Fri, 25 May 2018

New package mQTL with initial version 1.0
Package: mQTL
Type: Package
Title: Metabolomic Quantitative Trait Locus Mapping
Version: 1.0
Date: 2013-09-18
Author: Lyamine Hedjazi and Jean-Baptiste Cazier
Maintainer: Lyamine Hedjazi <l.hedjazi@fondation-ican.com>
Description: mQTL provides a complete QTL analysis pipeline for metabolomic data. Distinctive features include normalisation using PQN approach, peak alignment using RSPA approach, dimensionality reduction using SRV approach and finally QTL mapping using R/qtl package.
License: GPL
LazyLoad: yes
LazyData: yes
NeedsCompilation: yes
Repository: CRAN
Depends: R (>= 2.15.0), qtl, MASS, outliers
Packaged: 2013-10-21 09:31:01 UTC; Utilisateur
Date/Publication: 2013-10-21 12:44:23

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Package kohonen updated to version 3.0.5 with previous version 3.0.4 dated 2017-08-28

Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens and Johannes Kruisselbrink
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>

Diff between kohonen versions 3.0.4 dated 2017-08-28 and 3.0.5 dated 2018-05-25

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Package aws.s3 updated to version 0.3.12 with previous version 0.3.11 dated 2018-04-11

Title: 'AWS S3' Client Package
Description: A simple client package for the Amazon Web Services ('AWS') Simple Storage Service ('S3') 'REST' 'API' <https://aws.amazon.com/s3/>.
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>), Boettiger Carl [ctb], Andrew Martin [ctb], Mark Thompson [ctb], Tyler Hunt [ctb], Steven Akins [ctb], Bao Nguyen [ctb], Thierry Onkelinx [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

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Package googleway updated to version 2.7.0 with previous version 2.6 dated 2018-04-29

Title: Accesses Google Maps APIs to Retrieve Data and Plot Maps
Description: Provides a mechanism to plot a 'Google Map' from 'R' and overlay it with shapes and markers. Also provides access to 'Google Maps' APIs, including places, directions, roads, distances, geocoding, elevation and timezone.
Author: David Cooley [aut, cre], Paulo Barcelos [ctb] (Author of c++ decode_pl), Rstudio [ctb] (Functions written for the Leaflet pacakge)
Maintainer: David Cooley <dcooley@symbolix.com.au>

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Package googlePolylines updated to version 0.6.1 with previous version 0.6.0 dated 2018-04-26

Title: Encoding Coordinates into 'Google' Polylines
Description: Encodes simple feature ('sf') objects and coordinates, and decodes polylines using the 'Google' polyline encoding algorithm (<https://developers.google.com/maps/documentation/utilities/polylinealgorithm>).
Author: David Cooley [aut, cre], Paulo Barcelos [ctb] (Author of c++ decode_polyline)
Maintainer: David Cooley <dcooley@symbolix.com.au>

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Package mbest updated to version 0.6 with previous version 0.5 dated 2016-03-08

Title: Moment-Based Estimation for Hierarchical Models
Description: Fast moment-based hierarchical model fitting. Implements methods from the papers "Fast Moment-Based Estimation for Hierarchical Models," by Perry (2017) and "Fitting a Deeply Nested Hierarchical Model to a Large Book Review Dataset Using a Moment-Based Estimator," by Zhang, Schmaus, and Perry (2018).
Author: Patrick O. Perry [aut, cre], Timothy Sweetser [ctb], Kyle Schmaus [ctb], Ningshan Zhang [aut, ctb]
Maintainer: Patrick O. Perry <patperry@gmail.com>

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Package greybox updated to version 0.2.2 with previous version 0.2.1 dated 2018-05-01

Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its application to forecasting. The main scope of the package is in variables selection and models specification for cases of time series data. This includes promotional modelling, selection between different dynamic regressions with non-standard distributions of errors, selection based on cross validation, solutions to the fat regressions model problem and more. Models developed in the package are tailored specifically for forecasting purposes. So as a results there are several methods that allow producing forecasts from these models and visualising them.
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 glm2 updated to version 1.2 with previous version 1.1.3 dated 2017-10-24

Title: Fitting Generalized Linear Models
Description: Fits generalized linear models using the same model specification as glm in the stats package, but with a modified default fitting method that provides greater stability for models that may fail to converge using glm.
Author: Ian Marschner [aut] (using code from glm and glm.fit in the stats package), Mark W. Donoghoe [cre, ctb]
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>

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Package dtwSat updated to version 0.2.4 with previous version 0.2.3 dated 2017-05-16

Title: Time-Weighted Dynamic Time Warping for Satellite Image Time Series Analysis
Description: Provides an implementation of the Time-Weighted Dynamic Time Warping (TWDTW) method for land cover mapping using satellite image time series. TWDTW is based on the Dynamic Time Warping technique and has achieved high accuracy for land cover classification using satellite data. The method is based on comparing unclassified satellite image time series with a set of known temporal patterns (e.g. phenological cycles associated with the vegetation). Using 'dtwSat' the user can build temporal patterns for land cover types, apply the TWDTW analysis for satellite datasets, visualize the results of the time series analysis, produce land cover maps, create temporal plots for land cover change, and compute accuracy assessment metrics.
Author: Victor Maus [aut, cre] (<https://orcid.org/0000-0002-7385-4723>), Marius Appel [ctb], Toni Giorgino [ctb]
Maintainer: Victor Maus <vwmaus1@gmail.com>

