Thu, 22 Aug 2019

Package MixGHD updated to version 2.3.3 with previous version 2.3.2 dated 2019-04-12

Title: Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution. The first model 'MGHD' (Browne and McNicholas (2015) <doi:10.1002/cjs.11246>) is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' (Tortora et al. (2016) <doi:10.1007/s11634-015-0204-z>) is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD'(Tortora et al. (2016) <arXiv:1403.2332v7>), mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' (Tortora et al. (2016) <arXiv:1403.2332v7>) is a 'MSGHD' with convex contour plots. The 'MCGHD' (Tortora et al. (2016) <arXiv:1403.2332v7>), mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora [aut, cre, cph], Aisha ElSherbiny [com], Ryan P. Browne [aut, cph], Brian C. Franczak [aut, cph], and Paul D. McNicholas [aut, cph], and Donald D. Amos [ctb].
Maintainer: Cristina Tortora <grikris1@gmail.com>

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Package MetaboList updated to version 2.0 with previous version 1.4 dated 2019-06-04

Title: Annotation of Metabolites from Liquid Chromatography-Mass Spectrometry Data
Description: Automatic metabolite annotation from Liquid Chromatography-Mass Spectrometry (LC-MS and LC-MS/MS DIA) analysis.
Author: Manuel David Peris Diaz
Maintainer: Manuel David Peris Diaz <manuel.perisdiaz@uwr.edu.pl>

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Package FPDclustering updated to version 1.3.1 with previous version 1.3 dated 2019-04-12

Title: PD-Clustering and Factor PD-Clustering
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership, under the constraint that the product of the probability and the distance of each point to any cluster centre is a constant. PD-clustering is a flexible method that can be used with non-spherical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different size. Factor PD-clustering (FPDC) is a recently proposed factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high dimensional datasets.
Author: Cristina Tortora [aut, cre, cph], Noe Vidales [aut], and Paul D. McNicholas [fnd]
Maintainer: Cristina Tortora <grikris1@gmail.com>

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Package pmd updated to version 0.1.5 with previous version 0.1.1 dated 2018-12-02

Title: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis
Description: Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. A GUI for PMD analysis is also included as a 'shiny' application.
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>)
Maintainer: Miao YU <yufreecas@gmail.com>

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Package nat updated to version 1.8.13 with previous version 1.8.11 dated 2017-11-12

Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Author: Gregory Jefferis [aut, cre] (<https://orcid.org/0000-0002-0587-9355>), James Manton [aut] (<https://orcid.org/0000-0001-9260-3156>)
Maintainer: Gregory Jefferis <jefferis@gmail.com>

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Package tdthap updated to version 1.1-11 with previous version 1.1-9 dated 2018-06-30

Title: TDT Tests for Extended Haplotypes
Description: Functions and examples are provided for Transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes". Amer. J. Hum. Genet., 65:1161-1169, <doi:10.1086/302566>.
Author: David Clayton
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>

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Package GillespieSSA2 updated to version 0.2.5 with previous version 0.2.4 dated 2019-08-05

Title: Gillespie's Stochastic Simulation Algorithm for Impatient People
Description: A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package esquisse updated to version 0.2.2 with previous version 0.2.1 dated 2019-07-01

Title: Explore and Visualize Your Data Interactively
Description: A 'shiny' gadget to create 'ggplot2' charts interactively with drag-and-drop to map your variables. You can quickly visualize your data accordingly to their type, export to 'PNG' or 'PowerPoint', and retrieve the code to reproduce the chart.
Author: Fanny Meyer [aut], Victor Perrier [aut, cre], Ian Carroll [ctb] (Facets support)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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New package rscielo with initial version 1.0.0
Package: rscielo
Type: Package
Title: A Scraper for Scientific Journals Hosted on Scielo
Version: 1.0.0
Authors@R: c( person("Fernando", "Meireles", , "fernando.meireles@iesp.uerj.br", c("aut", "cre"), c(ORCID = "0000-0002-7027-2058")), person("Denisson", "Silva", , "silvadenisson@ufmg.br", c("aut"), c(ORCID = "0000-0003-2771-8146")), person("Rogerio", "Barbosa", , "antrologos@gmail.com", c("aut"), c(ORCID = "0000-0002-7027-2058")) )
Description: Scrapes data from scientific articles hosted on the Scientific Electronic Library Online Platform <http://www.scielo.br/>. The data information includes author's names, articles' metadata and contents, among others. The package also provides additional functions to easily summarize the scraped data.
License: GPL-3
Depends: R (>= 3.1)
Imports: graphics, magrittr, stats, xml2, httr (>= 0.5), rvest, stringr, tibble, purrr, dplyr
LazyData: TRUE
URL: https://github.com/meirelesff/rscielo
BugReports: https://github.com/meirelesff/rscielo/issues
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-21 15:44:21 UTC; meire
Author: Fernando Meireles [aut, cre] (<https://orcid.org/0000-0002-7027-2058>), Denisson Silva [aut] (<https://orcid.org/0000-0003-2771-8146>), Rogerio Barbosa [aut] (<https://orcid.org/0000-0002-7027-2058>)
Maintainer: Fernando Meireles <fernando.meireles@iesp.uerj.br>
Repository: CRAN
Date/Publication: 2019-08-22 12:10:02 UTC

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Package dexter updated to version 1.0.0 with previous version 0.8.5 dated 2019-04-25

Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris, Timo Bechger, Jesse Koops, Ivailo Partchev
Maintainer: Jesse Koops <jesse.koops@cito.nl>

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More information about dexter at CRAN
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Package apexcharter updated to version 0.1.2 with previous version 0.1.1 dated 2019-07-28

Title: Create Interactive Chart with the JavaScript 'ApexCharts' Library
Description: Provides an 'htmlwidgets' interface to 'apexcharts.js'. 'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API. 'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], Juned Chhipa [cph] (apexcharts.js library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between apexcharter versions 0.1.1 dated 2019-07-28 and 0.1.2 dated 2019-08-22

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New package gretel with initial version 0.0.1
Package: gretel
Title: Generalized Path Analysis for Social Networks
Version: 0.0.1
Date: 2019-08-09
Authors@R: person("David", "Buch", email = "davidbuch42@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4574-0075"))
Description: The social network literature features numerous methods for assigning value to paths as a function of their ties. 'gretel' systemizes these approaches, casting them as instances of a generalized path value function indexed by a penalty parameter. The package also calculates probabilistic path value and identifies optimal paths in either value framework. Finally, proximity matrices can be generated in these frameworks that capture high-order connections overlooked in primitive adjacency sociomatrices. Novel methods are described in Buch (2019) <https://davidbuch.github.io/analyzing-networks-with-gretel.html>. More traditional methods are also implemented, as described in Yang, Knoke (2001) <doi:10.1016/S0378-8733(01)00043-0>.
Maintainer: David Buch <davidbuch42@gmail.com>
URL: https://github.com/davidbuch/gretel
BugReports: https://github.com/davidbuch/gretel/issues
License: GPL-3
Depends: R (>= 3.0)
Imports: Rcpp (>= 1.0.0), ResistorArray (>= 1.0-32)
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, testthat (>= 2.1.0)
VignetteBuilder: knitr
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-08-21 11:38:45 UTC; Buch
Author: David Buch [aut, cre] (<https://orcid.org/0000-0002-4574-0075>)
Repository: CRAN
Date/Publication: 2019-08-22 12:00:02 UTC

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Package forecast updated to version 8.9 with previous version 8.8 dated 2019-08-02

Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>), George Athanasopoulos [aut], Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>), Gabriel Caceres [aut], Leanne Chhay [aut], Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>), Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>), Slava Razbash [aut], Earo Wang [aut], Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>), R Core Team [ctb, cph], Ross Ihaka [ctb, cph], Daniel Reid [ctb], David Shaub [ctb], Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>), Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>

Diff between forecast versions 8.8 dated 2019-08-02 and 8.9 dated 2019-08-22

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Package STMotif updated to version 1.0.3 with previous version 1.0.2 dated 2019-02-11

Title: Discovery of Motifs in Spatial-Time Series
Description: Allow to identify motifs in spatial-time series. A motif is a previously unknown subsequence of a (spatial) time series with relevant number of occurrences. For this purpose, the Combined Series Approach (CSA) is used.
Author: Heraldo Borges [aut, cre] (CEFET/RJ), Amin Bazaz [aut] (Polytech'Montpellier), Luciana Escobar [aut] (CEFET/RJ), Esther Pacitti [aut] (CEFET/RJ), Eduardo Ogasawara [aut] (CEFET/RJ)
Maintainer: Heraldo Borges <stmotif@eic.cefet-rj.br>

Diff between STMotif versions 1.0.2 dated 2019-02-11 and 1.0.3 dated 2019-08-22

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Package nandb updated to version 2.0.5 with previous version 2.0.4 dated 2019-07-08

Title: Number and Brightness Image Analysis
Description: Calculation of molecular number and brightness from fluorescence microscopy image series. The software was published in a 2016 paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for the technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>. A review of the technique was published in 2017 <doi:10.1016/j.ymeth.2017.12.001>.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>), Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>), Sergi Padilla-Parra [ctb, ths, cph] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between nandb versions 2.0.4 dated 2019-07-08 and 2.0.5 dated 2019-08-22

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New package simGWAS with initial version 0.2.0-2
Package: simGWAS
Type: Package
Title: Fast Simulation of Large Case-Control GWAS Summary Statistics
Version: 0.2.0-2
Date: 2019-08-19
Authors@R: c(person("Mary", "Fortune", role=c("aut"), email = "mdf34@cam.ac.uk"), person("Chris","Wallace", role=c("aut","cre"), email="cew54@cam.ac.uk"), person("Marcus", "Klarqvist", role=c("ctb")))
Author: Mary Fortune [aut], Chris Wallace [aut, cre], Marcus Klarqvist [ctb]
Maintainer: Chris Wallace <cew54@cam.ac.uk>
Description: Simulating output from a case-control genome wide association study (GWAS) with a given causal model. Fortune and Wallace (2019) <doi:10.1093/bioinformatics/bty898>.
License: GPL
LazyLoad: yes
OS_type: unix
Collate: 'simGWAS.R' 'compute_gamma0.R' 'vbeta.R' 'zscore.R' 'extractsnps.R' 'make_dataset.R' 'make_GenoProbList.R' 'RcppExports.R'
LinkingTo: Rcpp
Imports: Rcpp, dplyr, combinat, corpcor, mvtnorm
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
URL: https://github.com/chr1swallace/simGWAS
BugReports: https://github.com/chr1swallace/simGWAS/issues
NeedsCompilation: yes
Packaged: 2019-08-20 21:01:25 UTC; chris
Repository: CRAN
Date/Publication: 2019-08-22 08:20:02 UTC

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New package cursory with initial version 1.0.0
Package: cursory
Type: Package
Title: A Cursory Look at Variables
Version: 1.0.0
Authors@R: person("Andrew", "Redd", role = c("aut", "cre") , email = "Andrew.Redd@hsc.utah.edu" , comment = c(ORCID = "https://orcid.org/000-0002-6149-2438") )
Maintainer: Andrew Redd <Andrew.Redd@hsc.utah.edu>
Description: Provides functions for quickly looking at summary statistics for variables in a data set.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Language: en-US
RoxygenNote: 6.1.1
Imports: dplyr, methods, pkgcond, purrr, rlang, tibble, tidymargins, tidyr, tidyselect
Suggests: covr, forcats, datasets, dbplyr, testthat, testextra, DBI, RSQLite
URL: https://github.com/halpo/cursory
BugReports: https://github.com/halpo/cursory/issues
NeedsCompilation: no
Packaged: 2019-08-20 21:26:04 UTC; u0092104
Author: Andrew Redd [aut, cre] (<https://orcid.org/000-0002-6149-2438>)
Repository: CRAN
Date/Publication: 2019-08-22 08:40:02 UTC

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New package Rirt with initial version 0.0.1
Package: Rirt
Type: Package
Title: Item Response Theory Models
Version: 0.0.1
Date: 2019-08-05
Authors@R: c(person("Xiao", "Luo", role=c("aut","cre"), email="xluo1986@gmail.com"))
Author: Xiao Luo [aut, cre]
Maintainer: Xiao Luo <xluo1986@gmail.com>
Description: Parameter estimation, computation of probability, information, and (log-)likelihood, and visualization of item/test characteristic curves and item/test information functions for three uni-dimensional item response theory models: the 3-parameter-logistic model, generalized partial credit model, and graded response model. The full documentation and tutorials are at <https://github.com/xluo11/Rirt>.
License: GPL (>= 3)
Depends: R (>= 3.6.0)
URL: https://github.com/xluo11/Rirt
BugReports: https://github.com/xluo11/Rirt/issues
LinkingTo: Rcpp
Imports: ggplot2, Rcpp, reshape2, stats
Suggests: testthat
RoxygenNote: 6.1.1
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2019-08-20 18:14:03 UTC; Luo.Xiao
Repository: CRAN
Date/Publication: 2019-08-22 07:50:05 UTC

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New package QuantileNPCI with initial version 0.2.95
Package: QuantileNPCI
Type: Package
Title: Nonparametric Confidence Intervals for Quantiles
Version: 0.2.95
Authors@R: c( person("Nicholas", "Hutson", role = "aut"), person("Li", "Yan", role=c("aut", "cre"), email = "li.yan@roswellpark.org") )
Maintainer: Li Yan <li.yan@roswellpark.org>
Description: Based on Alan D. Hutson (1999) <doi:10.1080/02664769922458>, "Calculating nonparametric confidence intervals for quantiles using fractional order statistics", Journal of Applied Statistics, 26:3, 343-353.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports:
Suggests: dplyr, kableExtra, knitr, rmarkdown, testthat (>= 2.1.0)
Depends: R (>= 2.10)
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-20 19:30:03 UTC; liyan
Author: Nicholas Hutson [aut], Li Yan [aut, cre]
Repository: CRAN
Date/Publication: 2019-08-22 07:20:02 UTC

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New package mRpostman with initial version 0.2.0
Package: mRpostman
Type: Package
Title: IMAP Tools in a Tidy Way
Version: 0.2.0
Date: 2019-08-18
Authors@R: c( person(given="Allan", family="Quadros", email = "allanvcq@gmail.com", role = c("aut", "cre")))
Description: Multiple IMAP (Internet Message Access Protocol) commands based on the RFC 3501 manual (Crispin, 2003, <doi:10.17487/RFC3501>), its updates, and other related documents. Besides other features, 'mRpostman' provides functions for listing, selecting and renaming mailboxes, as well as moving, fetching, and searching for messages using several criteria.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: curl, stringr, magrittr, assertthat, base64enc
Depends: R (>= 3.1.0)
BugReports: https://github.com/allanvc/mRpostman/issues
SystemRequirements: libcurl: libcurl-devel (rpm) or libcurl4-openssl-dev (deb)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-20 19:12:26 UTC; allan
Author: Allan Quadros [aut, cre]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Repository: CRAN
Date/Publication: 2019-08-22 07:30:02 UTC

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New package DoE.multi.response with initial version 0.1.0
Package: DoE.multi.response
Title: Construct Multi-Response Experimental Designs
Version: 0.1.0
Authors@R: person("Wilmina", "Marget", email = "margetw@augsburg.edu", role = c("aut", "cre"))
Description: Construct multi-response experimental designs, such as a Unique Factor Central Composite Design (UF-CCD), given information (from screening or expert knowledge) about which factors are related to each response variable (Wilmina M. Marget & Max D. Morris, 2019 <doi:10.1080/00401706.2018.1549102>).
Depends: R (>= 3.6), DoE.wrapper (>= 0.10)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2019-08-21 15:01:29 UTC; margetw
Author: Wilmina Marget [aut, cre]
Maintainer: Wilmina Marget <margetw@augsburg.edu>
Repository: CRAN
Date/Publication: 2019-08-22 07:10:02 UTC

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New package bigutilsr with initial version 0.1.1
Package: bigutilsr
Title: Utility Functions for Large-scale Data
Version: 0.1.1
Date: 2019-08-20
Authors@R: person("Florian", "Privé", email = "florian.prive.21@gmail.com", role = c("aut", "cre"))
Description: Utility functions for large-scale data. For now, package 'bigutilsr' mainly includes functions for outlier detection.
License: GPL-3
Encoding: UTF-8
Language: en-US
LazyData: TRUE
ByteCompile: TRUE
RoxygenNote: 6.1.0
URL: https://github.com/privefl/bigutilsr
BugReports: https://github.com/privefl/bigutilsr/issues
LinkingTo: Rcpp
Imports: hdpca, nabor, Rcpp, robustbase, robust, stats
Suggests: covr, spelling, testthat
NeedsCompilation: yes
Packaged: 2019-08-20 20:32:14 UTC; privef
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Repository: CRAN
Date/Publication: 2019-08-22 07:50:02 UTC

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Package SECFISH (with last version 0.1.5) was removed from CRAN

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

2019-08-21 0.1.5

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Package units updated to version 0.6-4 with previous version 0.6-3 dated 2019-05-03

Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion. Documentation about 'units' is provided in the paper by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a vignette; see 'citation("units")' for details.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Thomas Mailund [aut], Tomasz Kalinowski [aut], James Hiebert [ctb], Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package radiant.data updated to version 1.0.6 with previous version 1.0.0 dated 2019-07-18

Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant.data versions 1.0.0 dated 2019-07-18 and 1.0.6 dated 2019-08-22

