: Mutation Models for Pedigree Likelihood Computations
Version: 0.1.0
Authors@R: person("Magnus Dehli", "Vigeland", email = "m.d.vigeland@medisin.uio.no", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9134-4962"))
Description: A collection of functions for modeling mutations in pedigrees with marker data, as used e.g. in likelihood computations with microsatellite data. Implemented models include proportional and stepwise models, as well as random models for experimental work, and custom models allowing the user to apply any valid mutation matrix. Allele lumping is done following the lumpability criteria of Kemeny and Snell (1976), ISBN:0387901922.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2019-09-30 18:06:12 UTC; magnusdv
Author: Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Repository: CRAN
Date/Publication: 2019-10-01 12:00:02 UTC

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New package kubik with initial version 0.1.1
Package: kubik
Title: Cubic Hermite Splines
Version: 0.1.1
Date: 2019-10-01
License: GPL (>= 2)
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Author: Abby Spurdle
URL: https://sites.google.com/site/spurdlea/r
Description: Computes (constructs, plots and evaluates) constrained cubic Hermite splines, which can be used to construct monotonic splines. Computes their first derivatives, indefinite integrals and smooth approximations of their first, second and higher derivatives. Also, computes their roots, including their argmins, argmaxs and inflection points.
Imports: intoo
Suggests: zeallot
NeedsCompilation: no
Packaged: 2019-10-01 01:38:36 UTC; Student9
Repository: CRAN
Date/Publication: 2019-10-01 12:00:05 UTC

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New package goffda with initial version 0.0.5
Package: goffda
Type: Package
Title: Goodness-of-Fit Tests for Functional Data
Version: 0.0.5
Date: 2019-09-30
Authors@R: c( person(given = "Eduardo", family = "García-Portugués", role = c("aut", "cre"), email = "edgarcia@est-econ.uc3m.es"), person("Javier", "Álvarez-Liébana", role = "aut", email = "alvarezljavier@uniovi.es"), person("Gonzalo", "Álvarez-Pérez", role = "ctb", email = "gonzaloalvarez@uniovi.es"), person("Manuel", "Febrero-Bande", role = "ctb", email = "manuel.febrero@usc.es") )
Description: Implementation of several goodness-of-fit tests for functional data. Currently, mostly related with the functional linear model with functional/scalar response and functional/scalar predictor. The package allows for the replication of the data applications considered in García-Portugués, Álvarez-Liébana, Álvarez-Pérez and González-Manteiga (2019) <arXiv:1909.07686>.
License: GPL-3
LazyData: true
Depends: R (>= 3.5.0), Rcpp
Imports: fda.usc, glmnet, ks
Suggests: microbenchmark, knitr, viridisLite, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/egarpor/goffda
BugReports: https://github.com/egarpor/goffda
Encoding: UTF-8
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-10-01 07:18:49 UTC; Eduardo
Author: Eduardo García-Portugués [aut, cre], Javier Álvarez-Liébana [aut], Gonzalo Álvarez-Pérez [ctb], Manuel Febrero-Bande [ctb]
Maintainer: Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>
Repository: CRAN
Date/Publication: 2019-10-01 12:00:08 UTC

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New package gemma2 with initial version 0.1.1
Package: gemma2
Title: GEMMA Multivariate Linear Mixed Model
Version: 0.1.1
Authors@R: c( person(given = "Frederick", family = "Boehm", email = "frederick.boehm@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1644-5931") ) )
Description: Fits a multivariate linear mixed effects model that uses a polygenic term, after Zhou & Stephens (2014) (<https://www.nature.com/articles/nmeth.2848>). Of particular interest is the estimation of variance components with restricted maximum likelihood (REML) methods. Genome-wide efficient mixed-model association (GEMMA), as implemented in the package 'gemma2', uses an expectation-maximization algorithm for variance components inference for use in quantitative trait locus studies.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/fboehm/gemma2
BugReports: https://github.com/fboehm/gemma2/issues
Suggests: covr, testthat, knitr, rmarkdown
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Imports: readr, Matrix
Language: en-US
NeedsCompilation: no
Packaged: 2019-09-30 15:47:45 UTC; fred
Author: Frederick Boehm [aut, cre] (<https://orcid.org/0000-0002-1644-5931>)
Maintainer: Frederick Boehm <frederick.boehm@gmail.com>
Repository: CRAN
Date/Publication: 2019-10-01 12:00:11 UTC