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Package bigsplines updated to version 1.1-1 with previous version 1.1-0 dated 2017-02-03

Title: Smoothing Splines for Large Samples
Description: Fits smoothing spline regression models using scalable algorithms designed for large samples. Seven marginal spline types are supported: linear, cubic, different cubic, cubic periodic, cubic thin-plate, ordinal, and nominal. Random effects and parametric effects are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>

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Package bigRR (with last version 1.3-10) was removed from CRAN

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2014-08-23 1.3-10

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

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2013-10-21 1.0

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Package ldlasso (with last version 3.2) was removed from CRAN

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2013-01-03 3.2
2011-02-15 3.1

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Package RepeatABEL (with last version 1.1) was removed from CRAN

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2016-08-19 1.1
2015-11-24 1.0

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

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2017-11-20 0.1.1
2017-07-25 0.1.0

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Package Haplin (with last version 6.2.1) was removed from CRAN

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2017-10-18 6.2.1
2017-02-28 6.2.0
2016-05-26 6.0.1
2016-05-25 6.0
2015-05-15 5.5
2013-05-23 5.3
2013-05-02 5.2
2013-03-18 5.0.2
2013-03-08 5.0.1
2013-02-06 5.0
2012-03-16 4.1
2012-01-27 4.0
2010-05-26 3.5
2010-01-10 3.0.2
2009-05-27 3.0.1

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Package GENEAclassify (with last version 1.4.11) was removed from CRAN

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2018-03-29 1.4.11
2018-02-13 1.4.9
2018-01-16 1.4.8
2018-01-08 1.4.7
2017-08-30 1.4.5

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Package GENEAread (with last version 1.1.1) was removed from CRAN

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2013-04-23 1.1.1
2012-06-28 1.0

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Package GENEAsphere (with last version 1.4) was removed from CRAN

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2017-12-13 1.4

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Package DatABEL (with last version 0.9-6) was removed from CRAN

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2015-03-31 0.9-6
2014-09-11 0.9-5
2014-07-27 0.9-4.1
2013-03-12 0.9-4
2010-10-20 0.9-2
2010-08-07 0.9-0
2010-06-22 0.1-6
2010-06-04 0.1-4
2010-05-11 0.1-2
2010-05-07 0.1-0
2010-04-04 0.0-7
2010-03-07 0.0-6

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Package GenABEL (with last version 1.8-0) was removed from CRAN

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2013-12-27 1.8-0
2013-05-16 1.7-6
2013-02-23 1.7-4
2013-01-09 1.7-3
2012-09-17 1.7-2
2011-12-21 1.7-0
2011-08-30 1.6-8
2011-08-30 1.6-9
2011-05-18 1.6-7
2011-05-02 1.6-6
2011-02-08 1.6-5
2010-08-31 1.6-4
2010-08-08 1.6-2
2010-06-22 1.6-0
2010-06-11 1.5-8
2010-05-30 1.5-6
2010-05-11 1.5-4
2010-05-07 1.5-2
2010-04-04 1.5-1
2009-09-03 1.4-4
2009-07-23 1.4-3
2009-01-29 1.4-2
2008-11-27 1.4-1
2008-08-22 1.4-0
2008-05-07 1.3-9
2008-04-17 1.3-7
2008-02-17 1.3-5
2007-11-07 1.3-1
2007-09-04 1.2-8
2007-08-07 1.2-6
2007-07-10 1.2-4
2007-03-21 1.1-8

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Package reReg updated to version 1.1-3 with previous version 1.1-2 dated 2018-04-17

Title: Recurrent Event Regression
Description: A collection of regression models for recurrent event process and failure time. Available methods include these from Xu et al. (2017) <doi:10.1080/01621459.2016.1173557>, Lin et al. (2000) <doi:10.1111/1467-9868.00259>, Wang et al. (2001) <doi:10.1198/016214501753209031>, Ghosh and Lin (2003) <doi:10.1111/j.0006-341X.2003.00102.x>, and Huang and Wang (2004) <doi:10.1198/016214504000001033>.
Author: Sy Han (Steven) Chiou
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>

Diff between reReg versions 1.1-2 dated 2018-04-17 and 1.1-3 dated 2018-05-25

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More information about reReg at CRAN
Permanent link

Package phyloclim updated to version 0.9.5 with previous version 0.9-4 dated 2013-07-13

Title: Integrating Phylogenetics and Climatic Niche Modeling
Description: Implements some methods in phyloclimatic modeling: estimation of ancestral climatic niches, age-range-correlation, niche equivalency test and background-similarity test.
Author: Christoph Heibl, Clement Calenge (\code{import.ascii})
Maintainer: Christoph Heibl <christoph.heibl@gmx.net>

Diff between phyloclim versions 0.9-4 dated 2013-07-13 and 0.9.5 dated 2018-05-25

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More information about phyloclim at CRAN
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Package ppitables updated to version 0.2.0 with previous version 0.1.2 dated 2018-03-05