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Package geohashTools (with last version 0.2.2) was removed from CRAN

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

2019-08-21 0.2.2

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Package rpart.plot updated to version 3.0.8 with previous version 3.0.7 dated 2019-04-12

Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

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Package paws updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Software Development Kit
Description: Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

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Package enviGCMS updated to version 0.5.7 with previous version 0.5.5 dated 2019-05-14

Title: GC/LC-MS Data Analysis for Environmental Science
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>), Thanh Wang [ctb] (<https://orcid.org/0000-0002-5729-1908>)
Maintainer: Miao YU <yufreecas@gmail.com>

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Package Eagle updated to version 1.5.2 with previous version 1.5.1 dated 2019-05-24

Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre], Joshua Bowden [ctb], Ryan Stephenson [ctb], Hyun Kang [ctb], Noah Zaitlen [ctb], Claire Wade [ctb], Andrew Kirby [ctb], David Heckerman [ctb], Mark Daly [ctb], Eleazar Eskin [ctb]
Maintainer: Andrew George <andrew.george@csiro.au>

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Wed, 21 Aug 2019

Package rdlocrand updated to version 0.5 with previous version 0.4 dated 2019-03-13

Title: Local Randomization Methods for RD Designs
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. Under the local randomization approach, RD designs can be interpreted as randomized experiments inside a window around the cutoff. This package provides tools to perform randomization inference for RD designs under local randomization: rdrandinf() to perform hypothesis testing using randomization inference, rdwinselect() to select a window around the cutoff in which randomization is likely to hold, rdsensitivity() to assess the sensitivity of the results to different window lengths and null hypotheses and rdrbounds() to construct Rosenbaum bounds for sensitivity to unobserved confounders. See Cattaneo, Titiunik and Vazquez-Bare (2016) <https://sites.google.com/site/rdpackages/rdlocrand/Cattaneo-Titiunik-VazquezBare_2016_Stata.pdf> for further methodological details.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@econ.ucsb.edu>

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Package dtw updated to version 1.21-1 with previous version 1.20-1 dated 2018-05-18

Title: Dynamic Time Warping Algorithms
Description: A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on. Provides cumulative distances, alignments, specialized plot styles, etc.
Author: Toni Giorgino <toni.giorgino@gmail.com>,
Maintainer: Toni Giorgino <toni.giorgino@gmail.com>

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Package DataSpaceR updated to version 0.7.2 with previous version 0.6.3 dated 2019-04-05

Title: Interface to 'the CAVD DataSpace'
Description: Provides a convenient API interface to access immunological data within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing and discovery tool that facilitates exploration of HIV immunological data from pre-clinical and clinical HIV vaccine studies.
Author: Ju Yeong Kim [aut, cre, cph], Sean Hughes [rev] (Sean reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/261>), Jason Taylor [aut]
Maintainer: Ju Yeong Kim <jkim2345@fredhutch.org>

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Package burnr updated to version 0.5.0 with previous version 0.4.0 dated 2019-07-09

Title: Forest Fire History Analysis
Description: Tools to read, write, parse, and analyze forest fire history data (e.g. FHX). Described in Malevich et al. (2018) <doi:10.1016/j.dendro.2018.02.005>.
Author: Steven Malevich [aut, cre] (<https://orcid.org/0000-0002-4752-8190>), Christopher Guiterman [ctb] (<https://orcid.org/0000-0002-9706-9332>), Ellis Margolis [ctb] (<https://orcid.org/0000-0002-0595-9005>)
Maintainer: Steven Malevich <sbmalev@gmail.com>

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New package xgxr with initial version 1.0.2
Package: xgxr
Title: Exploratory Graphics for Pharmacometrics
Version: 1.0.2
Authors@R: c(person(given = "Andrew", family = "Stein", role = c("aut", "cre"), email = "andy.stein@gmail.com"), person(given = "Alison", family = "Margolskee", role = "aut", email = "alison.margolskee@gmail.com"), person(given = "Fariba", family = "Khanshan", role = "aut", email = "faribashan@gmail.com"), person(given = "Konstantin", family = "Krismer", role = "aut", email = "krismer@mit.edu", comment = c(ORCID = "0000-0001-8994-3416")), person(given = "Matthew", family = "Fidler", role = "ctb", email = "matthew.fidler@gmail.com", comment = c(ORCID = "0000-0001-8538-6691")), person("Novartis Pharma AG", role = c("cph","fnd")))
Description: Supports a structured approach for exploring PKPD data <https://opensource.nibr.com/xgx>. It also contains helper functions for enabling the modeler to follow best R practices (by appending the program name, figure name location, and draft status to each plot). In addition, it enables the modeler to follow best graphical practices (by providing a theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, it provides some data checking and summarizing functions for rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
License: MIT + file LICENSE
URL: https://opensource.nibr.com/xgx
Depends: R (>= 3.4.0)
Imports: assertthat, binom, dplyr, ggplot2, graphics, grDevices, labeling, magrittr, pander, png, scales, stats, tibble, utils
Suggests: caTools, gridExtra, knitr, rmarkdown, RxODE, stringr, testthat, tidyr
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-21 18:13:04 UTC; steinanf
Author: Andrew Stein [aut, cre], Alison Margolskee [aut], Fariba Khanshan [aut], Konstantin Krismer [aut] (<https://orcid.org/0000-0001-8994-3416>), Matthew Fidler [ctb] (<https://orcid.org/0000-0001-8538-6691>), Novartis Pharma AG [cph, fnd]
Maintainer: Andrew Stein <andy.stein@gmail.com>
Repository: CRAN
Date/Publication: 2019-08-21 21:50:02 UTC

More information about xgxr at CRAN
Permanent link

New package SWMPrExtension with initial version 1.1.1
Package: SWMPrExtension
Type: Package
Title: Functions for Analyzing and Plotting Estuary Monitoring Data
Version: 1.1.1
Maintainer: Dave Eslinger <dave.eslinger@noaa.gov>
Description: Tools for performing routine analysis and plotting tasks with environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System <http://cdmo.baruch.sc.edu/>. This package builds on the functionality of the SWMPr package <https://cran.r-project.org/web/packages/SWMPr/index.html>, which is used to retrieve and organize the data. The combined set of tools address common challenges associated with continuous time series data for environmental decision making, and are intended for use in annual reporting activities. References: Beck, Marcus W. (2016) <ISSN 2073-4859><https://journal.r-project.org/archive/2016-1/beck.pdf> Rudis, Bob (2014) <https://rud.is/b/2014/11/16/moving-the-earth-well-alaska-hawaii-with-r/>. United States Environmental Protection Agency (2015) <https://cfpub.epa.gov/si/si_public_record_Report.cfm?dirEntryId=327030>. United States Environmental Protection Agency (2012) <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.646.1973&rep=rep1&type=pdf>.
BugReports: https://github.com/NOAA-OCM/SWMPrExtension/issues
License: CC0
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.2.0), SWMPr
Imports: broom, dplyr, EnvStats, flextable, ggplot2, ggthemes, grDevices, leaflet, lubridate, magrittr, maptools, methods, officer, tidyr, scales, RColorBrewer, rgdal, rgeos, rlang, sp
Authors@R: c( person(given = "Julie", family = "Padilla", role = c("aut", "ctb"), email = "jpadilla@limno.com"), person(given = "Marcus", family = "Beck", role = c("ctb"), email = "marcus@sccwrp.org"), person(given = "Kimberly", family = "Cressman", role = c("ctb"), email = "kimberly.cressman@dmr.ms.gov"), person(given = "Dave", family = "Eslinger", role = c("cre", "ctb"), email = "dave.eslinger@noaa.gov"), person(given = "Bob", family = "Rudis", role = c("ctb"), email = "bob@rud.is") )
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-19 15:37:44 UTC; Dave.Eslinger
Author: Julie Padilla [aut, ctb], Marcus Beck [ctb], Kimberly Cressman [ctb], Dave Eslinger [cre, ctb], Bob Rudis [ctb]
Repository: CRAN
Date/Publication: 2019-08-21 21:50:09 UTC

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Permanent link

Package pccc updated to version 1.0.3 with previous version 1.0.2 dated 2018-07-02

Title: Pediatric Complex Chronic Conditions
Description: An implementation of the pediatric complex chronic conditions (CCC) classification system using R and C++.
Author: Peter DeWitt [aut], Tell Bennett [aut], James Feinstein [aut], Seth Russell [aut, cre]
Maintainer: Seth Russell <seth.russell@ucdenver.edu>

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New package KernSmoothIRT with initial version 6.2
Package: KernSmoothIRT
Type: Package
Title: Nonparametric Item Response Theory
Version: 6.2
Date: 2019-08-08
Author: Angelo Mazza, Antonio Punzo, Brian McGuire
Maintainer: Brian McGuire <mcguirebc@gmail.com>
Description: Fits nonparametric item and option characteristic curves using kernel smoothing. It allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools. The kernel smoothing is based on methods described in Silverman, B.W. (1986). Density Estimation for Statistics and Data Analysis. Chapman & Hall, London.
License: GPL-2
LazyLoad: yes
Imports: Rcpp, plotrix, rgl
LinkingTo: Rcpp
Packaged: 2019-08-21 17:18:47 UTC; BrianMcGuire
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2019-08-21 21:50:13 UTC

More information about KernSmoothIRT at CRAN
Permanent link

Package ICD10gm updated to version 1.0.4 with previous version 1.0.3 dated 2019-02-12

Title: Metadata Processing for the German Modification of the ICD-10 Coding System
Description: Provides convenient access to the German modification of the International Classification of Diagnoses, 10th revision (ICD-10-GM). It provides functionality to aid in the identification, specification and historisation of ICD-10 codes. Its intended use is the analysis of routinely collected data in the context of epidemiology, medical research and health services research. The underlying metadata are released by the German Institute for Medical Documentation and Information <https://www.dimdi.de>, and are redistributed in accordance with their license.
Author: Ewan Donnachie [aut, cre] (<https://orcid.org/0000-0002-0668-0049>)
Maintainer: Ewan Donnachie <ewan@donnachie.net>

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Package DTRreg updated to version 1.4 with previous version 1.3 dated 2017-08-30

Title: DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
Description: Dynamic treatment regime estimation and inference via G-estimation, dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via bootstrap and (for G-estimation) recursive sandwich estimation. Estimation and inference for survival outcomes via Dynamic Weighted Survival Modeling (DWSurv).
Author: Michael Wallace, Erica E M Moodie, David A Stephens and Gabrielle Simoneau
Maintainer: Michael Wallace <michael.wallace@uwaterloo.ca>

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Package DClusterm updated to version 1.0-0 with previous version 0.2-1 dated 2018-05-28

Title: Model-Based Detection of Disease Clusters
Description: Model-based methods for the detection of disease clusters using GLMs, GLMMs and zero-inflated models. These methods are described in 'V. Gómez-Rubio et al.' (2019) <doi:10.18637/jss.v090.i14> and 'V. Gómez-Rubio et al.' (2018) <doi:10.1007/978-3-030-01584-8_1>.
Author: Virgilio Gomez-Rubio, Paula Esther Moraga Serrano, Barry Rowlingson
Maintainer: Virgilio Gomez-Rubio <virgilio.gomez@uclm.es>

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Package NetworkToolbox updated to version 1.3.0 with previous version 1.2.3 dated 2019-01-31

Title: Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis
Description: Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershogoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Author: Alexander Christensen [aut, cre], Guido Previde Massara [ctb]
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>

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Package pagedown updated to version 0.4 with previous version 0.3 dated 2019-07-15

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>

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Package circlize updated to version 0.4.7 with previous version 0.4.6 dated 2019-04-03

Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>

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Package shinylogs updated to version 0.1.7 with previous version 0.1.6 dated 2019-07-18

Title: Record Everything that Happens in a 'Shiny' Application
Description: Track and record the use of applications and the user's interactions with 'Shiny' inputs. Allow to save inputs clicked, output generated and eventually errors.
Author: Fanny Meyer [aut], Victor Perrier [aut, cre], Silex Technologies [fnd] (https://www.silex-ip.com), iamkun [cph] (dayjs library), Mozilla [cph] (localForage library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package ggimage updated to version 0.2.2 with previous version 0.2.1 dated 2019-01-16

Title: Use Image in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package GENEAclassify updated to version 1.4.18 with previous version 1.4.17 dated 2019-05-14

Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://www.activinsights.com/products/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing. Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut], Aimee Gott [aut], Joss Langford [aut], Charles Sweetland [aut, cre], Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>

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Package circumplex updated to version 0.3.2 with previous version 0.3.1 dated 2019-05-15

Title: Analysis and Visualization of Circular Data
Description: Tools for analyzing and visualizing circular data, including scoring functions for relevant instruments and a generalization of the bootstrapped structural summary method from Zimmermann & Wright (2017) <doi:10.1177/1073191115621795> and functions for creating publication-ready tables and figures from the results. Future versions will include tools for circular fit and reliability analyses, as well as visualization enhancements.
Author: Jeffrey Girard [aut, cre] (<https://orcid.org/0000-0002-7359-3746>), Johannes Zimmermann [aut] (<https://orcid.org/0000-0001-6975-2356>), Aidan Wright [aut] (<https://orcid.org/0000-0002-2369-0601>)
Maintainer: Jeffrey Girard <me@jmgirard.com>

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Package lumberjack updated to version 1.0.2 with previous version 0.3.0 dated 2018-07-20

Title: Track Changes in Data
Description: A framework that allows for easy logging of changes in data. Main features: start tracking changes by adding a single line of code to an existing script. Track changes in multiple datasets, using multiple loggers. Add custom-built loggers or use loggers offered by other packages.
Author: Mark van der Loo [aut, cre] (<https://orcid.org/0000-0002-9807-4686>)
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

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Package av updated to version 0.3 with previous version 0.2 dated 2018-09-30

Title: Working with Audio and Video
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with audio and video in R. Generate high quality videos files by capturing images from the R graphics device combined with custom audio stream. Also offers tools to convert between countless audio / video formats, or convert images to video and vice versa. This package interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package ludic updated to version 0.1.7 with previous version 0.1.6 dated 2018-01-28

Title: Linkage Using Diagnosis Codes
Description: Probabilistic record linkage without direct identifiers using only diagnosis codes. Method is detailed in: Hejblum, Weber, Liao, Palmer, Churchill, Szolovits, Murphy, Kohane & Cai (2019) <doi: 10.1038/sdata.2018.298>.
Author: Boris P Hejblum [aut, cre], Tianxi Cai [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>

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Package bookdown updated to version 0.13 with previous version 0.12 dated 2019-07-11

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], 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], 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), 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>

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Package sys updated to version 3.3 with previous version 3.2 dated 2019-04-23

Title: Powerful and Reliable Tools for Running System Commands in R
Description: Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between sys versions 3.2 dated 2019-04-23 and 3.3 dated 2019-08-21

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Package geometry updated to version 0.4.3 with previous version 0.4.2 dated 2019-07-12

Title: Mesh Generation and Surface Tessellation
Description: Makes the 'Qhull' library <http://www.qhull.org> available in R, in a similar manner as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2D, 3D, 4D, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this.
Author: Jean-Romain Roussel [cph, ctb] (wrote tsearch function with QuadTrees), C. B. Barber [cph], Kai Habel [cph, aut], Raoul Grasman [cph, aut], Robert B. Gramacy [cph, aut], Pavlo Mozharovskyi [cph, aut], David C. Sterratt [cph, aut, cre] (<https://orcid.org/0000-0001-9092-9099>)
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>

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New package geohashTools with initial version 0.2.2
Package: geohashTools
Version: 0.2.2
Title: Tools for Working with Geohashes
Author: Michael Chirico, Hiroaki Kawai
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Depends: R (>= 3.0.0)
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, ported to R from Hiroaki Kawai's 'Python' implementation and embellished to sit naturally in the R ecosystem.
URL: https://github.com/MichaelChirico/geohashTools
License: MIT + file LICENSE
Imports: Rcpp (>= 1.0.0)
Suggests: rgdal, sf, sp, testthat, mockery
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2019-08-21 12:18:15 UTC; michael.chirico
Repository: CRAN
Date/Publication: 2019-08-21 14:20:04 UTC

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Package GD updated to version 1.7 with previous version 1.6 dated 2018-07-02

Title: Geographical Detectors
Description: Geographical detectors for measuring spatial stratified heterogeneity, as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the optimal discretization of continuous data, four primary functions of geographical detectors, comparison of size effects of spatial unit and the visualizations of results. The descriptions of the package, methods and case datasets refer to the citation information below.
Author: Yongze Song [aut, cre] (<https://orcid.org/0000-0003-3420-9622>)
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>

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Package AzureAuth updated to version 1.2.0 with previous version 1.1.1 dated 2019-06-07

Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], httr development team [ctb] (Original OAuth listener code), Scott Holden [ctb] (Advice on AAD authentication), Chris Stone [ctb] (Advice on AAD authentication), Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

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Package denvax updated to version 0.1.1 with previous version 0.1.0 dated 2019-07-19