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Package rsggm updated to version 0.3.1 with previous version 0.3 dated 2015-08-21

Title: Robust Sparse Gaussian Graphical Modeling via the Gamma-Divergence
Description: Robust estimation of sparse inverse covariance matrix via the gamma-divergence.
Author: Kei Hirose
Maintainer: Kei Hirose <mail@keihirose.com>

Diff between rsggm versions 0.3 dated 2015-08-21 and 0.3.1 dated 2019-10-01

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Package excelR updated to version 0.3.1 with previous version 0.3.0 dated 2019-09-07

Title: A Wrapper of the 'JavaScript' Library 'jExcel'
Description: An R interface to 'jExcel' library to create web-based interactive tables and spreadsheets compatible with 'Excel' or any other spreadsheet software.
Author: Swechhya Bista [aut, cre], Kent Russell [ctb], Mārcis Bratka [ctb]
Maintainer: Swechhya Bista <swechhyabista@gmail.com>

Diff between excelR versions 0.3.0 dated 2019-09-07 and 0.3.1 dated 2019-10-01

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Package zipfR updated to version 0.6-66 with previous version 0.6-10 dated 2017-08-17

Title: Statistical Models for Word Frequency Distributions
Description: Statistical models and utilities for the analysis of word frequency distributions. The utilities include functions for loading, manipulating and visualizing word frequency data and vocabulary growth curves. The package also implements several statistical models for the distribution of word frequencies in a population. (The name of this package derives from the most famous word frequency distribution, Zipf's law.)
Author: Stefan Evert <stefan.evert@fau.de>, Marco Baroni <marco.baroni@unitn.it>
Maintainer: Stefan Evert <stefan.evert@fau.de>

Diff between zipfR versions 0.6-10 dated 2017-08-17 and 0.6-66 dated 2019-10-01

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More information about zipfR at CRAN
Permanent link

Package rvcheck updated to version 0.1.5 with previous version 0.1.3 dated 2018-12-06

Title: R/Package Version Check
Description: Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
Author: Guangchuang Yu [aut, cre], Chun-hui Gao [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between rvcheck versions 0.1.3 dated 2018-12-06 and 0.1.5 dated 2019-10-01

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Package pagedown updated to version 0.5 with previous version 0.4 dated 2019-08-21

Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>), Brent Thorne [aut] (<https://orcid.org/0000-0002-1099-3857>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), RStudio, Inc. [cph], Adam Hyde [ctb] (paged.js in resources/js/), Min-Zhong Lu [ctb] (resume.css in resources/css/), Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between pagedown versions 0.4 dated 2019-08-21 and 0.5 dated 2019-10-01

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Package future.batchtools updated to version 0.8.1 with previous version 0.8.0 dated 2019-05-05

Title: A Future API for Parallel and Distributed Processing using 'batchtools'
Description: Implementation of the Future API on top of the 'batchtools' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, not only on your local machine or ad-hoc cluster of machines, but also via high-performance compute ('HPC') job schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS', e.g. 'y <- future.apply::future_lapply(files, FUN = process)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between future.batchtools versions 0.8.0 dated 2019-05-05 and 0.8.1 dated 2019-10-01

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Package politeness updated to version 0.3.3 with previous version 0.3.2 dated 2019-07-02

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 <myeomans@hbs.edu>

Diff between politeness versions 0.3.2 dated 2019-07-02 and 0.3.3 dated 2019-10-01

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Package pins updated to version 0.2.0 with previous version 0.1.2 dated 2019-09-04

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 0.1.2 dated 2019-09-04 and 0.2.0 dated 2019-10-01

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Package MSEtool updated to version 1.3.0 with previous version 1.2.1 dated 2019-07-29

Title: Management Strategy Evaluation Toolkit
Description: Simulation tools for management strategy evaluation are provided for the 'DLMtool' operating model to inform data-rich fisheries. 'MSEtool' provides complementary assessment models of varying complexity with standardized reporting, diagnostic tools for evaluating assessment models within closed-loop simulation, and helper functions for building more complex operating models and management procedures.
Author: Quang Huynh [aut], Tom Carruthers [aut, cre], Adrian Hordyk [aut], Chris Grandin [ctb] (iSCAM functions)
Maintainer: Tom Carruthers <t.carruthers@oceans.ubc.ca>

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Package dials updated to version 0.0.3 with previous version 0.0.2 dated 2018-12-09

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 0.0.2 dated 2018-12-09 and 0.0.3 dated 2019-10-01

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