Title: Lookup Tables to Generate Poverty Likelihoods and Rates using the Poverty Probability Index (PPI)
Description: The Poverty Probability Index (PPI) is a poverty measurement tool for organizations and businesses with a mission to serve the poor. The PPI is statistically-sound, yet simple to use: the answers to 10 questions about a household’s characteristics and asset ownership are scored to compute the likelihood that the household is living below the poverty line – or above by only a narrow margin. This package contains country-specific lookup data tables used as reference to determine the poverty likelihood of a household based on their score from the country-specific PPI questionnaire. These lookup tables have been extracted from documentation of the PPI found at <https://www.povertyindex.org> and managed by Innovations for Poverty Action <https://www.poverty-action.org>.
Author: Ernest Guevarra [aut, cre] (<https://orcid.org/0000-0002-4887-4415>)
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>

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Thu, 24 May 2018

Package WVPlots updated to version 1.0.0 with previous version 0.3.2 dated 2018-05-08

Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'. Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions, conditioned scatter plot with marginal densities, box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package edgarWebR updated to version 1.0.0 with previous version 0.3.1 dated 2018-02-13

Title: SEC Filings Access
Description: A set of methods to access and parse live filing information from the U.S. Securities and Exchange Commission (SEC - <https://sec.gov>) including company and fund filings along with all associated metadata.
Author: Micah J Waldstein [aut, cre]
Maintainer: Micah J Waldstein <micah@waldste.in>

Diff between edgarWebR versions 0.3.1 dated 2018-02-13 and 1.0.0 dated 2018-05-24

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Package tclust updated to version 1.4-1 with previous version 1.3-1 dated 2017-08-24

Title: Robust Trimmed Clustering
Description: Provides functions for robust trimmed clustering. The methods are described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>, Fritz et al. (2012) <doi:10.18637/jss.v047.i12> and others.
Author: Agustin Mayo Iscar, Luis Angel Garcia Escudero, Heinrich Fritz
Maintainer: Valentin Todorov <valentin.todorov@chello.at>

Diff between tclust versions 1.3-1 dated 2017-08-24 and 1.4-1 dated 2018-05-24

 ChangeLog                |   13 
 DESCRIPTION              |   11 
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 NAMESPACE                |   30 -
 R/print.tclust.R         |   22 
 build/vignette.rds       |binary
 inst/doc/tclust.R        |   16 
 inst/doc/tclust.pdf      |binary
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 man/DiscrFact.Rd         |    7 
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 src/R_package.cpp        |    2 
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 src/clust.h              |    2 
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 src/tkmeans.cpp          |   29 +
 src/tkmeans.h            |    6 
 tests/ttclust.R          |   22 
 tests/ttclust.Rout.save  | 1155 +++++++++++++++++++++++------------------------
 vignettes/tclust.bib     |   42 -
 vignettes/tclust.rnw     |   16 
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Package h2o updated to version 3.18.0.11 with previous version 3.18.0.8 dated 2018-05-02

Title: R Interface for 'H2O'
Description: R scripting functionality for 'H2O', the open source math engine for big data that computes parallel distributed machine learning algorithms such as generalized linear models, gradient boosting machines, random forests, and neural networks (deep learning) within various cluster environments.
Author: Tom Kraljevic [aut, cre], H2O.ai [cph]
Maintainer: Tom Kraljevic <tomk@0xdata.com>

Diff between h2o versions 3.18.0.8 dated 2018-05-02 and 3.18.0.11 dated 2018-05-24

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Package MVar.pt updated to version 2.0.1 with previous version 2.0.0 dated 2018-05-01

Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise de cluster hierarquico e nao hierarquico, regressao linear, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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Package rscopus updated to version 0.5.11 with previous version 0.5.3 dated 2017-10-11

Title: Scopus Database 'API' Interface
Description: Uses Elsevier 'Scopus' 'API' <https://dev.elsevier.com/sc_apis.html> to download information about authors and their citations.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package neurohcp updated to version 0.8.1 with previous version 0.8.0 dated 2018-04-11

Title: Human 'Connectome' Project Interface
Description: Downloads and reads data from Human 'Connectome' Project <https://db.humanconnectome.org> using Amazon Web Services ('AWS') 'S3' buckets.
Author: John Muschelli [aut, cre], Adi Gherman [ctb]
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package ncf updated to version 1.2-5 with previous version 1.2-4 dated 2018-05-06

Title: Spatial Covariance Functions
Description: R functions for analyzing spatial (cross-)covariance: the nonparametric (cross-)covariance function, the spline correlogram, the nonparametric phase coherence function, local indicators of spatial association (LISA), (Mantel) correlogram, (Partial) Mantel test.
Author: Ottar N. Bjornstad [aut, cre], Jun Cai [ctb]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>

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Package labelled updated to version 1.1.0 with previous version 1.0.1 dated 2017-12-19

Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS' or 'Stata' with 'haven' or 'foreign'.
Author: Joseph Larmarange [aut, cre], Daniel Ludecke [ctb], Hadley Wickham [ctb], Bojanowski Michał [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>

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Package knitrBootstrap updated to version 1.0.2 with previous version 1.0.1 dated 2017-07-19

Title: 'knitr' Bootstrap Framework
Description: A framework to create Bootstrap <http://getbootstrap.com/> HTML reports from 'knitr' 'rmarkdown'.
Author: Jim Hester
Maintainer: Jim Hester <james.f.hester@gmail.com>

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Package event updated to version 1.1.1 with previous version 1.1.0 dated 2016-12-06

Title: Event History Procedures and Models
Description: Functions for setting up and analyzing event history data.
Author: Bruce Swihart [cre, aut], Jim Lindsey [aut] (Jim created this package, Bruce is maintaining the CRAN version)
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>