Title: Simple Dengue Test and Vaccinate Cost Thresholds
Description: Provides the mathematical model described by "Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds" in <doi:10.1098/rsif.2019.0234>. Using the functions in the package, that analysis can be repeated using sample life histories, either synthesized from local seroprevalence data using other functions in this package (as in the manuscript) or from some other source. The package provides a vignette which walks through the analysis in the publication, as well as a function to generate a project skeleton for such an analysis.
Author: Carl A. B. Pearson [aut, cre] (<https://orcid.org/0000-0003-0701-7860>), Kaja M. Abbas [aut] (<https://orcid.org/0000-0003-0563-1576>), Samuel Clifford [aut] (<https://orcid.org/0000-0002-3774-3882>), Stefan Flasche [aut] (<https://orcid.org/0000-0002-5808-2606>), Thomas J. Hladish [aut] (<https://orcid.org/0000-0003-1819-6235>)
Maintainer: Carl A. B. Pearson <carl.pearson@lshtm.ac.uk>

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Package billboarder updated to version 0.2.7 with previous version 0.2.6 dated 2019-05-07

Title: Create Interactive Chart with the JavaScript 'Billboard' Library
Description: Provides an 'htmlwidgets' interface to 'billboard.js', a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], NAVER Corp [cph] (billboard library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package xfun updated to version 0.9 with previous version 0.8 dated 2019-06-25

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]
Maintainer: Yihui Xie <xie@yihui.name>

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Package webutils updated to version 1.0 with previous version 0.6 dated 2017-06-23

Title: Utility Functions for Developing Web Applications
Description: Parses http request data in application/json, multipart/form-data, or application/x-www-form-urlencoded format. Includes example of hosting and parsing html form data in R using either 'httpuv' or 'Rhttpd'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package umap updated to version 0.2.3.1 with previous version 0.2.3 dated 2019-08-19

Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique for dimension reduction. The algorithm was described by McInnes and Healy (2018) in <arXiv:1802.03426>. This package provides an interface for two implementations. One is written from scratch, including components for nearest-neighbor search and for embedding. The second implementation is a wrapper for 'python' package 'umap-learn' (requires separate installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>

Diff between umap versions 0.2.3 dated 2019-08-19 and 0.2.3.1 dated 2019-08-21

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

Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, and plotting. The package implements lazy evaluation and multithreading. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] (<https://orcid.org/0000-0001-5281-3896>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb], Lewis Van Winkle [cph], Ole Christian Eidheim [cph], Niels Lohmann [cph], Howard Hinnant [cph], Adrian Colomitchi [cph], Florian Dang [cph], Paul Thompson [cph], Tomasz Kamiński [cph]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>

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Package spANOVA updated to version 0.99.1 with previous version 0.99.0 dated 2019-07-02

Title: Spatial Analysis of Field Trials Experiments using Geostatistics and Spatial Autoregressive Model
Description: Perform analysis of variance when the experimental units are spatially correlated. There are two methods to deal with spatial dependence: Spatial autoregressive models (see Rossoni, D. F., & Lima, R. R. (2019) <doi:10.28951/rbb.v37i2.388>) and geostatistics (see Pontes, J. M., & Oliveira, M. S. D. (2004) <doi:10.1590/S1413-70542004000100018>). For both methods, there are three multicomparison procedure available: Tukey, multivariate T, and Scott-Knott.
Author: Lucas Roberto de Castro, Renato Ribeiro de Lima, Diogo Francisco Rossoni, Cristina Henriques Nogueira
Maintainer: Lucas Roberto de Castro <lrcastro@estudante.ufla.br>

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New package SECFISH with initial version 0.1.5
Package: SECFISH
Type: Package
Title: Disaggregate Variable Costs
Version: 0.1.5
Author: Isabella Bitetto (COISPA), Loretta Malvarosa (NISEA), Maria Teresa Spedicato (COISPA), Ralf Doering (THUENEN), Joerg Berkenhagen (THUENEN)
Maintainer: Isabella Bitetto <bitetto@coispa.it>
Description: These functions were developed within SECFISH project (Strengthening regional cooperation in the area of fisheries data collection-Socio-economic data collection for fisheries, aquaculture and the processing industry at EU level). They are aimed at identifying correlations between costs and transversal variables by metier using individual vessel data and for disaggregating variable costs from fleet segment to metier level.
License: GPL-2
Depends: R (>= 3.5)
Imports: ggplot2, Hmisc, optimization
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2019-08-21 08:42:10 UTC; Bitetto Isabella
Repository: CRAN
Date/Publication: 2019-08-21 11:20:09 UTC

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Package qs updated to version 0.18.3 with previous version 0.17.3 dated 2019-07-08

Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd and lz4 code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Romain Francois [ctb, cph] (Derived example/tutorials for Alt-Rep structures), Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc library)
Maintainer: Travers Ching <traversc@gmail.com>

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Package durmod updated to version 1.1-2 with previous version 1.1-1 dated 2019-07-25

Title: Mixed Proportional Hazard Competing Risk Model
Description: Estimation of piecewise constant mixed proportional hazard competing risk model with NPMLE. The model is described in S. Gaure et al. (2007) <doi:10.1016/j.jeconom.2007.01.015>, J. Heckman and B. Singer (1984) <doi:10.2307/1911491>, and B.G. Lindsay (1983) <doi:10.1214/aos/1176346059>.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>)
Maintainer: Simen Gaure <simen@gaure.no>

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Package Countr updated to version 3.5.4 with previous version 3.5.2 dated 2018-10-04

Title: Flexible Univariate Count Models Based on Renewal Processes
Description: Flexible univariate count models based on renewal processes. The models may include covariates and can be specified with familiar formula syntax as in glm() and package 'flexsurv'. The methodology is described in a forthcoming paper in the Journal of Statistical Software <10.18637/jss.v090.i13> (included as vignette 'Countr_guide' in the package).
Author: Tarak Kharrat [aut, cre], Georgi N. Boshnakov [aut]
Maintainer: Tarak Kharrat <Tarak.Kharrat@liverpool.ac.uk>

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Package clustree updated to version 0.4.1 with previous version 0.4.0 dated 2019-04-18

Title: Visualise Clusterings at Different Resolutions
Description: Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
Author: Luke Zappia [aut, cre] (<https://orcid.org/0000-0001-7744-8565>), Alicia Oshlack [aut] (<https://orcid.org/0000-0001-9788-5690>), Andrea Rau [ctb], Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>)
Maintainer: Luke Zappia <luke@lazappi.id.au>

Diff between clustree versions 0.4.0 dated 2019-04-18 and 0.4.1 dated 2019-08-21

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Package splot updated to version 0.5.0 with previous version 0.4.2 dated 2019-04-28

Title: Split Plot
Description: Automates common plotting tasks to ease data exploration. Makes density plots (potentially overlaid on histograms), scatter plots with prediction lines, or bar or line plots with error bars. For each type, y, or x and y variables can be plotted at levels of other variables, all with minimal specification.
Author: Micah Iserman
Maintainer: Micah Iserman <micah.iserman@ttu.edu>

Diff between splot versions 0.4.2 dated 2019-04-28 and 0.5.0 dated 2019-08-21

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Package rmarkdown updated to version 1.15 with previous version 1.14 dated 2019-07-12

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)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between rmarkdown versions 1.14 dated 2019-07-12 and 1.15 dated 2019-08-21

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Package paws.storage updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Storage APIs
Description: Interface to Amazon Web Services storage APIs, including 'Simple Storage Service' ('S3') and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.storage versions 0.1.3 dated 2019-07-28 and 0.1.4 dated 2019-08-21

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Package paws.security.identity updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Security, Identity, & Compliance APIs
Description: Interface to Amazon Web Services security, identity, and compliance APIs, including the 'Identity & Access Management' ('IAM') service for managing access to services and resources, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

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Package paws.networking updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Networking & Content Delivery APIs
Description: Interface to Amazon Web Services networking and content delivery APIs, including 'Route 53' Domain Name System service, 'CloudFront' content delivery, load balancing, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

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Package paws.management updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Management & Governance APIs
Description: Interface to Amazon Web Services management and governance APIs, including 'CloudWatch' application and infrastructure monitoring, 'Auto Scaling' for automatically scaling resources, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

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Package paws.machine.learning updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Machine Learning APIs
Description: Interface to Amazon Web Services machine learning APIs, including 'SageMaker' managed machine learning service, natural language processing, speech recognition, translation, and more <https://aws.amazon.com/machine-learning/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.machine.learning versions 0.1.3 dated 2019-07-28 and 0.1.4 dated 2019-08-21

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Package paws.database updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Database APIs
Description: Interface to Amazon Web Services database APIs, including 'Relational Database Service' ('RDS'), 'DynamoDB' 'NoSQL' database, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.database versions 0.1.3 dated 2019-07-27 and 0.1.4 dated 2019-08-21

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Package paws.customer.engagement updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Customer Engagement APIs
Description: Interface to Amazon Web Services customer engagement APIs, including 'Simple Email Service', 'Connect' contact center service, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

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Package paws.cost.management updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Cost Management APIs
Description: Interface to Amazon Web Services cost management APIs, including cost and usage reports, budgets, pricing, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.cost.management versions 0.1.3 dated 2019-07-27 and 0.1.4 dated 2019-08-21

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Package paws.compute updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Compute APIs
Description: Interface to Amazon Web Services compute APIs, including 'Elastic Compute Cloud' ('EC2'), 'Lambda' functions-as-a-service, containers, batch processing, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.compute versions 0.1.3 dated 2019-07-27 and 0.1.4 dated 2019-08-21

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 R/elasticbeanstalk_service.R                |    2 +-
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Package paws.application.integration updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Application Integration APIs
Description: Interface to Amazon Web Services application integration APIs, including 'Simple Queue Service' ('SQS') message queue, 'Simple Notification Service' ('SNS') publish/subscribe messaging, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.application.integration versions 0.1.3 dated 2019-07-27 and 0.1.4 dated 2019-08-21

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Package paws.analytics updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Analytics APIs
Description: Interface to Amazon Web Services analytics APIs, including 'Elastic MapReduce' 'Hadoop' and 'Spark' big data service, 'Elasticsearch' search engine, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

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Package optionstrat updated to version 1.4.0 with previous version 1.3.0 dated 2019-06-20

Title: Utilizes the Black-Scholes Option Pricing Model to Perform Strategic Option Analysis and Plot Option Strategies
Description: Utilizes the Black-Scholes-Merton option pricing model to calculate key option analytics and perform graphical analysis of various option strategies. Provides functions to calculate the option premium and option greeks of European-style options.
Author: John T. Buynak [aut, cre]
Maintainer: John T. Buynak <jbuynak94@gmail.com>

Diff between optionstrat versions 1.3.0 dated 2019-06-20 and 1.4.0 dated 2019-08-21

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Package deTestSet updated to version 1.1.6 with previous version 1.1.5 dated 2017-01-19

Title: Test Set for Differential Equations
Description: Solvers and test set for stiff and non-stiff differential equations, and differential algebraic equations. 'Mazzia, F., Cash, J.R. and K. Soetaert, 2012. DOI: 10.1016/j.cam.2012.03.014'.
Author: Karline Soetaert [aut, cre], Jeff Cash [aut], Francesca Mazzia [aut], LAPACK authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>

Diff between deTestSet versions 1.1.5 dated 2017-01-19 and 1.1.6 dated 2019-08-21

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Package d3r updated to version 0.8.7 with previous version 0.8.6 dated 2019-07-23

Title: 'd3.js' Utilities for R
Description: Provides a suite of functions to help ease the use of 'd3.js' in R. These helpers include 'htmltools::htmlDependency' functions, hierarchy builders, and conversion tools for 'partykit', 'igraph,' 'table', and 'data.frame' R objects into the 'JSON' that 'd3.js' expects.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Kent Russell [aut, cre] (R interface), Gregor Aisch [aut, cph] (d3-jetpack creator, https://github.com/gka/d3-jetpack), Adam Pearce [aut] (core contributor to d3-jetpack), Ben Ortiz [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between d3r versions 0.8.6 dated 2019-07-23 and 0.8.7 dated 2019-08-21

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Package Chaos01 updated to version 1.2.1 with previous version 1.2.0 dated 2019-08-02

Title: 0-1 Test for Chaos
Description: Computes and visualize the results of the 0-1 test for chaos proposed by Gottwald and Melbourne (2004) <DOI:10.1137/080718851>. The algorithm is available in parallel for the independent values of parameter c. Additionally, fast RQA is added to distinguish chaos from noise.
Author: Tomas Martinovic [aut, cre]
Maintainer: Tomas Martinovic <tomas.martinovic@vsb.cz>

Diff between Chaos01 versions 1.2.0 dated 2019-08-02 and 1.2.1 dated 2019-08-21

 DESCRIPTION  |    6 +++---
 MD5          |    6 +++---
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 4 files changed, 14 insertions(+), 7 deletions(-)

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New package vici with initial version 0.5.2
Package: vici
Title: Vaccine Induced Cellular Immunogenicity with Bivariate Modeling
Version: 0.5.2
Date: 2019-08-20
Authors@R: person('Boris', 'Hejblum', email = 'boris.hejblum@u-bordeaux.fr', role = c('cre', 'aut'))
Description: A shiny app for accurate estimation of vaccine induced immunogenicity with bivariate linear modeling. Method is detailed in: Lhomme E, Hejblum BP, Lacabaratz C, Wiedemann A, Lelièvre J-D, Levy Y, Thiebaut R & Richert L (2019). Submitted.
BugReports: https://github.com/borishejblum/vici/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: cowplot, DT, ggplot2, grDevices, ggpubr, nlme, shiny, stats, tidyr, utils
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-20 14:04:39 UTC; borishejblum
Author: Boris Hejblum [cre, aut]
Maintainer: Boris Hejblum <boris.hejblum@u-bordeaux.fr>
Repository: CRAN
Date/Publication: 2019-08-21 09:20:02 UTC

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New package samc with initial version 1.0.3
Package: samc
Type: Package
Title: Spatial Absorbing Markov Chains
Version: 1.0.3
Date: 2019-08-20
Authors@R: c( person("Andrew", "Marx", , "andrewjmarx@ufl.edu", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-7456-1631") ), person("Robert", "Fletcher", , , role = c("ctb"), comment = c(ORCID = "0000-0003-1717-5707") ), person("Miguel", "Acevedo", , , role = c("ctb"), comment = c(ORCID = "0000-0002-8289-1497") ), person("Jorge", "Sefair", , , role = c("ctb"), comment = c() ), person("Chao", "Wang", , , role = c("ctb"), comment = c() ) )
Description: An implementation of the framework described in "Toward a unified framework for connectivity that disentangles movement and mortality in space and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>. Incorporates both resistance and absorption with spatial absorbing Markov chains (SAMC) to provide several short-term and long-term predictions for metrics related to connectivity in landscapes.
License: GPL (>= 3)
URL: https://andrewmarx.github.io/samc
BugReports: https://github.com/andrewmarx/samc/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Imports: methods, gdistance, Matrix, raster
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, testthat, ggplot2, png, viridis, gifski, gganimate
VignetteBuilder: knitr
Collate: 'RcppExports.R' 'samc-class.R' 'check.R' 'data.R' 'visitation.R' 'dispersal.R' 'distribution.R' 'map.R' 'mortality.R' 'samc.R' 'survival.R'
LinkingTo: Rcpp (>= 1.0.1), RcppEigen (>= 0.3.3.5.0)
NeedsCompilation: yes
Packaged: 2019-08-20 14:42:48 UTC; andrewjmarx
Author: Andrew Marx [aut, cre, cph] (<https://orcid.org/0000-0002-7456-1631>), Robert Fletcher [ctb] (<https://orcid.org/0000-0003-1717-5707>), Miguel Acevedo [ctb] (<https://orcid.org/0000-0002-8289-1497>), Jorge Sefair [ctb], Chao Wang [ctb]
Maintainer: Andrew Marx <andrewjmarx@ufl.edu>
Repository: CRAN
Date/Publication: 2019-08-21 09:40:02 UTC

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Package longitudinalcascade updated to version 0.3.2.1 with previous version 0.3.1.1 dated 2019-06-13

Title: Longitudinal Cascade
Description: Creates a series of set of graphics and statistics related to the longitudinal cascade, all included in a single object. The longitudinal cascade inputs longitudinal data to identify gaps in the HIV and related cascades by observing differences using time to event and survival methods. The stage definitions are set by the user, with default standard options. Outputs include graphics, datasets, and formal statistical tests.
Author: Noah Haber [aut, cre]
Maintainer: Noah Haber <noahhaber@gmail.com>

Diff between longitudinalcascade versions 0.3.1.1 dated 2019-06-13 and 0.3.2.1 dated 2019-08-21

 DESCRIPTION             |    6 +++---
 MD5                     |    4 ++--
 R/longitudinalcascade.R |   15 +++++++--------
 3 files changed, 12 insertions(+), 13 deletions(-)

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New package ipfr with initial version 1.0.0
Package: ipfr
Title: List Balancing for Reweighting and Population Synthesis
Version: 1.0.0
Authors@R: c( person( "Kyle", "Ward", email = "kyleward084@gmail.com", role = c("aut", "cre", "cph") ), person("Greg", "Macfarlane", email = "gregmacfarlane@byu.edu", role = c("ctb")))
Description: Performs iterative proportional updating given a seed table and an arbitrary number of marginal distributions. This is commonly used in population synthesis, survey raking, matrix rebalancing, and other applications. For example, a household survey may be weighted to match the known distribution of households by size from the census. An origin/ destination trip matrix might be balanced to match traffic counts. The approach used by this package is based on a paper from Arizona State University (Ye, Xin, et. al. (2009) <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.537.723&rep=rep1&type=pdf>). Some enhancements have been made to their work including primary and secondary target balance/importance, general marginal agreement, and weight restriction.
License: Apache License (== 2.0)
URL: https://github.com/dkyleward/ipfr
BugReports: https://github.com/dkyleward/ipfr/issues
Depends: R (>= 3.2.0)
Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.2.1), magrittr (>= 1.5), tidyr (>= 0.5.1), mlr (>= 2.11)
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 2.1.0), covr
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-20 14:15:20 UTC; kyle
Author: Kyle Ward [aut, cre, cph], Greg Macfarlane [ctb]
Maintainer: Kyle Ward <kyleward084@gmail.com>
Repository: CRAN
Date/Publication: 2019-08-21 09:30:03 UTC

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New package genodds with initial version 1.0.0
Package: genodds
Type: Package
Title: Generalized Odds Ratios
Version: 1.0.0
Date: 2019-08-14
Encoding: UTF-8
Authors@R: person("Hannah","Johns", role=c("aut","cre"),email="htjohns@gmail.com",comment=c(ORCID="0000-0003-2135-0504"))
Maintainer: Hannah Johns <htjohns@gmail.com>
Description: Calculates Agresti's (1980) <https://www.jstor.org/stable/2530495> generalized odds ratios. For a randomly selected pair of observations from two groups, calculates the odds that the second group will have a higher scoring outcome than that of the first group. Package provides hypothesis testing for if this odds ratio is significantly different to 1 (equal chance).
License: GPL (>= 2)
LazyData: TRUE
Depends: R (>= 2.10)
Imports: Rcpp (>= 0.12.3)
LinkingTo: Rcpp
RoxygenNote: 6.1.1
Suggests: testthat (>= 2.1.0)
NeedsCompilation: yes
Packaged: 2019-08-20 14:30:17 UTC; hannah
Author: Hannah Johns [aut, cre] (<https://orcid.org/0000-0003-2135-0504>)
Repository: CRAN
Date/Publication: 2019-08-21 09:30:06 UTC

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New package Biopeak with initial version 1.0
Package: Biopeak
Type: Package
Title: Identification of Impulse-Like Gene Expression Changes in Short Genomic Series Data
Version: 1.0
Author: David Lauenstein
Maintainer: David Lauenstein <david.lauenstein@gmail.com>
Description: Enables the user to systematically identify and visualize impulse-like gene expression changes within short genomic series experiments. In order to detect such activation peaks, the gene expression is treated as a signal that propagates along an experimental axis (time, temperature or other series conditions). Peaks are selected by exhaustive identification of local maximums and subsequent filtering based on a range of controllable parameters. Moreover, the 'Biopeak' package provides a series of data exploration tools including: expression profile plots, correlation heat maps and clustering functionalities.
License: GPL (>= 2)
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: cluster, dbscan, factoextra, gplots, RColorBrewer, stats, graphics
LazyData: True
RoxygenNote: 6.1.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2019-08-09 09:40:11 UTC; David
Repository: CRAN
Date/Publication: 2019-08-21 09:40:06 UTC

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Package bfa (with last version 0.4) was removed from CRAN

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

2016-09-29 0.4
2014-02-11 0.3.1
2013-05-11 0.3
2012-03-15 0.2.3
2011-11-02 0.2.2

Permanent link
New package viromeBrowser with initial version 1.0.0
Package: viromeBrowser
Type: Package
Title: Virome Sequencing Analysis Result Browser
Version: 1.0.0
Authors@R: person("David", "Nieuwenhuijse", email = "d.nieuwenhuijse@erasmusmc.nl", role = c("aut", "cre"))
Description: Experiments in which highly complex virome sequencing data is generated are difficult to visualize and unpack for a person without programming experience. After processing of the raw sequencing data by a next generation sequencing (NGS) processing pipeline the usual output consists of contiguous sequences (contigs) in fasta format and an annotation file linking the contigs to a reference sequence. The virome analysis browser app imports an annotation file and a corresponding fasta file containing the annotated contigs. It facilitates browsing of annotations in multiple files and allows users to select and export specific annotated sequences from the associated fasta files. Various annotation quality thresholds can be set to filter contigs from the annotation files. Further inspection of selected contigs can be done in the form of automatic open reading frame (ORF) detection. Separate contigs and/or separate ORFs can be downloaded in nucleotide or amino acid format for further analysis.
Depends: R (>= 3.4)
Imports: shiny (>= 1.3.2), shinyWidgets, plyr, ggplot2, shinydashboard, DT, reshape, rbokeh, Biostrings, Rsamtools, data.table, markdown, stringr, shinycssloaders
License: AGPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-20 12:02:54 UTC; david
Author: David Nieuwenhuijse [aut, cre]
Maintainer: David Nieuwenhuijse <d.nieuwenhuijse@erasmusmc.nl>
Repository: CRAN
Date/Publication: 2019-08-21 08:10:02 UTC

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New package scorepeak with initial version 0.1.2
Package: scorepeak
Type: Package
Title: Peak Functions for Peak Detection in Univariate Time Series
Version: 0.1.2
Authors@R: c( person("Shota", "Ochi", email = "shotaochi1990@gmail.com", role = c("aut", "cre", "cph")))
Maintainer: Shota Ochi <shotaochi1990@gmail.com>
Description: Provides peak functions, which enable us to detect peaks in time series. The methods implemented in this package are based on Girish Keshav Palshikar (2009) <https://www.researchgate.net/publication/228853276_Simple_Algorithms_for_Peak_Detection_in_Time-Series>.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: checkmate (>= 1.9.1), Rcpp (>= 1.0.0)
Suggests: knitr, rmarkdown, testthat (>= 2.0.0), cluster
URL: https://github.com/ShotaOchi/scorepeak
BugReports: https://github.com/ShotaOchi/scorepeak/issues
NeedsCompilation: yes
LinkingTo: Rcpp
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Encoding: UTF-8
Packaged: 2019-08-20 12:16:24 UTC; shota
Author: Shota Ochi [aut, cre, cph]
Repository: CRAN
Date/Publication: 2019-08-21 08:20:02 UTC

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New package partitionBEFsp with initial version 1.0
Package: partitionBEFsp
Title: Methods for Calculating the Loreau & Hector 2001 BEF Partition
Version: 1.0
Author: Adam Clark
Maintainer: Adam Clark <adam.tclark@gmail.com>
Description: A collection of functions that can be used to estimate selection and complementarity effects, sensu Loreau & Hector (2001) <doi:10.1038/35083573>, even in cases where data are only available for a random subset of species (i.e. incomplete sample-level data). A full derivation and explanation of the statistical corrections used here is available in Clark et al. (2019) <doi:10.1111/2041-210X.13285>.
Depends: R (>= 3.4)
Imports: graphics, stats
License: GPL-3
LazyData: true
NeedsCompilation: no
Packaged: 2019-08-20 12:36:15 UTC; atclark
Repository: CRAN
Date/Publication: 2019-08-21 08:20:05 UTC

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Package heuristica updated to version 1.0.2 with previous version 1.0.1 dated 2016-07-17

Title: Heuristics Including Take the Best and Unit-Weight Linear
Description: Implements various heuristics like Take The Best and unit-weight linear, which do two-alternative choice: which of two objects will have a higher criterion? Also offers functions to assess performance, e.g. percent correct across all row pairs in a data set and finding row pairs where models disagree. New models can be added by implementing a fit and predict function-- see vignette.
Author: Jean Whitmore [aut, cre], Daniel Barkoczi [aut]
Maintainer: Jean Whitmore <jeanimal@gmail.com>

Diff between heuristica versions 1.0.1 dated 2016-07-17 and 1.0.2 dated 2019-08-21

 DESCRIPTION                                  |   12 
 LICENSE                                      |    2 
 MD5                                          |  146 ++++----
 NEWS.md                                      |    5 
 R/heuristics.R                               |   36 ++
 README.md                                    |    2 
 build/vignette.rds                           |binary
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 inst/doc/confusion-matrix.Rmd                |    2 
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 inst/doc/cross-validation.R                  |   15 
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 inst/doc/how-to-make-heuristic.html          |  479 ++++++++++++++++++++-------
 inst/doc/reproducing-results.R               |   61 +++
 inst/doc/reproducing-results.Rmd             |   80 ++++
 inst/doc/reproducing-results.html            |  417 ++++++++++++++++++++---
 man/accuracyFromConfusionMatrix3x3.Rd        |    1 
 man/city_population.Rd                       |    1 
 man/city_population_original.Rd              |    1 
 man/collapseConfusionMatrix3x3To2x2.Rd       |    1 
 man/conditionalCueValidityComplete.Rd        |    1 
 man/confusionMatrixFor_Neg1_0_1.Rd           |    1 
 man/correctGreater.Rd                        |    1 
 man/createFunction.Rd                        |    1 
 man/createFunction.heuristics.Rd             |    1 
 man/cueAccuracy.Rd                           |    1 
 man/cueValidity.Rd                           |    1 
 man/cueValidityAppliedToColumns.Rd           |    1 
 man/cueValidityComplete.Rd                   |    5 
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 man/heuristics.Rd                            |    1 
 man/heuristicsList.Rd                        |    1 
 man/heuristicsProb.Rd                        |    1 
 man/highschool_dropout.Rd                    |    1 
 man/lmWrapper.Rd                             |    4 
 man/logRegModel.Rd                           |    1 
 man/minModel.Rd                              |    1 
 man/oneRow.Rd                                |    1 
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 man/percentCorrectList.Rd                    |    1 
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 man/percentCorrectListReturnMatrix.Rd        |    1 
 man/predictPair.Rd                           |    1 
 man/predictPairInternal.Rd                   |    1 
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 man/predictPairSummary.Rd                    |    1 
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 man/probGreater.Rd                           |    1 
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 man/regModel.Rd                              |    1 
 man/reverseRowsAndReverseColumns.Rd          |    1 
 man/rowIndexes.Rd                            |    1 
 man/rowPairApply.Rd                          |    1 
 man/rowPairApply2Rows.Rd                     |    1 
 man/rowPairApplyList.Rd                      |    1 
 man/singleCueModel.Rd                        |    5 
 man/statsFromConfusionMatrix.Rd              |    1 
 man/ttbGreedyModel.Rd                        |    1 
 man/ttbModel.Rd                              |    1 
 man/unitWeightModel.Rd                       |    5 
 man/validityWeightModel.Rd                   |    1 
 man/zzDocumentationStubFormulaModelParams.Rd |    4 
 man/zzDocumentationStubModelParams.Rd        |    1 
 man/zzDocumentationStubReverseCues.Rd        |    1 
 tests/testthat/test-aggregators.R            |   91 ++---
 tests/testthat/test-heuristics.R             |   65 +++
 tests/testthat/test-heuristics_benchmark.R   |   11 
 vignettes/README.Rmd                         |    2 
 vignettes/confusion-matrix.Rmd               |    2 
 vignettes/cross-validation.Rmd               |   18 -
 vignettes/reproducing-results.Rmd            |   80 ++++
 74 files changed, 2213 insertions(+), 679 deletions(-)

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New package factory with initial version 0.1.0
Package: factory
Type: Package
Title: Build Function Factories
Version: 0.1.0
Authors@R: c(person(given = "Jon", family = "Harmon", role = c("aut", "cre"), email = "jonthegeek@gmail.com") )
Description: Function factories are functions that make functions. They can be confusing to construct. Straightforward techniques can produce functions that are fragile or hard to understand. While more robust techniques exist to construct function factories, those techniques can be confusing. This package is designed to make it easier to construct function factories.
URL: https://github.com/jonthegeek/factory
BugReports: https://github.com/jonthegeek/factory/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: purrr (>= 0.3.2), rlang (>= 0.4.0)
Suggests: testthat (>= 2.1.0), covr, roxygen2, knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-20 13:44:54 UTC; Jon.Harmon
Author: Jon Harmon [aut, cre]
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Repository: CRAN
Date/Publication: 2019-08-21 09:00:07 UTC

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New package DRAYL with initial version 1.0
Package: DRAYL
Version: 1.0
Title: Computation of Rayleigh Densities of Arbitrary Dimension
Author: Martin Wiegand
Maintainer: Martin Wiegand <Martin.Wiegand@manchester.ac.uk>
Depends: R (>= 3.0.1)
Description: We offer an implementation of the series representation put forth in "A series representation for multidimensional Rayleigh distributions" by Wiegand and Nadarajah <DOI: 10.1002/dac.3510>. Furthermore we have implemented an integration approach proposed by Beaulieu et al. for 3 and 4-dimensional Rayleigh densities (Beaulieu, Zhang, "New simplest exact forms for the 3D and 4D multivariate Rayleigh PDFs with applications to antenna array geometrics", <DOI: 10.1109/TCOMM.2017.2709307>).
License: GPL-2
Imports: stats,pracma,RConics,rmutil,cubature
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2019-08-20 12:56:17 UTC; mbbxwmw4
Repository: CRAN
Date/Publication: 2019-08-21 08:20:07 UTC

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Package rticles updated to version 0.10 with previous version 0.9 dated 2019-07-12

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>)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between rticles versions 0.9 dated 2019-07-12 and 0.10 dated 2019-08-21

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Package NPP updated to version 0.2.0 with previous version 0.1.0 dated 2019-07-11

Title: Normalized Power Prior Bayesian Analysis
Description: Posterior sampling in several commonly used distributions using normalized power prior as described in Duan, Ye and Smith (2006) <doi:10.1002/env.752> and Ibrahim et.al. (2015) <doi:10.1002/sim.6728>. Sampling of the power parameter is achieved via either independence Metropolis-Hastings or random walk Metropolis-Hastings based on transformation.
Author: Zifei Han, Tianyu Bai and Keying Ye
Maintainer: Zifei Han <hanzifei1@gmail.com>

Diff between NPP versions 0.1.0 dated 2019-07-11 and 0.2.0 dated 2019-08-21

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Package CBPS updated to version 0.21 with previous version 0.20 dated 2019-03-22

Title: Covariate Balancing Propensity Score
Description: Implements the covariate balancing propensity score (CBPS) proposed by Imai and Ratkovic (2014) <DOI:10.1111/rssb.12027>. The propensity score is estimated such that it maximizes the resulting covariate balance as well as the prediction of treatment assignment. The method, therefore, avoids an iteration between model fitting and balance checking. The package also implements optimal CBPS from Fan et al. (2016) <https://imai.fas.harvard.edu/research/CBPStheory.html>, several extensions of the CBPS beyond the cross-sectional, binary treatment setting. They include the CBPS for longitudinal settings so that it can be used in conjunction with marginal structural models from Imai and Ratkovic (2015) <DOI:10.1080/01621459.2014.956872>, treatments with three- and four-valued treatment variables, continuous-valued treatments from Fong, Hazlett, and Imai (2018) <DOI:10.1214/17-AOAS1101>, propensity score estimation with a large number of covariates from Ning, Peng, and Imai (2018) <arXiv:1812.08683>, and the situation with multiple distinct binary treatments administered simultaneously. In the future it will be extended to other settings including the generalization of experimental and instrumental variable estimates.
Author: Christian Fong [aut, cre], Marc Ratkovic [aut], Kosuke Imai [aut], Chad Hazlett [ctb], Xiaolin Yang [ctb], Sida Peng [ctb]
Maintainer: Christian Fong <cjfong@umich.edu>

Diff between CBPS versions 0.20 dated 2019-03-22 and 0.21 dated 2019-08-21

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Package bnviewer updated to version 0.1.4 with previous version 0.1.3 dated 2019-06-08

Title: Interactive Visualization of Bayesian Networks
Description: Bayesian networks provide an intuitive framework for probabilistic reasoning and its graphical nature can be interpreted quite clearly. Graph based methods of machine learning are becoming more popular because they offer a richer model of knowledge that can be understood by a human in a graphical format. The 'bnviewer' is an R Package that allows the interactive visualization of Bayesian Networks. The aim of this package is to improve the Bayesian Networks visualization over the basic and static views offered by existing packages.
Author: Robson Fernandes
Maintainer: Robson Fernandes <robson.fernandes@usp.br>

Diff between bnviewer versions 0.1.3 dated 2019-06-08 and 0.1.4 dated 2019-08-21

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Package blogdown updated to version 0.15 with previous version 0.14 dated 2019-07-13

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 0.14 dated 2019-07-13 and 0.15 dated 2019-08-21

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Package apcluster updated to version 1.4.8 with previous version 1.4.7 dated 2018-05-29

Title: Affinity Propagation Clustering
Description: Implements Affinity Propagation clustering introduced by Frey and Dueck (2007) <DOI:10.1126/science.1136800>. The algorithms are largely analogous to the 'Matlab' code published by Frey and Dueck. The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.
Author: Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier, Nikola Kostic
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

Diff between apcluster versions 1.4.7 dated 2018-05-29 and 1.4.8 dated 2019-08-21

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Tue, 20 Aug 2019

Package visualR updated to version 2.0.2 with previous version 2.0.1 dated 2019-05-05

Title: 3D Visualization of Option Greeks and Volatility Skew
Description: Generates a 3D graph which plots the volatility skew of a stock or a selected stock option parameter over time. The default setting plots the net parameter position of a double vertical spread over time.
Author: John T. Buynak
Maintainer: John T. Buynak <jbuynak94@gmail.com>

Diff between visualR versions 2.0.1 dated 2019-05-05 and 2.0.2 dated 2019-08-20

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Package scoringRules updated to version 1.0.0 with previous version 0.9.6 dated 2019-05-27