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Package utf8 updated to version 1.1.4 with previous version 1.1.3 dated 2018-01-03

Title: Unicode Text Processing
Description: Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.
Author: Patrick O. Perry [aut, cph, cre], Unicode, Inc. [cph, dtc] (Unicode Character Database)
Maintainer: Patrick O. Perry <patperry@gmail.com>

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Package locpol updated to version 0.7-0 with previous version 0.6-0 dated 2012-10-25

Title: Kernel Local Polynomial Regression
Description: Computes local polynomial estimators for the regression and also density. It comprises several different utilities to handle kernel estimators.
Author: Jorge Luis Ojeda Cabrera <jojeda@unizar.es>
Maintainer: Jorge Luis Ojeda Cabrera <jojeda@unizar.es>

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Package dfmta updated to version 1.7-0 with previous version 1.6-2 dated 2018-01-10

Title: Phase I/II Adaptive Dose-Finding Design for MTA
Description: Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper "Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization", Riviere Marie-Karelle et al. (2016) <doi:10.1177/0962280216631763>.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Jacques-Henri Jourdan <jacques-henri.jourdan@normalesup.org>

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Package dfcomb updated to version 2.5-0 with previous version 2.4-2 dated 2018-01-10

Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination studies. Several methods are proposed depending on the type of combinations: (1) the combination of two cytotoxic agents, and (2) combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Jacques-Henri Jourdan <jacques-henri.jourdan@normalesup.org>

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Package BETS updated to version 0.4.2 with previous version 0.3.6 dated 2018-04-02

Title: Brazilian Economic Time Series
Description: It provides access to and information about the most important Brazilian economic time series - from the Getulio Vargas Foundation <http://portal.fgv.br/en>, the Central Bank of Brazil <http://www.bcb.gov.br> and the Brazilian Institute of Geography and Statistics <http://www.ibge.gov.br>. It also presents tools for managing, analysing (e.g. generating dynamic reports with a complete analysis of a series) and exporting these time series.
Author: Pedro Costa Ferreira [aut], Talitha Speranza [aut, cre], Jonatha Costa [aut], Fernando Teixeira [ctb], Daiane Marcolino [ctb]
Maintainer: Talitha Speranza <talitha.speranza@fgv.br>

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Package mfGARCH updated to version 0.1.3 with previous version 0.1.2 dated 2018-02-19

Title: Mixed-Frequency GARCH Models
Description: Estimating GARCH-MIDAS (MIxed-DAta-Sampling) models (Engle, Ghysels, Sohn, 2013, <doi:10.1162/REST_a_00300>) and related statistical inference, accompanying the paper "Two are better than one: volatility forecasting using multiplicative component GARCH models" by Conrad and Kleen (2018, Working Paper, <doi:10.2139/ssrn.2752354>). The GARCH-MIDAS model decomposes the conditional variance of (daily) stock returns into a short- and long-term component, where the latter may depend on an exogenous covariate sampled at a lower frequency.
Author: Onno Kleen [aut, cre]
Maintainer: Onno Kleen <r@onnokleen.de>

Diff between mfGARCH versions 0.1.2 dated 2018-02-19 and 0.1.3 dated 2018-05-24

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Package ALEPlot updated to version 1.1 with previous version 1.0 dated 2017-11-13

Title: Accumulated Local Effects (ALE) Plots and Partial Dependence (PD) Plots
Description: Visualizes the main effects of individual predictor variables and their second-order interaction effects in black-box supervised learning models. The package creates either Accumulated Local Effects (ALE) plots and/or Partial Dependence (PD) plots, given a fitted supervised learning model.
Author: Dan Apley
Maintainer: Dan Apley <apley@northwestern.edu>

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Package Rdpack updated to version 0.8-0 with previous version 0.7-0 dated 2018-03-26

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

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Package uwIntroStats (with last version 0.0.5) was removed from CRAN

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

2018-04-03 0.0.5
2017-11-19 0.0.4
2016-09-22 0.0.3

Permanent link
Package tccox (with last version 0.1.0) was removed from CRAN

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

2017-12-03 0.1.0

Permanent link
Package gamlss.spatial updated to version 2.0.0 with previous version 1.3.5 dated 2018-02-17

Title: Spatial Terms in Generalized Additive Models for Location Scale and Shape Models
Description: It allows us to fit Gaussian Markov Random Field within the Generalized Additive Models for Location Scale and Shape algorithms.
Author: Fernanda De Bastiani [aut, cre, cph], Mikis Stasinopoulos [aut], Robert Rigby [aut]
Maintainer: Fernanda De Bastiani <fernandadebastiani@gmail.com>

Diff between gamlss.spatial versions 1.3.5 dated 2018-02-17 and 2.0.0 dated 2018-05-24

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New package sklarsomega with initial version 1.0
Package: sklarsomega
Type: Package
Title: Measuring Agreement Using Sklar's Omega Coefficient
Version: 1.0
Date: 2018-05-22
Author: John Hughes <jphughesjr@gmail.com>
Maintainer: John Hughes <jphughesjr@gmail.com>
Imports: hash, LaplacesDemon, Matrix, numDeriv, spam
Suggests: lattice, parallel, pbapply
Description: Provides tools for applying Sklar's Omega (Hughes, 2018) <arXiv:1706.04651> methodology to nominal, ordinal, interval, or ratio scores. The framework can accommodate any number of units, any number of coders, and missingness; and can be used to measure agreement with a gold standard, intra-coder agreement, and/or inter-coder agreement.
License: GPL (>= 2)
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2018-05-22 16:17:46 UTC; jphughesjr
Repository: CRAN
Date/Publication: 2018-05-24 13:10:46 UTC