Title: Scoring Rules for Parametric and Simulated Distribution Forecasts
Description: Dictionary-like reference for computing scoring rules in a wide range of situations. Covers both parametric forecast distributions (such as mixtures of Gaussians) and distributions generated via simulation.
Author: Alexander Jordan, Fabian Krueger, Sebastian Lerch
Maintainer: Fabian Krueger <Fabian.Krueger83@gmail.com>

Diff between scoringRules versions 0.9.6 dated 2019-05-27 and 1.0.0 dated 2019-08-20

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Package clustrd updated to version 1.3.4 with previous version 1.3.2 dated 2019-07-11

Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>

Diff between clustrd versions 1.3.2 dated 2019-07-11 and 1.3.4 dated 2019-08-20

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Package xlink updated to version 1.0.1 with previous version 1.0.0 dated 2019-07-03

Title: Genetic Association Models for X-Chromosome SNPS on Continuous, Binary and Survival Outcomes
Description: The expression of X-chromosome undergoes three possible biological processes: X-chromosome inactivation (XCI), escape of the X-chromosome inactivation (XCI-E),and skewed X-chromosome inactivation (XCI-S). To analyze the X-linked genetic association for phenotype such as continuous, binary, and time-to-event outcomes with the actual process unknown, we propose a unified approach of maximizing the likelihood or partial likelihood over all of the potential biological processes. The methods are described in Wei Xu, Meiling Hao (2017) <doi:10.1002/gepi.22097>. And also see Dongxiao Han, Meiling Hao, Lianqiang Qu, Wei Xu (2019) <doi:10.1177/0962280219859037>.
Author: Wei Xu [aut], Meiling Hao [aut], Yi Zhu [cre]
Maintainer: Yi Zhu <yizhu87@gmail.com>

Diff between xlink versions 1.0.0 dated 2019-07-03 and 1.0.1 dated 2019-08-20

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Package Seurat updated to version 3.1.0 with previous version 3.0.2 dated 2019-06-14

Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>), Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>), Jeff Farrell [ctb], Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Patrick Roelli [ctb], Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>

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Package orthoDr updated to version 0.6.2 with previous version 0.5 dated 2018-03-25

Title: Semi-Parametric Dimension Reduction Models Using Orthogonality Constrained Optimization
Description: Utilize an orthogonality constrained optimization algorithm of Wen & Yin (2013) <DOI:10.1007/s10107-012-0584-1> to solve a variety of dimension reduction problems in the semiparametric framework, such as Ma & Zhu (2012) <DOI:10.1080/01621459.2011.646925>, Ma & Zhu (2013) <DOI:10.1214/12-AOS1072>, Sun, Zhu, Wang & Zeng (2017) <arXiv:1704.05046> and Zhou & Zhu (2018+) <arXiv:1802.06156>. It also serves as a general purpose optimization solver for problems with orthogonality constraints. Parallel computing for approximating the gradient is enabled through `OpenMP'.
Author: Ruilin Zhao, Ruoqing Zhu, Jiyang Zhang, Wenzhuo Zhou and Peng Xu
Maintainer: Ruoqing Zhu <teazrq@gmail.com>

Diff between orthoDr versions 0.5 dated 2018-03-25 and 0.6.2 dated 2019-08-20

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Package kernscr updated to version 1.0.5 with previous version 1.0.3 dated 2016-06-28

Title: Kernel Machine Score Test for Semi-Competing Risks
Description: Kernel Machine Score Test for Pathway Analysis in the Presence of Semi-Competing Risks. Method is detailed in: Neykov, Hejblum & Sinnott (2018) <doi: 10.1177/0962280216653427>.
Author: Matey Neykov [aut], Boris P Hejblum [aut, cre], Jennifer A Sinnot [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>

Diff between kernscr versions 1.0.3 dated 2016-06-28 and 1.0.5 dated 2019-08-20

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Package gtsummary updated to version 1.2.1 with previous version 1.2.0 dated 2019-08-19

Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers. The package is enhanced when the 'gt' package is installed. Use this code to install: 'remotes::install_github("rstudio/gt")'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>), Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>), Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>), Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>), Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>), Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>), Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

Diff between gtsummary versions 1.2.0 dated 2019-08-19 and 1.2.1 dated 2019-08-20

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Package dlsem updated to version 2.4.3 with previous version 2.4.2 dated 2019-05-27

Title: Distributed-Lag Linear Structural Equation Models
Description: Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs are Markovian structural causal models where each factor of the joint probability distribution is a distributed-lag linear regression (Magrini, 2018 <doi:10.2478/bile-2018-0012>; Magrini et al., 2019 <doi:10.1007/s11135-019-00855-z>). DLSEMs account for temporal delays in the dependence relationships among the variables and allow to perform dynamic causal inference by assessing causal effects at different time lags. Endpoint-constrained quadratic, quadratic decreasing and gamma lag shapes are available.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <alessandro.magrini@unifi.it>

Diff between dlsem versions 2.4.2 dated 2019-05-27 and 2.4.3 dated 2019-08-20

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Package bestNormalize updated to version 1.4.2 with previous version 1.4.0 dated 2019-05-13

Title: Normalizing Transformation Functions
Description: Estimate a suite of normalizing transformations, including a new adaptation of a technique based on ranks which can guarantee normally distributed transformed data if there are no ties: ordered quantile normalization (ORQ). ORQ normalization combines a rank-mapping approach with a shifted logit approximation that allows the transformation to work on data outside the original domain. It is also able to handle new data within the original domain via linear interpolation. The package is built to estimate the best normalizing transformation for a vector consistently and accurately. It implements the Box-Cox transformation, the Yeo-Johnson transformation, three types of Lambert WxF transformations, and the ordered quantile normalization transformation. It also estimates the normalization efficacy of other commonly used transformations.
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>

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Package BallMapper updated to version 0.2.0 with previous version 0.1.0 dated 2019-07-26

Title: The Ball Mapper Algorithm
Description: The core algorithm is described in "Ball mapper: a shape summary for topological data analysis" by Pawel Dlotko, (2019) <arXiv:1901.07410>. Please consult the following youtube video <https://www.youtube.com/watch?v=M9Dm1nl_zSQfor> the idea of functionality. Ball Mapper provide a topologically accurate summary of a data in a form of an abstract graph. To create it, please provide the coordinates of points (in the points array), values of a function of interest at those points (can be initialized randomly if you do not have it) and the value epsilon which is the radius of the ball in the Ball Mapper construction. It can be understood as the minimal resolution on which we use to create the model of the data.
Author: Pawel Dlotko [aut, cre]
Maintainer: Pawel Dlotko <pdlotko@gmail.com>

Diff between BallMapper versions 0.1.0 dated 2019-07-26 and 0.2.0 dated 2019-08-20

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Package vcr updated to version 0.3.0 with previous version 0.2.6 dated 2019-02-12

Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>

Diff between vcr versions 0.2.6 dated 2019-02-12 and 0.3.0 dated 2019-08-20

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Package MazamaCoreUtils updated to version 0.3.1 with previous version 0.2.0 dated 2019-07-18

Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly needed for production level projects such as logging, error handling, and cache management.
Author: Jonathan Callahan [aut, cre], Spencer Pease [aut], Thomas Bergamaschi [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>

Diff between MazamaCoreUtils versions 0.2.0 dated 2019-07-18 and 0.3.1 dated 2019-08-20

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Package RCzechia updated to version 1.4.2 with previous version 1.4.1 dated 2019-07-01

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

Diff between RCzechia versions 1.4.1 dated 2019-07-01 and 1.4.2 dated 2019-08-20

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Package GENEAread updated to version 2.0.7 with previous version 2.0.6 dated 2018-11-16

Title: Package for Reading Binary Files
Description: Functions and analytics for GENEA-compatible accelerometer data into R objects. See topic 'GENEAread' for an introduction to the package.
Author: Zhou Fang [aut], Joss Langford [aut], Charles Sweetland [aut, cre]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>

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New package lactcurves with initial version 1.0.0
Package: lactcurves
Type: Package
Title: Lactation Curve Parameter Estimation
Version: 1.0.0
Author: Eva M. Strucken
Maintainer: Eva M. Strucken <estrucke@une.edu.au>
Description: AllCurves() runs multiple lactation curve models and extracts selection criteria for each model. This package summarises the most common lactation curve models from the last century and provides a tool for researchers to quickly decide on which model fits their data best to proceed with their analysis. Start parameters were optimized based on a dataset with 1.7 million Holstein-Friesian cows. If convergence fails, the start parameters need to be manually adjusted. The models included in the package are taken from: (1) Michaelis-Menten: Michaelis, L. and M.L. Menten (1913). <www.plantphys.info/plant_physiology/copyright/MichaelisMentenTranslation2.pdf> (1a) Michaelis-Menten (Rook): Rook, A.J., J. France, and M.S. Dhanoa (1993). <doi:10.1017/S002185960007684X> (1b) Michaelis-Menten + exponential (Rook): Rook, A.J., J. France, and M.S. Dhanoa (1993). <doi:10.1017/S002185960007684X> (2) Brody (1923): Brody, S., A.C. Ragsdale, and C.W. Turner (1923). <doi:10.1085/jgp.5.6.777> (3) Brody (1924): Brody, S., C.W. Tuner, and A.C. Ragsdale (1924). <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2140670/> (4) Schumacher: Schumacher, F.X. (1939) in Thornley, J.H.M. and J. France (2007). <https://books.google.com.au/books/about/Mathematical_Models_in_Agriculture.html?id=rlwBCRSHobcC&redir_esc=y> (4a) Schumacher (Lopez et al. 2015): Lopez, S. J. France, N.E. Odongo, R.A. McBride, E. Kebreab, O. AlZahal, B.W. McBride, and J. Dijkstra (2015). <doi:10.3168/jds.2014-8132> (5) Parabolic exponential (Adediran): Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012). <doi:10.3168/jds.2011-4663> (6) Wood: Wood, P.D.P. (1967). <doi:10.1038/216164a0> (6a) Wood reparameterized (Dhanoa): Dhanoa, M.S. (1981). <doi:10.1017/S0003356100027276> (6b) Wood non-linear (Cappio-Borlino): Cappio-Borlino, A., G. Pulina, and G. Rossi (1995). <doi:10.1016/0921-4488(95)00713-U> (7) Quadratic Polynomial (Dave): Dave, B.K. (1971) in Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012). <doi:10.3168/jds.2011-4663> (8) Cobby and Le Du (Vargas): Vargas, B., W.J. Koops, M. Herrero, and J.A.M Van Arendonk (2000). <doi:10.3168/jds.S0022-0302(00)75005-3> (9) Papajcsik and Bodero 1: Papajcsik, I.A. and J. Bodero (1988). <doi:10.1017/S0003356100003275> (10) Papajcsik and Bodero 2: Papajcsik, I.A. and J. Bodero (1988). <doi:10.1017/S0003356100003275> (11) Papajcsik and Bodero 3: Papajcsik, I.A. and J. Bodero (1988). <doi:10.1017/S0003356100003275> (12) Papajcsik and Bodero 4: Papajcsik, I.A. and J. Bodero (1988). <doi:10.1017/S0003356100003275> (13) Papajcsik and Bodero 6: Papajcsik, I.A. and J. Bodero (1988). <doi:10.1017/S0003356100003275> (14) Mixed log model 1 (Guo and Swalve): Guo, Z. and H.H. Swalve (1995). <https://journal.interbull.org/index.php/ib/issue/view/11> (15) Mixed log model 3 (Guo and Swalve): Guo, Z. and H.H. Swalve (1995). <https://journal.interbull.org/index.php/ib/issue/view/11> (16) Log-quadratic (Adediran et al. 2012): Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012). <doi:10.3168/jds.2011-4663> (17) Wilmink: J.B.M. Wilmink (1987). <doi:10.1016/0301-6226(87)90003-0> (17a) modified Wilmink (Jakobsen): Jakobsen J.H., P. Madsen, J. Jensen, J. Pedersen, L.G. Christensen, and D.A. Sorensen (2002). <doi:10.3168/jds.S0022-0302(02)74231-8> (17b) modified Wilmink (Laurenson & Strucken): in preparation (2019). (18) Bicompartemental (Ferguson and Boston 1993): Ferguson, J.D., and R. Boston (1993) in Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012). <doi:10.3168/jds.2011-4663> (19) Dijkstra: Dijkstra, J., J. France, M.S. Dhanoa, J.A. Maas, M.D. Hanigan, A.J. Rook, and D.E. Beever (1997). <doi10.3168/jds.S0022-0302(97)76185-X> (20) Morant and Gnanasakthy (Pollott et al 2000): Pollott, G.E. and E. Gootwine (2000). <doi10.1017/S1357729800055028> (21) Morant and Gnanasakthy (Vargas et al 2000): Vargas, B., W.J. Koops, M. Herrero, and J.A.M Van Arendonk (2000). <doi:10.3168/jds.S0022-0302(00)75005-3> (22) Morant and Gnanasakthy (Adediran et al. 2012): Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012). <doi:10.3168/jds.2011-4663> (23) Khandekar (Guo and Swalve): Guo, Z. and H.H. Swalve (1995). <https://journal.interbull.org/index.php/ib/issue/view/11> (24) Ali and Schaeffer: Ali, T.E. and L.R. Schaeffer (1987). <https://www.nrcresearchpress.com/doi/pdf/10.4141/cjas87-067> (25) Fractional Polynomial (Elvira et al. 2013): Elvira, L., F. Hernandez, P. Cuesta, S. Cano, J.-V. Gonzalez-Martin, and S. Astiz (2012). <doi:10.1017/S175173111200239X> (26) Pollott multiplicative (Elvira): Elvira, L., F. Hernandez, P. Cuesta, S. Cano, J.-V. Gonzalez-Martin, and S. Astiz (2012). <doi:10.1017/S175173111200239X> (27) Pollott modified: Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012). <doi:10.3168/jds.2011-4663> (28) Monophasic Grossman: Grossman, M. and W.J. Koops (1988). <doi:10.3168/jds.S0022-0302(88)79723-4> (29) Monophasic Power Transformed (Grossman 1999): Grossman, M., S.M. Hartz, and W.J. Koops (1999). <doi:10.3168/jds.S0022-0302(99)75464-0> (30) Diphasic (Grossman 1999): Grossman, M., S.M. Hartz, and W.J. Koops (1999). <doi:10.3168/jds.S0022-0302(99)75464-0> (31) Diphasic Power Transformed (Grossman 1999): Grossman, M., S.M. Hartz, and W.J. Koops (1999). <doi:10.3168/jds.S0022-0302(99)75464-0> (32) Legendre Polynomial (3th order): Jakobsen J.H., P. Madsen, J. Jensen, J. Pedersen, L.G. Christensen, and D.A. Sorensen (2002). <doi:10.3168/jds.S0022-0302(02)74231-8> (33) Legendre Polynomial (4th order): Jakobsen J.H., P. Madsen, J. Jensen, J. Pedersen, L.G. Christensen, and D.A. Sorensen (2002). <doi:10.3168/jds.S0022-0302(02)74231-8> (34) Legendre + Wilmink (Lidauer): Lidauer, M. and E.A. Mantysaari (1999). <https://journal.interbull.org/index.php/ib/article/view/417> (35) Natural Cubic Spline (3 percentiles): White, I.M.S., R. Thompson, and S. Brotherstone (1999). <doi:10.3168/jds.S0022-0302(99)75277-X> (36) Natural Cubic Spline (4 percentiles): White, I.M.S., R. Thompson, and S. Brotherstone (1999). <doi:10.3168/jds.S0022-0302(99)75277-X> (37) Natural Cubic Spline (5 percentiles): White, I.M.S., R. Thompson, and S. Brotherstone (1999) <doi:10.3168/jds.S0022-0302(99)75277-X> (38) Natural Cubic Spline (defined knots according to Harrell 2001): Jr. Harrell, F.E. (2001). <https://link.springer.com/book/10.1007/978-3-319-19425-7> The selection criteria measure the goodness of fit of the model and include: Residual standard error (RSE), R-square (R2), log likelihood, Akaike information criterion (AIC), Akaike information criterion corrected (AICC), Bayesian Information Criterion (BIC), Durbin Watson coefficient (DW). The following model parameters are included: Residual sum of squares (RSS), Residual standard deviation (RSD), F-value (F) based on F-ratio test.
License: GPL-3
Depends: orthopolynom,splines
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2019-08-20 05:10:34 UTC; estrucke
Repository: CRAN
Date/Publication: 2019-08-20 16:30:02 UTC

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Package blackbox updated to version 1.1.27 with previous version 1.1.25 dated 2018-06-08

Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 <doi:10.1093/molbev/MSR262>; Leblois et al., 2014 <doi:10.1093/molbev/msu212>; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph] (<https://orcid.org/0000-0003-4670-0371>), Raphaël Leblois [ctb] (<https://orcid.org/0000-0002-3051-4497>)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>

Diff between blackbox versions 1.1.25 dated 2018-06-08 and 1.1.27 dated 2019-08-20

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New package spread with initial version 2019.8.5
Package: spread
Title: Infectious Disease Spread Models
Version: 2019.8.5
Authors@R: c( person("Solveig", "Engebretsen", email = "solveig.engebretsen@medisin.uio.no", role = c("aut")), person("Andreas Nygård", "Osnes", email = "andreas.n.osnes@gmail.com", role = c("aut")), person("Richard", "White", email = "w@rwhite.no", role = c("aut", "cre")))
Description: A stochastic SEIIaR (susceptible, exposed, infectious, infectious asymptomatic, recovered) metapopulation model that including commuting. Each location has a local infection system, while the locations are connected by people who commute each day. The model differentiates between day and night. During the day you can infect/be infected in the location where you work, while during the night you can infect/be infected in the location where you live. It is the same commuters who travel back and forth each day. At the start of a day, all commuters are sent to their work location, where they mix for 12 hours. The commuters are then sent to their respective home locations, where they mix for 12 hours. The model is loosely based upon a published model by Engebretsen (2019) <doi:10.1371/journal.pcbi.1006879>.
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 0.9.4), RcppProgress (>= 0.1), data.table, fhidata, stringr, readxl, zoo
Suggests: testthat, knitr, ggplot2, glue, rmarkdown
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
LinkingTo: Rcpp, RcppProgress
VignetteBuilder: knitr
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2019-08-20 06:47:56 UTC; rstudio
Author: Solveig Engebretsen [aut], Andreas Nygård Osnes [aut], Richard White [aut, cre]
Maintainer: Richard White <w@rwhite.no>
Repository: CRAN
Date/Publication: 2019-08-20 15:50:02 UTC

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New package pass.lme with initial version 0.9.0
Package: pass.lme
Type: Package
Title: Power and Sample Size for Linear Mixed Effect Models
Version: 0.9.0
Depends: R (>= 3.2.5)
Author: Marco Chak Yan YU
Maintainer: Marco Chak Yan YU <marcocyyu@gmail.com>
Description: Power and sample size calculation for testing fixed effect coefficients in multilevel linear mixed effect models with one or more than one independent populations. Laird, Nan M. and Ware, James H. (1982) <doi:10.2307/2529876>.
License: GPL-3
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-20 08:34:36 UTC; marco
Repository: CRAN
Date/Publication: 2019-08-20 15:50:05 UTC

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Package overlapping updated to version 1.5.4 with previous version 1.5.3 dated 2019-05-28

Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>

Diff between overlapping versions 1.5.3 dated 2019-05-28 and 1.5.4 dated 2019-08-20

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Package mDAG updated to version 1.2.2 with previous version 1.2 dated 2019-03-13

Title: Inferring Causal Network from Mixed Observational Data Using a Directed Acyclic Graph
Description: Learning a mixed directed acyclic graph based on both continuous and categorical data.
Author: Wujuan Zhong, Li Dong, Quefeng Li, Xiaojing Zheng
Maintainer: Wujuan Zhong <zhongwujuan@gmail.com>

Diff between mDAG versions 1.2 dated 2019-03-13 and 1.2.2 dated 2019-08-20

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Package lgr updated to version 0.3.2 with previous version 0.3.1 dated 2019-06-13

Title: A Fully Featured Logging Framework
Description: A flexible, feature-rich yet light-weight logging framework based on 'R6' classes. It supports hierarchical loggers, custom log levels, arbitrary data fields in log events, logging to plaintext, 'JSON', (rotating) files, memory buffers, and databases, as well as email and push notifications. For a full list of features with examples please refer to the package vignette.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>

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New package implicitMeasures with initial version 0.1.0
Package: implicitMeasures
Type: Package
Title: Computes the Scores for Different Implicit Measures
Version: 0.1.0
Author: Ottavia M. Epifania [aut, cre], Pasquale Anselmi [ctb], Egidio Robusto [ctb]
Maintainer: Ottavia M. Epifania <otta.epifania@gmail.com>
Description: A tool for computing the scores for the Implicit Association Test (IAT; Greenwald, McGhee & Schwartz (1998) <doi:10.1037/0022-3514.74.6.1464>) and the Single Category-IAT (SC-IAT: Karpinski & Steinman (2006) <doi:10.1037/0022-3514.91.1.16>). Functions for preparing the data (both for the IAT and the SC-IAT), plotting the results, and obtaining a table with the scores of implicit measures descriptive statistics are provided.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: dplyr, ggplot2, methods, plyr, qpdf, tidyr, xtable
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, tableHTML, data.table
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-02 11:46:22 UTC; huawei
Repository: CRAN
Date/Publication: 2019-08-20 15:40:05 UTC

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Package bioacoustics updated to version 0.2.1 with previous version 0.2.0.1 dated 2019-06-09

Title: Analyse Audio Recordings and Automatically Extract Animal Vocalizations
Description: Contains all the necessary tools to process audio recordings of various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files, display audio signals, detect and extract automatically acoustic features for further analysis such as classification.
Author: Jean Marchal [aut, cre], Francois Fabianek [aut], Christopher Scott [aut], Chris Corben [ctb, cph] (Read ZC files, original C code), David Riggs [ctb, cph] (Read GUANO metadata, original R code), Peter Wilson [ctb, cph] (Read ZC files, original R code), Wildlife Acoustics, inc. [ctb, cph] (Read WAC files, original C code), WavX, inc. [cph]
Maintainer: Jean Marchal <jean.marchal@wavx.ca>

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Package ssizeRNA updated to version 1.3.2 with previous version 1.3.1 dated 2019-02-19

Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes. To install this package, please use 'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'. For R version 3.5 or greater, please use 'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}; BiocManager::install("ssizeRNA")'.
Author: Ran Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb]
Maintainer: Ran Bi <biranpier@gmail.com>

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New package electivity with initial version 1.0.2
Package: electivity
Type: Package
Title: Algorithms for Electivity Indices
Version: 1.0.2
Date: 2019-08-13
Authors@R: person("Desi", "Quintans", email = "science@desiquintans.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3356-0293"))
Description: Provides all electivity algorithms (including Vanderploeg and Scavia electivity) that were examined in Lechowicz (1982) <doi:10.1007/BF00349007>, plus the example data that were provided for moth resource utilisation.
URL: https://github.com/DesiQuintans/electivity
BugReports: https://github.com/DesiQuintans/electivity/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0)
Suggests: utils (>= 3.4.2), usethis (>= 1.0.0)
RoxygenNote: 6.1.1
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2019-08-19 21:38:27 UTC; 90928711
Author: Desi Quintans [aut, cre] (<https://orcid.org/0000-0003-3356-0293>)
Maintainer: Desi Quintans <science@desiquintans.com>
Repository: CRAN
Date/Publication: 2019-08-20 14:50:05 UTC

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Package comorbidity updated to version 0.5.0 with previous version 0.4.1 dated 2019-06-27

Title: Computing Comorbidity Scores
Description: Computing comorbidity scores such as the weighted Charlson score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>) using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>).
Author: Alessandro Gasparini [aut, cre] (<https://orcid.org/0000-0002-8319-7624>), Hojjat Salmasian [ctb] (ICD-9-CM scores), Jonathan Williman [ctb] (<https://orcid.org/0000-0001-5080-4435>)
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>

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Package sugarbag updated to version 0.1.1 with previous version 0.1.0 dated 2019-06-14

Title: Create Tessellated Hexagon Maps
Description: Create a hexagon tilegram from spatial polygons. Each polygon is represented by a hexagon tile, placed as close to it's original centroid as possible, with a focus on maintaining spatial relationship to a focal point. Developed to aid visualisation and analysis of spatial distributions across Australia, which can be challenging due to the concentration of the population on the coast and wide open interior.
Author: Stephanie Kobakian [aut, cre], Dianne Cook [aut, ths]
Maintainer: Stephanie Kobakian <stephanie.kobakian@gmail.com>

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Package suddengains updated to version 0.3.0 with previous version 0.2.1 dated 2019-05-21

Title: Identify Sudden Gains in Longitudinal Data
Description: Identify sudden gains based on the three criteria outlined by Tang and DeRubeis (1999) <doi:10.1037/0022-006X.67.6.894> to a selection of repeated measures. Sudden losses, defined as the opposite of sudden gains can also be identified. Two different datasets can be created, one including all sudden gains/losses and one including one selected sudden gain/loss for each case. It can extract scores around sudden gains/losses. It can plot the average change around sudden gains/losses and trajectories of individual cases.
Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>), Graham M Thew [ctb] (<https://orcid.org/0000-0003-2851-1315>), Richard Stott [ctb] (<https://orcid.org/0000-0003-2533-5504>), Anke Ehlers [ctb, ths] (<https://orcid.org/0000-0002-8742-0192>)
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>

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Package RgoogleMaps updated to version 1.4.4 with previous version 1.4.3 dated 2018-11-07

Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>

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Package highfrequency updated to version 0.6.0 with previous version 0.5.3 dated 2018-03-03

Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency trades and quotes data, calculate various liquidity measures, estimate and forecast volatility, detect price jumps and investigate microstructure noise and intraday periodicity.
Author: Kris Boudt [aut, cre], Jonathan Cornelissen [aut], Scott Payseur [aut], Giang Nguyen [ctb], Onno Kleen [ctb] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Kris Boudt <Kris.Boudt@econ.kuleuven.be>

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Package difNLR updated to version 1.3.0 with previous version 1.2.2 dated 2018-05-06

Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Drabinova and Martinkova, 2017, doi:10.1111/jedm.12158).
Author: Adela Hladka [aut, cre], Patricia Martinkova [aut], Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>

Diff between difNLR versions 1.2.2 dated 2018-05-06 and 1.3.0 dated 2019-08-20

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Package cbsodataR updated to version 0.3.4 with previous version 0.3.2 dated 2019-02-21

Title: Statistics Netherlands (CBS) Open Data API Client
Description: The data and meta data from Statistics Netherlands (<https://www.cbs.nl>) can be browsed and downloaded. The client uses the open data API of Statistics Netherlands.
Author: Edwin de Jonge [aut, cre], Sara Houweling [ctb]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>

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Package semPlot updated to version 1.1.2 with previous version 1.1.1 dated 2019-04-05

Title: Path Diagrams and Visual Analysis of Various SEM Packages' Output
Description: Path diagrams and visual analysis of various SEM packages' output.
Author: Sacha Epskamp [aut, cre], Simon Stuber [ctb], Jason Nak [ctb], Myrthe Veenman [ctb], Terrence D. Jorgensen [ctb] (<https://orcid.org/0000-0001-5111-6773>)
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package Peptides updated to version 2.4.1 with previous version 2.4 dated 2018-06-08

Title: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences
Description: Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio [aut, cre], Paola Rondon-Villarreal [aut, ths], Rodrigo Torres [aut, ths], J. Sebastian Paez [ctb]
Maintainer: Daniel Osorio <dcosorioh@tamu.edu>

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New package NetSimR with initial version 0.1.0
Package: NetSimR
Type: Package
Title: Actuarial Functions for Non-Life Insurance Modelling
Version: 0.1.0
Author: Yiannis Parizas [aut, cre]
Authors@R: person("Yiannis", "Parizas", email = "yiannis.parizas@gmail.com", role = c("aut", "cre"))
Maintainer: Yiannis Parizas <yiannis.parizas@gmail.com>
Description: Assists actuaries and other insurance modellers in pricing, reserving and capital modelling for non-life insurance and reinsurance modelling. Provides functions that help model excess levels, capping and pure Incurred but not reported claims (pure IBNR). Includes capped mean, exposure curves and increased limit factor curves (ILFs) for LogNormal, Gamma, Pareto, Sliced LogNormal-Pareto and Sliced Gamma-Pareto distributions. Includes mean, probability density function (pdf), cumulative probability function (cdf) and inverse cumulative probability function for Sliced LogNormal-Pareto and Sliced Gamma-Pareto distributions. Includes calculating pure IBNR exposure with LogNormal and Gamma distribution for reporting delay.
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: knitr, crch, testthat
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-19 16:31:54 UTC; yiann
Repository: CRAN
Date/Publication: 2019-08-20 11:30:12 UTC

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New package ihpdr with initial version 1.0.0
Package: ihpdr
Title: Download Data from the International House Price Database
Version: 1.0.0
Authors@R: person(given = "Kostas", family = "Vasilopoulos", role = c("aut", "cre"), email = "k.vasilopoulo@gmail.com")
Description: Web scraping the <https://www.dallasfed.org> for up-to-date data on international house prices and exuberance indicators. Download data in tidy format.
Encoding: UTF-8
LazyData: true
Imports: rvest (>= 0.3.4), xml2 (>= 1.2.0), magrittr (>= 1.5), httr (>= 1.4.0), readxl (>= 1.3.1), dplyr (>= 0.8.3), lubridate (>= 1.7.4), purrr (>= 0.3.2), rlang (>= 0.4.0), tidyr (>= 0.8.3)
RoxygenNote: 6.1.1
URL: https://github.com/kvasilopoulos/ihpdr
BugReports: https://github.com/kvasilopoulos/ihpdr/issues
Suggests: spelling, testthat (>= 2.1.0), covr
Language: en-US
License: GPL-3
NeedsCompilation: no
Packaged: 2019-08-19 16:26:00 UTC; T460p
Author: Kostas Vasilopoulos [aut, cre]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>
Repository: CRAN
Date/Publication: 2019-08-20 11:30:06 UTC

More information about ihpdr at CRAN
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Package hutilscpp updated to version 0.2.0 with previous version 0.1.0 dated 2019-02-03

Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used, but may require higher performance that what can be obtained from base R. Incidentally provides support for 'reverse geocoding', such as matching a point with its nearest neighbour in another array. Used as a complement to package 'hutils' by sacrificing compilation or installation time for higher running speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>

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Package graphlayouts updated to version 0.5.0 with previous version 0.2.0 dated 2019-07-04

Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'. Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>

Diff between graphlayouts versions 0.2.0 dated 2019-07-04 and 0.5.0 dated 2019-08-20

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Package dtpcrm updated to version 0.1.1 with previous version 0.1.0 dated 2019-04-10

Title: Dose Transition Pathways for Continual Reassessment Method
Description: Provides the dose transition pathways (DTP) to project in advance the doses recommended by a model-based design for subsequent patients (stay, escalate, deescalate or stop early) using all the accumulated toxicity information; See Yap et al (2017) <doi: 10.1158/1078-0432.CCR-17-0582>. DTP can be used as a design and an operational tool and can be displayed as a table or flow diagram. The 'dtpcrm' package also provides the modified continual reassessment method (CRM) and time-to-event CRM (TITE-CRM) with added practical considerations to allow stopping early when there is sufficient evidence that the lowest dose is too toxic and/or there is a sufficient number of patients dosed at the maximum tolerated dose.
Author: Christina Yap [aut, cre], Daniel Slade [aut], Kristian Brock [aut], Yi Pan [aut]
Maintainer: Christina Yap <yapchristina17@gmail.com>

Diff between dtpcrm versions 0.1.0 dated 2019-04-10 and 0.1.1 dated 2019-08-20

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Package DataVisualizations updated to version 1.1.8 with previous version 1.1.6 dated 2019-03-08

Title: Visualizations of High-Dimensional Data
Description: Gives access to data visualisation methods that are relevant from the data scientist's point of view. The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) for either classified or non-classified multivariate data presented in Thrun et al. (2019) <arXiv:1908.06081>. The MD-plot outperforms the box-and-whisker diagram (box plot) and bean plot. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables as well as the Shepard density plot and the Bland-Altman plot are presented here. Pertaining to classified high-dimensional data, a number of visualizations are described, such as f.ex. the heat map and silhouette plot. A political map of the world or Germany can be visualized with the additional information defined by a classification of countries or regions. By extending the political map further, an uncomplicated function for a Choropleth map can be used which is useful for measurements across a geographic area. For categorical features, the Pie charts, slope charts and fan plots, improved by the ABC analysis, become usable. More detailed explanations are found in the book by Thrun, M.C.: "Projection-Based Clustering through Self-Organization and Swarm Intelligence" (2018) <doi:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph] (<https://orcid.org/0000-0001-9542-5543>), Felix Pape [aut, rev], Onno Hansen-Goos [ctr, ctb], Alfred Ultsch [dtc, ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>

Diff between DataVisualizations versions 1.1.6 dated 2019-03-08 and 1.1.8 dated 2019-08-20

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Package clean updated to version 1.1.0 with previous version 1.0.0 dated 2019-07-28

Title: Fast and Easy Data Cleaning
Description: Data cleaning functions for classes 'logical', 'factor', 'numeric', 'character', 'currency' and 'Date' to make data cleaning fast and easy. Relying on very few dependencies, it provides smart guessing, but with user options to override anything if needed.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

Diff between clean versions 1.0.0 dated 2019-07-28 and 1.1.0 dated 2019-08-20

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Package bvartools updated to version 0.0.2 with previous version 0.0.1 dated 2019-06-11

Title: Bayesian Inference of Vector Autoregressive Models
Description: Assists in the set-up of algorithms for Bayesian inference of vector autoregressive (VAR) models. Functions for posterior simulation, forecasting, impulse response analysis and forecast error variance decomposition are largely based on the introductory texts of Koop and Korobilis (2010) <doi:10.1561/0800000013> and Luetkepohl (2007, ISBN: 9783540262398).
Author: Franz X. Mohr [aut, cre]
Maintainer: Franz X. Mohr <bvartools@outlook.com>

Diff between bvartools versions 0.0.1 dated 2019-06-11 and 0.0.2 dated 2019-08-20