More information about sklarsomega at CRAN
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Package PCPS updated to version 1.0.6 with previous version 1.0.5 dated 2018-04-09

Title: Principal Coordinates of Phylogenetic Structure
Description: Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).
Author: Vanderlei Julio Debastiani
Maintainer: Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>

Diff between PCPS versions 1.0.5 dated 2018-04-09 and 1.0.6 dated 2018-05-24

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New package MMPPsampler with initial version 1.0
Package: MMPPsampler
Type: Package
Title: Efficient Gibbs-Sampler for Markov-Modulated-Poisson-Processes
Version: 1.0
Date: 2018-05-15
Author: Henry Clausen
Maintainer: Henry Clausen <henry.clausen@ed.ac.uk>
Description: Efficient implementation of the Gibbs sampler by Fearnheard and Sherlock (2006) <DOI:10.1111/j.1467-9868.2006.00566.x> for the Markov modulated Poisson process that uses 'C++' via the 'Rcpp' interface. Fearnheard and Sherlock proposed an exact Gibbs-sampler for performing Bayesian inference on Markov Modulated Poisson processes. This package is an efficient implementation of their proposal for binned data. Furthermore, the package contains an efficient implementation of the hierarchical MMPP framework, proposed by Clausen, Adams, and Briers (2017) <https://github.com/hc2116/MMPPsampler/blob/master/Master_thesis_Henry.pdf>, that is tailored towards inference on network flow arrival data and extends Fearnheard and Sherlock's Gibbs sampler. Both frameworks harvests greatly from routines that are optimised for this specific problem in order to remain scalable and efficient for large amounts of input data. These optimised routines include matrix exponentiation and multiplication, and endpoint-conditioned Markov process sampling. Both implementations require an input vector that contains the binned observations, the length of a binning interval, the number of states of the hidden Markov process, and lose prior hyperparameters. As a return, the user receives the desired number of sample trajectories of the hidden Markov process as well as the likelihood of each trajectory.
License: GPL-3
SystemRequirements: C++11
Imports: Rcpp (>= 0.12.16), MASS (>= 7.3-48), gtools (>= 3.5.0), ggplot2(>= 2.2.1), cowplot(>= 0.9.2)
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/hc2116/MMPPsampler
NeedsCompilation: yes
Packaged: 2018-05-22 14:23:14 UTC; henryclausen
Repository: CRAN
Date/Publication: 2018-05-24 13:07:43 UTC

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New package epiphy with initial version 0.3.4
Package: epiphy
Type: Package
Title: Analysis of Plant Disease Epidemics
Version: 0.3.4
Authors@R: c( person("Christophe", "Gigot", email = "ch.gigot@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1748-2902")))
Description: A toolbox to make it easy to analyze plant disease epidemics. It provides a common framework for plant disease intensity data recorded over time and/or space. Implemented statistical methods are currently mainly focused on spatial pattern analysis (e.g., aggregation indices, Taylor and binary power laws, distribution fitting, SADIE and mapcomp methods). See Madden LV, Hughes G, van den Bosch F (2007, ISBN: 978-089054-354-2) for further information on these methods. Several data sets that were mainly published in plant disease epidemiology literature are also included in this package.
License: MIT + file LICENSE
URL: http://epiphy.org, https://github.com/chgigot/epiphy
BugReports: https://github.com/chgigot/epiphy/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
LinkingTo: Rcpp
Depends: R (>= 2.15.1)
Imports: stats, methods, utils, grDevices, ggplot2, transport, msm, pbapply, Rcpp
Suggests: magrittr, dplyr, tidyr, spdep, emdist, vegan, MASS, emdbook, knitr, rmarkdown
Collate: 'RcppExports.R' 'betabinom.R' 'data.R' 'utils.R' 'mle-factory.R' 'epiphy.R' 'intensity-classes.R' 'distr-fitting.R' 'indices.R' 'mapcomp.R' 'power-law.R' 'sadie.R' 'spatial-hier.R'
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-05-22 19:20:57 UTC; tof
Author: Christophe Gigot [aut, cre] (<https://orcid.org/0000-0002-1748-2902>)
Maintainer: Christophe Gigot <ch.gigot@gmail.com>
Repository: CRAN
Date/Publication: 2018-05-24 13:37:06 UTC

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New package deeplr with initial version 0.1.0
Package: deeplr
Type: Package
Title: Interface to the 'DeepL' Translation API
Version: 0.1.0
Authors@R: person("David", "Zumbach", role = c("aut", "cre"), email = "david.zumbach@gfzb.ch")
Description: A wrapper for the 'DeepL' API (see <https://www.deepl.com/translator>), a web service that translates texts between different languages. Access to the API is subject to a monthly fee.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
URL: <https://www.deepl.com/translator
BugReports: https://github.com/zumbov2/deeplr/issues
RoxygenNote: 6.0.1
Imports: utf8, httr, tibble
Suggests: purrr, dplyr
NeedsCompilation: no
Packaged: 2018-05-21 23:39:17 UTC; David Zumbach
Author: David Zumbach [aut, cre]
Maintainer: David Zumbach <david.zumbach@gfzb.ch>
Repository: CRAN
Date/Publication: 2018-05-24 13:26:47 UTC