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New package tidycells with initial version 0.2.0
Type: Package
Package: tidycells
Title: Read Tabular Data from Diverse Sources and Easily Make Them Tidy
Version: 0.2.0
Authors@R: person(given = "Indranil", family = "Gayen", role = c("aut", "cre"), email = "nil.gayen@gmail.com", comment = c(ORCID = "0000-0003-0197-1944"))
Description: Provides utilities to read, cells from complex tabular data and heuristic detection based 'structural assignment' of those cells to a columnar or tidy format. Read functionality has the ability to read structured, partially structured or unstructured tabular data from various types of documents. The 'structural assignment' functionality has both supervised and unsupervised way of assigning cells data to columnar/tidy format. Multiple disconnected blocks of tables in a single sheet are also handled appropriately. These tools are suitable for unattended conversation of messy tables into a consumable format(usable for further analysis and data wrangling).
License: MIT + file LICENSE
URL: https://r-rudra.github.io/tidycells/, https://github.com/r-rudra/tidycells
BugReports: https://github.com/r-rudra/tidycells/issues
Depends: R (>= 3.2.0)
Imports: dplyr (>= 0.8.1), ggplot2, graphics, magrittr, methods, purrr (>= 0.3.2), rlang, stats, stringr (>= 1.4.0), tibble, tidyr, unpivotr (>= 0.5.1), utils
Suggests: cli, covr, docxtractr, DT, knitr, miniUI, plotly, readr, readxl, rmarkdown, rstudioapi, shiny, shinytest, stringdist, tabulizer, testthat (>= 2.1.0), tidyxl, xlsx, XML
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-19 13:36:24 UTC; igayen
Author: Indranil Gayen [aut, cre] (<https://orcid.org/0000-0003-0197-1944>)
Maintainer: Indranil Gayen <nil.gayen@gmail.com>
Repository: CRAN
Date/Publication: 2019-08-20 10:30:02 UTC

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Package qrandom updated to version 1.2 with previous version 1.1 dated 2019-02-14

Title: True Random Numbers using the ANU Quantum Random Numbers Server
Description: The ANU Quantum Random Number Generator provided by the Australian National University generates true random numbers in real-time by measuring the quantum fluctuations of the vacuum. This package offers an interface using their API. The electromagnetic field of the vacuum exhibits random fluctuations in phase and amplitude at all frequencies. By carefully measuring these fluctuations, one is able to generate ultra-high bandwidth random numbers. The quantum Random Number Generator is based on the papers by Symul et al., (2011) <doi:10.1063/1.3597793> and Haw, et al. (2015) <doi:10.1103/PhysRevApplied.3.054004>. The package offers functions to retrieve a sequence of random integers or hexadecimals and true random samples from a normal or uniform distribution.
Author: Siegfried Köstlmeier [aut, cre] (<https://orcid.org/0000-0002-7221-6981>), Boris Steipe [ctb] (<https://orcid.org/0000-0002-1134-6758>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

Diff between qrandom versions 1.1 dated 2019-02-14 and 1.2 dated 2019-08-20

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Package metadynminer updated to version 0.1.6 with previous version 0.1.5 dated 2019-07-18

Title: Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'
Description: Metadynamics is a state of the art biomolecular simulation technique. 'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes it possible to perform metadynamics using various simulation codes. The results of metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package 'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package. It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037> to calculate a free energy surface from hills. Minima can be located and plotted on the free energy surface. Transition states can be analyzed by Nudged Elastic Band method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy surfaces, minima and transition paths can be plotted to produce publication quality images.
Author: Vojtech Spiwok [aut, cre] (<https://orcid.org/0000-0001-8108-2033>)
Maintainer: Vojtech Spiwok <spiwokv@vscht.cz>

Diff between metadynminer versions 0.1.5 dated 2019-07-18 and 0.1.6 dated 2019-08-20

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Package HiCblock updated to version 1.5 with previous version 1.4 dated 2018-04-18

Title: Systematic Analysis of Architectural Proteins and Functional Elements in Blocking Long-Range Contacts Between Loci
Description: Here we propose a model to systematically analyze the roles of architectural proteins and functional elements in blocking long-range contacts between loci. The proposed model does not rely on topologically associating domain (TAD) mapping from Hi-C data. Instead of testing the enrichment or influence of protein binding at TAD borders, the model directly estimates the blocking effect of proteins on long-range contacts between flanking loci, making the model intuitive and biologically meaningful.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>

Diff between HiCblock versions 1.4 dated 2018-04-18 and 1.5 dated 2019-08-20

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New package disk.frame with initial version 0.1.0
Type: Package
Package: disk.frame
Title: Larger-than-RAM Disk-Based Data Manipulation Framework
Version: 0.1.0
Date: 2019-08-03
Authors@R: person("Dai", "ZJ", email = "zhuojia.dai@gmail.com", role = c("aut", "cre"))
Maintainer: Dai ZJ <zhuojia.dai@gmail.com>
Description: A disk-based data manipulation tool for working with arbitrarily large datasets as long as they fit on disk.
License: MIT + file LICENSE
Imports: Rcpp (>= 0.12.13), glue (>= 1.3.1), rlang (>= 0.4.0), furrr (>= 0.1.0), future.apply (>= 1.3.0), fs (>= 1.3.1), jsonlite (>= 1.6), pryr (>= 0.1.4), stringr (>= 1.4.0), fst (>= 0.8.0), assertthat (>= 0.2.1), globals (>= 0.12.4), future (>= 1.14.0), data.table (>= 1.12.2), crayon (>= 1.3.4)
Depends: R (>= 3.5.0), dplyr (>= 0.8.3), purrr (>= 0.3.2)
Suggests: testthat, knitr, rmarkdown, nycflights13, magrittr, shiny
LinkingTo: Rcpp
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Encoding: UTF-8
URL: http://diskframe.com
BugReports: https://github.com/xiaodaigh/disk.frame/issues
NeedsCompilation: yes
Packaged: 2019-08-19 13:19:13 UTC; RTX2080
Author: Dai ZJ [aut, cre]
Repository: CRAN
Date/Publication: 2019-08-20 10:10:02 UTC

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Package dexterMST updated to version 0.1.2 with previous version 0.1.1 dated 2018-10-29

Title: CML Calibration of Multi Stage Tests
Description: Conditional Maximum Likelihood Calibration and data management of multistage tests. Functions for calibration of the Extended Nominal Response and the Interaction models, DIF and profile analysis. See Robert J. Zwitser and Gunter Maris (2015)<doi:10.1007/s11336-013-9369-6>.
Author: Timo Bechger [aut, cre], Jesse Koops [aut], Ivailo Partchev [aut], Gunter Maris [aut], Robert Zwitser [ctb]
Maintainer: Timo Bechger <tmbechger@gmail.com>

Diff between dexterMST versions 0.1.1 dated 2018-10-29 and 0.1.2 dated 2019-08-20

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New package testequavar with initial version 0.1.2
Package: testequavar
Type: Package
Title: Bootstrap Tests for Equality of 2, 3, or 4 Population Variances
Version: 0.1.2
Author: Dexter Cahoy
Maintainer: Dexter Cahoy <cahoyd@uhd.edu>
Description: Tests the hypothesis that variances are homogeneous or not using bootstrap. The procedure uses a variance-based statistic, and is derived from a normal-theory test. The test equivalently expressed the hypothesis as a function of the log contrasts of the population variances. A box-type acceptance region is constructed to test the hypothesis. See Cahoy (2010) <doi:10.1016/j.csda.2010.04.012>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: stats
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-19 12:27:57 UTC; cahoyd
Repository: CRAN
Date/Publication: 2019-08-20 09:30:02 UTC

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New package TestDesign with initial version 0.2.2
Package: TestDesign
Type: Package
Title: Optimal Test Design Approach to Fixed and Adaptive Test Construction
Version: 0.2.2
Date: 2019-08-10
Authors@R: c( person("Seung W.", "Choi", email = "schoi@austin.utexas.edu", role = c("aut", "cre")), person("Sangdon", "Lim", email = "sangdonlim@utexas.edu", role = "aut"))
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Description: Use the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and van der Linden (2018) <doi:10.1201/9781315117430> in constructing fixed and adaptive tests. Supports the following mixed-integer programming (MIP) solver packages: 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package is not available from CRAN; see <https://www.gurobi.com/downloads>. See vignette for installing 'Rsymphony' package on Mac systems.
License: GPL (>= 2)
Depends: R (>= 2.10)
Imports: Rcpp (>= 1.0.0), methods, Matrix, lpSolve, foreach, logitnorm, Rdpack, crayon
Suggests: gurobi, Rsymphony, Rglpk, shiny, shinythemes, shinyWidgets, shinyjs, DT, knitr, rmarkdown, testthat (>= 2.1.0)
LinkingTo: Rcpp
RoxygenNote: 6.1.1
Encoding: UTF-8
LazyData: true
RdMacros: Rdpack
VignetteBuilder: knitr
Collate: 'import.R' 'RcppExports.R' 'item_class.R' 'item_functions.R' 'loading_functions.R' 'ATA_class.R' 'ATA_functions.R' 'solver_functions.R' 'shadow_class.R' 'shadow_functions.R' 'datasets.R' 'runshiny.R'
NeedsCompilation: yes
Packaged: 2019-08-19 00:17:52 UTC; chois1
Author: Seung W. Choi [aut, cre], Sangdon Lim [aut]
Repository: CRAN
Date/Publication: 2019-08-20 09:10:05 UTC

More information about TestDesign at CRAN
Permanent link

New package ssr with initial version 0.1.0
Package: ssr
Type: Package
Title: Semi-Supervised Regression Methods
Version: 0.1.0
Authors@R: c(person("Enrique", "Garcia-Ceja", role = c("aut", "cre"), email = "e.g.mx@ieee.org", comment = c(ORCID = "0000-0001-6864-8557")))
Description: An implementation of semi-supervised regression methods including self-learning and co-training by committee based on Hady, M. F. A., Schwenker, F., & Palm, G. (2009) <doi:10.1007/978-3-642-04274-4_13>. Users can define which set of regressors to use as base models from the 'caret' package, other packages, or custom functions.
Depends: R (>= 3.6.0)
License: GPL-3
Encoding: UTF-8
URL: https://github.com/enriquegit/ssr
BugReports: https://github.com/enriquegit/ssr/issues
LazyData: true
Imports: caret
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, tgp
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-19 12:20:47 UTC; enriqueg
Author: Enrique Garcia-Ceja [aut, cre] (<https://orcid.org/0000-0001-6864-8557>)
Maintainer: Enrique Garcia-Ceja <e.g.mx@ieee.org>
Repository: CRAN
Date/Publication: 2019-08-20 09:30:05 UTC

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New package rSPDE with initial version 0.4.6
Package: rSPDE
Type: Package
Date: 2019-08-19
Title: Rational Approximations of Fractional Stochastic Partial Differential Equations
Version: 0.4.6
Authors@R: person("David","Bolin", email = "davidbolin@gmail.com", role = c("cre", "aut"))
Maintainer: David Bolin <davidbolin@gmail.com>
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main reference for the methods is Bolin and Kirchner (2019) <arXiv:1711.04333>, which can be generated by the citation function in R.
Depends: R (>= 3.2.0), Matrix
Imports: stats
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, INLA (>= 0.0-1468840039), testthat, excursions
Additional_repositories: https://inla.r-inla-download.org/R/stable
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-19 10:55:52 UTC; davidbolin
Author: David Bolin [cre, aut]
Repository: CRAN
Date/Publication: 2019-08-20 09:10:02 UTC

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New package noisyCE2 with initial version 1.0.0
Package: noisyCE2
Type: Package
Title: Cross-Entropy Optimisation of Noisy Functions
Date: 2019-08-15
Version: 1.0.0
Authors@R: person(given = "Flavio", family = "Santi", role = c("cre", "aut"), email = "flavio.santi@univr.it", comment = c(ORCID = "0000-0002-2014-1981"))
Author: Flavio Santi [cre, aut] (<https://orcid.org/0000-0002-2014-1981>)
Maintainer: Flavio Santi <flavio.santi@univr.it>
URL: https://www.flaviosanti.it/software/noisyCE2
BugReports: https://github.com/f-santi/noisyCE2
Description: Cross-Entropy optimisation of unconstrained deterministic and noisy functions illustrated in Rubinstein and Kroese (2004, ISBN: 978-1-4419-1940-3) through a highly flexible and customisable function which allows user to define custom variable domains, sampling distributions, updating and smoothing rules, and stopping criteria. Several built-in methods and settings make the package very easy-to-use under standard optimisation problems.
Imports: magrittr
Suggests: coda
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-19 12:51:27 UTC; flavio
Repository: CRAN
Date/Publication: 2019-08-20 09:50:02 UTC

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Package monotonicity updated to version 1.3 with previous version 1.2 dated 2019-02-14

Title: Test for Monotonicity in Expected Asset Returns, Sorted by Portfolios
Description: Test for monotonicity in financial variables sorted by portfolios. It is conventional practice in empirical research to form portfolios of assets ranked by a certain sort variable. A t-test is then used to consider the mean return spread between the portfolios with the highest and lowest values of the sort variable. Yet comparing only the average returns on the top and bottom portfolios does not provide a sufficient way to test for a monotonic relation between expected returns and the sort variable. This package provides nonparametric tests for the full set of monotonic patterns by Patton, A. and Timmermann, A. (2010) <doi:10.1016/j.jfineco.2010.06.006> and compares the proposed results with extant alternatives such as t-tests, Bonferroni bounds, and multivariate inequality tests through empirical applications and simulations.
Author: Siegfried Köstlmeier [aut, cre, trl] (<https://orcid.org/0000-0002-7221-6981>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

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Package ggforce updated to version 0.3.1 with previous version 0.3.0 dated 2019-08-09

Title: Accelerating 'ggplot2'
Description: The aim of 'ggplot2' is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialised plots. 'ggforce' aims to be a collection of mainly new stats and geoms that fills this gap. All additional functionality is aimed to come through the official extension system so using 'ggforce' should be a stable experience.
Author: Thomas Lin Pedersen [cre, aut] (<https://orcid.org/0000-0002-5147-4711>), RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between ggforce versions 0.3.0 dated 2019-08-09 and 0.3.1 dated 2019-08-20

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Package crseEventStudy updated to version 1.2 with previous version 1.1 dated 2019-02-13

Title: A Robust and Powerful Test of Abnormal Stock Returns in Long-Horizon Event Studies
Description: Based on Dutta et al. (2018) <doi:10.1016/j.jempfin.2018.02.004>, this package provides their standardized test for abnormal returns in long-horizon event studies. The methods used improve the major weaknesses of size, power, and robustness of long-run statistical tests described in Kothari/Warner (2007) <doi:10.1016/B978-0-444-53265-7.50015-9>. Abnormal returns are weighted by their statistical precision (i.e., standard deviation), resulting in abnormal standardized returns. This procedure efficiently captures the heteroskedasticity problem. Clustering techniques following Cameron et al. (2011) <10.1198/jbes.2010.07136> are adopted for computing cross-sectional correlation robust standard errors. The statistical tests in this package therefore accounts for potential biases arising from returns' cross-sectional correlation, autocorrelation, and volatility clustering without power loss.
Author: Siegfried Köstlmeier [aut, cre] (<https://orcid.org/0000-0002-7221-6981>), Seppo Pynnonen [aut]
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

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Package birdring updated to version 1.4 with previous version 1.3 dated 2015-10-13

Title: Methods to Analyse Ring Re-Encounter Data
Description: R functions to read EURING data and analyse re-encounter data of birds marked by metal rings. For a tutorial, go to <http://www.tandfonline.com/doi/full/10.1080/03078698.2014.933053>.
Author: Fraenzi Korner-Nievergelt, Rob Robinson
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@vogelwarte.ch>

Diff between birdring versions 1.3 dated 2015-10-13 and 1.4 dated 2019-08-20

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Package readabs updated to version 0.4.1 with previous version 0.4.0 dated 2019-06-07

Title: Download and Tidy Time Series Data from the Australian Bureau of Statistics
Description: Downloads, imports, and tidies time series data from the Australian Bureau of Statistics <https://www.abs.gov.au/>.
Author: Matt Cowgill [aut, cre], Zoe Meers [aut], Jaron Lee [aut], David Diviny [ctb]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>

Diff between readabs versions 0.4.0 dated 2019-06-07 and 0.4.1 dated 2019-08-20

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Package pksensi updated to version 1.1.3 with previous version 1.1.2 dated 2019-06-30

Title: Global Sensitivity Analysis in Physiologically Based Kinetic Modeling
Description: Applying the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in pharmacokinetic (PK) models, especially the physiologically-based pharmacokinetic (PBPK) model with multivariate outputs. The package also provide some functions to check the sensitivity measures and its convergence of model parameters.
Author: Nan-Hung Hsieh [aut, cre] (<https://orcid.org/0000-0003-0163-2766>), Brad Reisfeld [aut], Weihsueh A. Chiu [aut] (<https://orcid.org/0000-0002-7575-2368>)
Maintainer: Nan-Hung Hsieh <nhsieh@cvm.tamu.edu>

Diff between pksensi versions 1.1.2 dated 2019-06-30 and 1.1.3 dated 2019-08-20

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Package photobiologyInOut updated to version 0.4.21 with previous version 0.4.20 dated 2019-06-15

Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files containing spectral data from spectrometers and their associated software, output from daylight simulation models in common use, and some spectral data repositories. As well as functions for exchange of spectral data with other R packages. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

Diff between photobiologyInOut versions 0.4.20 dated 2019-06-15 and 0.4.21 dated 2019-08-20

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Package paws.common updated to version 0.2.0 with previous version 0.1.2 dated 2019-08-08

Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.common versions 0.1.2 dated 2019-08-08 and 0.2.0 dated 2019-08-20

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Package icarus updated to version 0.3.1 with previous version 0.3.0 dated 2017-03-04

Title: Calibrates and Reweights Units in Samples
Description: Provides user-friendly tools for calibration in survey sampling. The package is production-oriented, and its interface is inspired by the famous popular macro 'Calmar' for SAS, so that 'Calmar' users can quickly get used to 'icarus'. In addition to calibration (with linear, raking and logit methods), 'icarus' features functions for calibration on tight bounds and penalized calibration.
Author: Antoine Rebecq [aut, cre]
Maintainer: Antoine Rebecq <antoine.rebecq@m4x.org>

Diff between icarus versions 0.3.0 dated 2017-03-04 and 0.3.1 dated 2019-08-20

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Package dst updated to version 1.4.0 with previous version 1.3.0 dated 2018-12-05

Title: Using the Theory of Belief Functions
Description: Using the Theory of Belief Functions for evidence calculus. Basic probability assignments, or mass functions, can be defined on the subsets of a set of possible values and combined. A mass function can be extended to a larger frame. Marginalization, i.e. reduction to a smaller frame can also be done. These features can be combined to analyze small belief networks and take into account situations where information cannot be satisfactorily described by probability distributions.
Author: Claude Boivin, Stat.ASSQ <webapp.cb@gmail.com>
Maintainer: Claude Boivin <webapp.cb@gmail.com>

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Mon, 19 Aug 2019

Package GDINA updated to version 2.7.3 with previous version 2.7.0 dated 2019-08-08

Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070> for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre <DOI:10.1177/0146621613479818> for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.
Author: Wenchao Ma [aut, cre, cph], Jimmy de la Torre [aut, cph], Miguel Sorrel [ctb], Zhehan Jiang [ctb]
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>

Diff between GDINA versions 2.7.0 dated 2019-08-08 and 2.7.3 dated 2019-08-19

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Package miceFast updated to version 0.5.1 with previous version 0.2.3 dated 2018-05-06

Title: Fast Imputations Using 'Rcpp' and 'Armadillo'
Description: Fast imputations under the object-oriented programming paradigm. There was used quantitative models with a closed-form solution. Thus package is based on linear algebra operations. 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. Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>

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Package sparsevar updated to version 0.0.11 with previous version 0.0.10 dated 2016-11-07

Title: Sparse VAR/VECM Models Estimation
Description: A wrapper for sparse VAR/VECM time series models estimation using penalties like ENET (Elastic Net), SCAD (Smoothly Clipped Absolute Deviation) and MCP (Minimax Concave Penalty). Based on the work of Sumanta Basu and George Michailidis <doi:10.1214/15-AOS1315>.
Author: Simone Vazzoler [aut, cre]
Maintainer: Simone Vazzoler <svazzole@gmail.com>

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Package rmapzen updated to version 0.4.2 with previous version 0.4.1 dated 2018-10-07

Title: Client for 'Mapzen' and Related Map APIs
Description: Provides an interface to 'Mapzen'-based APIs (including geocode.earth, Nextzen, and NYC GeoSearch) for geographic search and geocoding, isochrone calculation, and vector data to draw map tiles. See <https://mapzen.com/documentation/> for more information. The original Mapzen has gone out of business, but 'rmapzen' can be set up to work with any provider who implements the Mapzen API.
Author: Tarak Shah [aut, cre], Daniel Possenriede [ctb]
Maintainer: Tarak Shah <tarak.shah@gmail.com>

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Package BNPTSclust updated to version 2.0 with previous version 1.1 dated 2015-04-19

Title: A Bayesian Nonparametric Algorithm for Time Series Clustering
Description: Performs the algorithm for time series clustering described in Nieto-Barajas and Contreras-Cristan (2014).
Author: Martell-Juarez, D.A. & Nieto-Barajas, L.E.
Maintainer: David Alejandro Martell Juarez <alex91599@gmail.com>

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Package mlflow updated to version 1.2.0 with previous version 1.1.0 dated 2019-07-23

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>

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Package MGDrivE updated to version 1.1.0 with previous version 1.0.0 dated 2019-07-12

Title: Mosquito Gene Drive Explorer
Description: Provides a model designed to be a reliable testbed where various gene drive interventions for mosquito-borne diseases control. It is being developed to accommodate the use of various mosquito-specific gene drive systems within a population dynamics framework that allows migration of individuals between patches in landscape. Previous work developing the population dynamics can be found in Deredec et al. (2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>, and extensions to accommodate basic CRISPR homing dynamics in Marshall et al. (2017) <doi:10.1038/s41598-017-02744-7>.
Author: Héctor Manuel Sánchez Castellanos [aut, cre], Jared Bennett [aut], Sean Wu [aut], John M. Marshall [aut]
Maintainer: Héctor Manuel Sánchez Castellanos <sanchez.hmsc@berkeley.edu>

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Package rnassqs updated to version 0.5.0 with previous version 0.4.0 dated 2019-05-03

Title: Access the NASS 'Quick Stats' API
Description: Interface to access data via the United States Department of Agriculture's National Agricultural Statistical Service (NASS) 'Quick Stats' web API <https://quickstats.nass.usda.gov/api>. Convenience functions facilitate building queries based on available parameters and valid parameter values.
Author: Nicholas Potter [aut, cre], Jonathan Adams [ctb], Joseph Stachelek [ctb], Julia Piaskowski [ctb], Adam Sparks [rev], Neal Richardson [ctb, rev]
Maintainer: Nicholas Potter <potter.nicholas@gmail.com>

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Package pangaear updated to version 0.8.0 with previous version 0.6.0 dated 2018-01-03

Title: Client for the 'Pangaea' Database
Description: Tools to interact with the 'Pangaea' Database (<https://www.pangaea.de>), including functions for searching for data, fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH' service.
Author: Scott Chamberlain [aut, cre], Kara Woo [aut], Andrew MacDonald [aut], Naupaka Zimmerman [aut], Gavin Simpson [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package HiCglmi updated to version 1.4 with previous version 1.3 dated 2018-04-18

Title: Probing Factor-Dependent Long-Range Contacts using Regression with Higher-Order Interaction Terms
Description: We propose a generalized linear regression with higher-order interaction terms to assess the influences of genomic features such as DNA-binding proteins and functional elements on long-range contacts from Hi-C experiments.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>

Diff between HiCglmi versions 1.3 dated 2018-04-18 and 1.4 dated 2019-08-19

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Package ari updated to version 0.3.2 with previous version 0.3.1 dated 2019-07-13

Title: Automated R Instructor
Description: Create videos from 'R Markdown' documents, or images and audio files. These images can come from image files or HTML slides, and the audio files can be provided by the user or computer voice narration can be created using 'Amazon Polly'. The purpose of this package is to allow users to create accessible, translatable, and reproducible lecture videos. See <https://aws.amazon.com/polly/> for more information.
Author: Sean Kross [aut, cre], John Muschelli [ctb]
Maintainer: Sean Kross <sean@seankross.com>

Diff between ari versions 0.3.1 dated 2019-07-13 and 0.3.2 dated 2019-08-19

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Package APfun updated to version 0.1.4 with previous version 0.1.3 dated 2018-04-03

Title: Geo-Processing Helper Functions
Description: Helper tools for facilitating basic geo-processing tasks, such as reading/writing Shapefiles, merging polygons or generating terrain contours.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>

Diff between APfun versions 0.1.3 dated 2018-04-03 and 0.1.4 dated 2019-08-19

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Package uroot updated to version 2.1-0 with previous version 2.0-11 dated 2019-08-19

Title: Unit Root Tests for Seasonal Time Series
Description: Seasonal unit roots and seasonal stability tests. P-values based on response surface regressions are available for both tests. P-values based on bootstrap are available for seasonal unit root tests.
Author: Javier López-de-Lacalle [aut], Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package umap updated to version 0.2.3 with previous version 0.2.2.0 dated 2019-05-13

Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique for dimension reduction. The algorithm was described by McInnes and Healy (2018) in <arXiv:1802.03426>. This package provides an interface for two implementations. One is written from scratch, including components for nearest-neighbor search and for embedding. The second implementation is a wrapper for 'python' package 'umap-learn' (requires separate installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>

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Package tidyLPA updated to version 1.0.4 with previous version 1.0.3 dated 2019-07-30

Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software
Description: An interface to the 'mclust' package to easily carry out latent profile analysis ("LPA"). Provides functionality to estimate commonly-specified models. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Also has functions to interface to the commercial 'MPlus' software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre], Caspar van Lissa [aut], Jennifer A Schmidt [ctb], Patrick N Beymer [ctb], Daniel Anderson [ctb], Matthew J. Schell [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>

Diff between tidyLPA versions 1.0.3 dated 2019-07-30 and 1.0.4 dated 2019-08-19

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Package smooth updated to version 2.5.3 with previous version 2.5.2 dated 2019-07-25

Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting. The package includes Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>), SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>), Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>), Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>), Vector Exponential Smoothing (de Silva et al., 2010, <doi: 10.1177/1471082X0901000401>) in state space forms, several simulation functions and intermittent demand state space models. It also allows dealing with intermittent demand based on the iETS framework (Svetunkov & Boylan, 2017, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>

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Package sharpData updated to version 1.2 with previous version 1.1 dated 2019-08-02

Title: Data Sharpening
Description: Functions and data sets inspired by data sharpening - data perturbation to achieve improved performance in nonparametric estimation, as described in Choi, E., Hall, P. and Rousson, V. (2000) <doi:10.1214/aos/1015957396>. Capabilities for enhanced local linear regression function and derivative estimation are included, as well as an asymptotically correct iterated data sharpening estimator for any degree of local polynomial regression estimation. A cross-validation-based bandwidth selector is included which, in concert with the iterated sharpener, will often provide superior performance, according to a median integrated squared error criterion. Sample data sets are provided to illustrate function usage.
Author: W.J. Braun
Maintainer: W.J. Braun <john.braun@ubc.ca>

Diff between sharpData versions 1.1 dated 2019-08-02 and 1.2 dated 2019-08-19

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Package RWsearch updated to version 4.6.2 with previous version 4.6 dated 2019-05-29

Title: Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One Download
Description: Search by keywords in R packages, task views, CRAN, the web and display the results in console, txt, html or pdf pages. Download the whole documentation (html index, pdf manual, vignettes, source code, etc) with a single instruction. Visualize the package dependencies. Several functions for task view maintenance and exploration of CRAN archive. Quick links to more than 70 web search engines. Lazy evaluation of non-standard content is available throughout the package and eases the use of many functions.
Author: Patrice Kiener [aut, cre] (<https://orcid.org/0000-0002-0505-9920>)
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>

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New package Rpoet with initial version 1.1.0
Package: Rpoet
Type: Package
Title: 'PoetryDB' API Wrapper
Version: 1.1.0
Author: Aaron Schlegel
Maintainer: Aaron Schlegel <aaron@aaronschlegel.me>
Description: Wrapper for the 'PoetryDB' API <http://poetrydb.org> that allows for interaction and data extraction from the database in an R interface. The 'PoetryDB' API is a database of poetry and poets implemented with 'MongoDB' to enable developers and poets to easily access one of the most comprehensive poetry databases currently available.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Suggests: testthat, knitr, rmarkdown, jsonlite, httr, stringr
NeedsCompilation: no
Packaged: 2019-08-19 18:01:10 UTC; aaronschlegel
Repository: CRAN
Date/Publication: 2019-08-19 18:30:06 UTC

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Package rgl updated to version 0.100.30 with previous version 0.100.26 dated 2019-07-08

Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>

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Package handlr updated to version 0.2.0 with previous version 0.1.0 dated 2019-02-27

Title: Convert Among Citation Formats
Description: Converts among many citation formats, including 'BibTeX', 'Citeproc', 'Codemeta', 'RDF XML', 'RIS', and 'Schema.org'. A low level 'R6' class is provided, as well as stand-alone functions for each citation format for both read and write.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>

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Package eSDM updated to version 0.3.0 with previous version 0.2.1 dated 2019-07-26

Title: Ensemble Tool for Predictions from Species Distribution Models
Description: A tool which allows users to create and evaluate ensembles of species distribution model (SDM) predictions. Functionality is offered through R functions or a GUI (R Shiny app). This tool can assist users in identifying spatial uncertainties and making informed conservation and management decisions. The package is further described in Woodman et al. (in press - contact author for paper).
Author: Sam Woodman [aut, cre]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>

Diff between eSDM versions 0.2.1 dated 2019-07-26 and 0.3.0 dated 2019-08-19

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Package envDocument updated to version 2.4.1 with previous version 2.4.0 dated 2017-09-19

Title: Document the R Working Environment
Description: Prints out information about the R working environment (system, R version,loaded and attached packages and versions) from a single function "env_doc()". Optionally adds information on git repository, tags, commits and remotes (if available).
Author: Donald Jackson [aut, cre]
Maintainer: Donald Jackson <donald.jackson@bms.com>

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Package cytometree updated to version 2.0.0 with previous version 1.3.0 dated 2019-01-12

Title: Automated Cytometry Gating and Annotation
Description: Given the hypothesis of a bi-modal distribution of cells for each marker, the algorithm constructs a binary tree, the nodes of which are subpopulations of cells. At each node, observed cells and markers are modeled by both a family of normal distributions and a family of bi-modal normal mixture distributions. Splitting is done according to a normalized difference of AIC between the two families.
Author: Chariff Alkhassim, Boris Hejblum, Anthony Devaux, Van Hung Huynh Tran
Maintainer: Boris Hejblum <boris.hejblum@u-bordeaux.fr>

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Package shinybusy updated to version 0.1.3 with previous version 0.1.2 dated 2019-05-07

Title: Busy Indicator for 'Shiny' Applications
Description: Add a global indicator (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy.
Author: Fanny Meyer [aut], Victor Perrier [aut, cre], Silex Technologies [fnd] (https://www.silex-ip.com), Tobias Ahlin [cph] (spin.css), Chris Antonellis [cph] (freezeframe.js), Jacobo Tabernero [cph] (nanobar.js)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package PLmixed updated to version 0.1.4 with previous version 0.1.3 dated 2018-05-02

Title: Estimate (Generalized) Linear Mixed Models with Factor Structures
Description: Utilizes the 'lme4' and 'optimx' packages (previously the optim() function from 'stats') to estimate (generalized) linear mixed models (GLMM) with factor structures using a profile likelihood approach, as outlined in Jeon and Rabe-Hesketh (2012) <doi:10.3102/1076998611417628> and Rockwood and Jeon (2019) <doi:10.1080/00273171.2018.1516541>. Factor analysis and item response models can be extended to allow for an arbitrary number of nested and crossed random effects, making it useful for multilevel and cross-classified models.
Author: Minjeong Jeon [aut], Nicholas Rockwood [aut, cre]
Maintainer: Nicholas Rockwood <nrockwood@llu.edu>

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Package outliertree updated to version 1.0.1 with previous version 1.0 dated 2019-07-31

Title: Explainable Outlier Detection Through Decision Tree Conditioning
Description: Will try to fit decision trees that try to "predict" values for each column based on the values of each other column. Along the way, each time a split is evaluated, it will take the observations that fall into each branch as a homogeneous cluster in which it will search for outliers in the 1-d distribution of the column being predicted. Outliers are determined according to confidence intervals on this 1-d distribution, and need to have a large gap with respect to the next observation in sorted order to be flagged as outliers. Since outliers are searched for in a decision tree branch, it will know the conditions that make it a rare observation compared to others that meet the same conditions, and the conditions will always be correlated with the target variable (as it's being predicted from them). Loosely based on the 'GritBot' <https://www.rulequest.com/gritbot-info.html> software.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package onewaytests updated to version 2.4 with previous version 2.3 dated 2019-05-17

Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs; one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second order test, Kruskal-Wallis test, Scott-Smith test, Box F test and Johansen F test, Generalized tests equivalent to Parametric Bootstrap and Fiducial tests. The package performs pairwise comparisons and graphical approaches. Also, the package includes Student's t test, Welch's t test and Mann-Whitney U test for two samples. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut], Sam Weerahandi [ctb], Malwane Ananda [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>

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Package multiDimBio updated to version 1.2.0 with previous version 1.1.1 dated 2016-12-16

Title: Multivariate Analysis and Visualization for Biological Data
Description: Code to support a systems biology research program from inception through publication. The methods focus on dimension reduction approaches to detect patterns in complex, multivariate experimental data and places an emphasis on informative visualizations. The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques. As a result, we encourage suggested additions to the package, both methodological and graphical.
Author: Samuel V. Scarpino
Maintainer: Samuel V. Scarpino <scarpino@utexas.edu>

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Package MetricsWeighted updated to version 0.2.0 with previous version 0.1.0 dated 2019-07-28

Title: Weighted Metrics, Scoring Functions and Performance Measures for Machine Learning
Description: Provides weighted versions of several metrics, scoring functions and performance measures used in machine learning, including average unit deviances of the Bernoulli, Tweedie, Poisson, and Gamma distributions, see Jorgensen B. (1997, ISBN: 978-0412997112). The package also contains a weighted version of generalized R-squared, see e.g. Cohen, J. et al. (2002, ISBN: 978-0805822236). Furthermore, 'dplyr' chains are supported.
Author: Michael Mayer [aut, cre, cph], Christian Lorentzen [rev]
Maintainer: Michael Mayer <mayermichael79@gmail.com>

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Package MEtest updated to version 1.1 with previous version 1.0 dated 2019-04-25

Title: A Homogeneity Test under the Presence of Measurement Errors
Description: Provides a function me.test() to test equality of distributions when observations are subject to measurement errors.
Author: DongHyuk Lee, Samiran Sinha
Maintainer: DongHyuk Lee <leedhyuk@gmail.com>

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