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New package SEA with initial version 1.0
Package: SEA
Type: Package
Title: Segregation Analysis
Version: 1.0
Date: 2018-5-20
Author: Zhang Ya-Wen, Du Ying-wen,Ren Wen-long and Zhang Yuan-ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Description: A few major genes and a series of polygene are responsive for each quantitative trait. Major genes are individually identified while polygene is collectively detected. This is mixed major genes plus polygene inheritance analysis or segregation analysis (SEA). In the SEA, phenotypes from a single or multiple segregation populations along with their parents are used to fit all the possible models and the best model is viewed as the model of the trait. There are fourteen combinations of populations available. Zhang YM, Gai JY, Yang YH (2003) <doi:10.1017/S0016672303006141>.
Depends: shiny,MASS,doParallel,foreach,methods
Imports: KScorrect,kolmim,utils,stats,grDevices,graphics,data.table
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-05-22 04:13:59 UTC; abc
Repository: CRAN
Date/Publication: 2018-05-24 12:35:11 UTC

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Package fastM updated to version 0.0-4 with previous version 0.0-3 dated 2018-03-10

Title: Fast Computation of Multivariate M-Estimators
Description: Implements the new algorithm for fast computation of M-scatter matrices using a partial Newton-Raphson procedure for several estimators. The algorithm is described in Duembgen, Nordhausen and Schuhmacher (2016) <doi:10.1016/j.jmva.2015.11.009>.
Author: Lutz Duembgen, Klaus Nordhausen, Heike Schuhmacher
Maintainer: Klaus Nordhausen <klaus.nordhausen@tuwien.ac.at>

Diff between fastM versions 0.0-3 dated 2018-03-10 and 0.0-4 dated 2018-05-24

 DESCRIPTION          |    8 ++++----
 MD5                  |    8 ++++----
 build/partial.rdb    |binary
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 5 files changed, 16 insertions(+), 20 deletions(-)

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New package DatabaseConnector with initial version 2.1.2
Package: DatabaseConnector
Type: Package
Title: Connecting to Various Database Platforms
Version: 2.1.2
Date: 2018-05-22
Authors@R: c( person("Martijn", "Schuemie", email = "schuemie@ohdsi.org", role = c("aut", "cre")), person("Marc", "Suchard", role = c("aut")), person("Observational Health Data Science and Informatics", role = c("cph")), person("Microsoft Inc.", role = c("cph"), comment = "SQL Server JDBC driver"), person("PostgreSQL Global Development Group", role = c("cph"), comment = "PostgreSQL JDBC driver"), person("Starschema Ltd.", role = c("cph"), comment = "BigQuery JDBC driver"), person("Oracle Inc.", role = c("cph"), comment = "Oracle JDBC driver"), person("Amazon Inc.", role = c("cph"), comment = "RedShift JDBC driver") )
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server', 'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', and 'Google BigQuery'). Also includes support for fetching data as 'ffdf' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases.
Imports: DatabaseConnectorJars, rJava, bit, ff, ffbase (>= 0.12.1), SqlRender, methods, utils, DBI, urltools
Suggests: aws.s3, uuid, R.utils, testthat, DBItest, knitr, rmarkdown,
License: Apache License
VignetteBuilder: knitr
URL: https://github.com/OHDSI/DatabaseConnector
BugReports: https://github.com/OHDSI/DatabaseConnector/issues
Copyright: See file COPYRIGHTS
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2018-05-22 11:51:53 UTC; mschuemi
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut], Observational Health Data Science and Informatics [cph], Microsoft Inc. [cph] (SQL Server JDBC driver), PostgreSQL Global Development Group [cph] (PostgreSQL JDBC driver), Starschema Ltd. [cph] (BigQuery JDBC driver), Oracle Inc. [cph] (Oracle JDBC driver), Amazon Inc. [cph] (RedShift JDBC driver)
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Repository: CRAN
Date/Publication: 2018-05-24 12:39:39 UTC

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Package compound.Cox updated to version 3.11 with previous version 3.10 dated 2018-03-26

Title: Univariate Feature Selection and Compound Covariate for Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (gene expressions). Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>, statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>, Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2018-)<submitted>. Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between compound.Cox versions 3.10 dated 2018-03-26 and 3.11 dated 2018-05-24

 DESCRIPTION                 |    8 ++++----
 MD5                         |    8 ++++----
 R/uni.selection.R           |   25 ++++++++++++++++++++++---
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 5 files changed, 37 insertions(+), 15 deletions(-)

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New package cmce with initial version 0.1.0
Package: cmce
Type: Package
Title: Computer Model Calibration for Deterministic and Stochastic Simulators
Version: 0.1.0
Date: 2018-05-12
Author: Matthew T. Pratola <mpratola@stat.osu.edu> [aut, cre, cph]
Maintainer: Matthew T. Pratola <mpratola@stat.osu.edu>
Description: Implements the Bayesian calibration model described in Pratola and Chkrebtii (2018) <DOI:10.5705/ss.202016.0403> for stochastic and deterministic simulators. Additive and multiplicative discrepancy models are currently supported. See <http://www.matthewpratola.com/software> for more information and examples.
Depends: R (>= 3.2.3)
Imports: stats
License: AGPL-3
LazyData: true
NeedsCompilation: no
Packaged: 2018-05-14 14:51:54 UTC; mpratola
Repository: CRAN
Date/Publication: 2018-05-24 12:31:59 UTC

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New package cfma with initial version 1.0
Package: cfma
Type: Package
Title: Causal Functional Mediation Analysis
Version: 1.0
Date: 2018-05-16
Author: Yi Zhao <zhaoyi1026@gmail.com>, Xi Luo <xi.rossi.luo@gmail.com>, Martin Lindquist <mal2053@gmail.com>, Brian Caffo <bcaffo@gmail.com>
Maintainer: Yi Zhao <zhaoyi1026@gmail.com>
Description: Performs causal functional mediation analysis (CFMA) for functional treatment, functional mediator, and functional outcome. This package includes two functional mediation model types: (1) a concurrent mediation model and (2) a historical influence mediation model. See Zhao et al. (2018), Functional Mediation Analysis with an Application to Functional Magnetic Resonance Imaging Data, <arXiv:1805.06923> for details.
License: GPL (>= 2)
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2018-05-22 14:15:59 UTC; yizhao
Repository: CRAN
Date/Publication: 2018-05-24 12:45:18 UTC

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New package tabulizer with initial version 0.2.1
Package: tabulizer
Type: Package
Title: Bindings for 'Tabula' PDF Table Extractor Library
Version: 0.2.1
Authors@R: c(person("Thomas J.", "Leeper", role = "aut", email = "thosjleeper@gmail.com", comment = c(ORCID = "0000-0003-4097-6326")), person("Tom", "Paskhalis", role = "cre", email = "tpaskhalis@gmail.com", comment = c(ORCID = "0000-0001-9298-8850")), person("David", "Gohel", role = "ctb", comment = "rOpenSci reviewer"), person("Lincoln", "Mullen", role = "ctb", comment = "rOpenSci reviewer"))
Maintainer: Tom Paskhalis <tpaskhalis@gmail.com>
Description: Bindings for the 'Tabula' <http://tabula.technology/> 'Java' library, which can extract tables from PDF documents. The 'tabulizerjars' package <https://github.com/ropensci/tabulizerjars> provides versioned 'Java' .jar files, including all dependencies, aligned to releases of 'Tabula'.
License: MIT + file LICENSE
URL: https://github.com/ropensci/tabulizer
BugReports: https://github.com/ropensci/tabulizer/issues
Imports: png, rJava, tabulizerjars, tools, utils
Suggests: graphics, grDevices, knitr, miniUI, shiny, testthat
SystemRequirements: Java (>= 7.0)
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-21 14:22:01 UTC; tom
Author: Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>), Tom Paskhalis [cre] (<https://orcid.org/0000-0001-9298-8850>), David Gohel [ctb] (rOpenSci reviewer), Lincoln Mullen [ctb] (rOpenSci reviewer)
Repository: CRAN
Date/Publication: 2018-05-24 11:55:24 UTC

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Package MXM updated to version 1.3.4 with previous version 1.3.3 dated 2018-03-30

Title: Feature Selection (Including Multiple Solutions) and Bayesian Networks
Description: Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. Reference: Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets, Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>.
Author: Michail Tsagris [aut, cre], Ioannis Tsamardinos [aut, cph], Vincenzo Lagani [aut, cph], Giorgos Athineou [aut], Giorgos Borboudakis [ctb], Anna Roumpelaki [ctb]
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>

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Package BiDAG updated to version 1.1.2 with previous version 1.1.1 dated 2018-03-16

Title: Bayesian Inference for Directed Acyclic Graphs (BiDAG)
Description: Implementation of a collection of MCMC methods for Bayesian structure learning of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient inference on larger DAGs, the space of DAGs is pruned according to the data. To filter the search space, the algorithm employs a hybrid approach, combining constraint-based learning with search and score. A reduced search space is initially defined on the basis of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with search and score. Search and score is then performed following two approaches: Order MCMC, or Partition MCMC. The BGe score is implemented for continuous data and the BDe score is implemented for binary data. The algorithms may provide the maximum a posteriori (MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data. References: N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>, D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>, J. Kuipers and G. Moffa (2016) <doi:10.1080/01621459.2015.1133426>, M. Kalisch et al.(2012) <doi:10.18637/jss.v047.i11>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.minkina@bsse.ethz.ch>

Diff between BiDAG versions 1.1.1 dated 2018-03-16 and 1.1.2 dated 2018-05-24

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New package weibullness with initial version 1.18.6
Package: weibullness
Version: 1.18.6
Date: 2018-05-21
Title: Goodness-of-Fit Test for Weibull (Weibullness Test)
Authors@R: person("Chanseok","Park", email="statpnu@gmail.com", role = c("aut", "cre"))
Author: Chanseok Park [aut, cre]
Maintainer: Chanseok Park <statpnu@gmail.com>
Depends: R (>= 3.1.0)
Description: Performs a goodness-of-fit test of Weibull distribution (weibullness test). For more details, see Park (2017) <http://journals.sfu.ca/ijietap/index.php/ijie/article/view/2848>. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (No. NRF-2017R1A2B4004169).
License: GPL-2 | GPL-3
URL: https://github.com/statpnu/R-package
LazyData: yes
NeedsCompilation: no
Packaged: 2018-05-21 01:52:05 UTC; cp
Repository: CRAN
Date/Publication: 2018-05-24 09:56:28 UTC

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New package TreeDep with initial version 0.1.0
Package: TreeDep
Type: Package
Title: Air Pollution Removal by Dry Deposition on Trees
Version: 0.1.0
Author: Silvestre Garcia de Jalon
Maintainer: Silvestre García de Jalón <s.garciadejalon@gmail.com>
Description: The model estimates air pollution removal by dry deposition on trees. The pollutants are nitrogen dioxide, ozone, sulphur dioxide, carbon monoxide and particulate matter. Baldocchi D (1994) <doi:10.1093/treephys/14.7-8-9.1069>. Nowak DJ, Crane DE, Stevens JC (2006) <doi:10.1016/j.ufug.2006.01.007>.
License: GPL-2
Depends: graphics, grDevices, stats, utils, lubridate
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-21 09:21:05 UTC; silvestre.garcia
Repository: CRAN
Date/Publication: 2018-05-24 09:59:25 UTC

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Package rrcov updated to version 1.4-4 with previous version 1.4-3 dated 2016-09-06

Title: Scalable Robust Estimators with High Breakdown Point
Description: Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point.
Author: Valentin Todorov <valentin.todorov@chello.at>
Maintainer: Valentin Todorov <valentin.todorov@chello.at>

Diff between rrcov versions 1.4-3 dated 2016-09-06 and 1.4-4 dated 2018-05-24

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Package ldat updated to version 0.2.0 with previous version 0.1.0 dated 2017-11-20

Title: Large Data Sets
Description: Tools for working with vectors and data sets that are too large to keep in memory. Extends the basic functionality provided in the 'lvec' package. Provides basis statistical functionality of 'lvec' objects, such as arithmetic operations and calculating means and sums. Also implements 'data.frame'-like objects storing its data in 'lvec' objects.
Author: Jan van der Laan
Maintainer: Jan van der Laan <djvanderlaan@unrealizedtime.nl>

Diff between ldat versions 0.1.0 dated 2017-11-20 and 0.2.0 dated 2018-05-24

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New package DPP with initial version 0.1.2
Package: DPP
Type: Package
Title: Inference of Parameters of Normal Distributions from a Mixture of Normals
Version: 0.1.2
Authors@R: c( person("Luis M.", "Avila", email = "lmavila@gmail.com", role = c("aut","cre")), person("Michael R.", "May", email = "mikeryanmay@ucdavis.edu", role = "aut"), person("Jeff", "Ross-Ibarra", email = "rossibarra@ucdavis.edu", role = "aut"))
Description: This MCMC method takes a data numeric vector (Y) and assigns the elements of Y to a (potentially infinite) number of normal distributions. The individual normal distributions from a mixture of normals can be inferred. Following the method described in Escobar (1994) <doi:10.2307/2291223> we use a Dirichlet Process Prior (DPP) to describe stochastically our prior assumptions about the dimensionality of the data.
License: MIT + file LICENSE
Depends: methods, Rcpp (>= 0.12.4), coda, stats
Suggests: R.rsp
VignetteBuilder: R.rsp
LinkingTo: Rcpp
RcppModules: DPPmcmc,Models
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-05-24 06:17:07 UTC; lavila
Author: Luis M. Avila [aut, cre], Michael R. May [aut], Jeff Ross-Ibarra [aut]
Maintainer: Luis M. Avila <lmavila@gmail.com>
Repository: CRAN
Date/Publication: 2018-05-24 08:38:30 UTC

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Package Compositional updated to version 3.0 with previous version 2.9 dated 2018-03-07

Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. The standard textbook for such data is John Aitchison's (1986). "The statistical analysis of compositional data". Chapman & Hall.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Compositional versions 2.9 dated 2018-03-07 and 3.0 dated 2018-05-24

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Package BNSP updated to version 2.0.4 with previous version 2.0.2 dated 2017-08-28

Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models: 1. Dirichlet process mixtures & 2. spike-slab for variable selection in mean/variance regression models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>

Diff between BNSP versions 2.0.2 dated 2017-08-28 and 2.0.4 dated 2018-05-24

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Package lvec updated to version 0.2.2 with previous version 0.2.1 dated 2018-05-17

Title: Out of Memory Vectors
Description: Core functionality for working with vectors (numeric, integer, logical and character) that are too large to keep in memory. The vectors are kept (partially) on disk using memory mapping. This package contains the basic functionality for working with these memory mapped vectors (e.g. creating, indexing, ordering and sorting) and provides C++ headers which can be used by other packages to extend the functionality provided in this package.
Author: Jan van der Laan
Maintainer: Jan van der Laan <djvanderlaan@unrealizedtime.nl>

Diff between lvec versions 0.2.1 dated 2018-05-17 and 0.2.2 dated 2018-05-24

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Package ica updated to version 1.0-2 with previous version 1.0-1 dated 2015-08-24

Title: Independent Component Analysis
Description: Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>

Diff between ica versions 1.0-1 dated 2015-08-24 and 1.0-2 dated 2018-05-24

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Package eegkit updated to version 1.0-3 with previous version 1.0-2 dated 2015-02-17

Title: Toolkit for Electroencephalography Data
Description: Analysis and visualization tools for electroencephalography (EEG) data. Includes functions for (i) plotting EEG caps, time courses, and spatial maps; (ii) spatial and/or temporal smoothing of EEG data; (iii) frequency domain analysis (FFT) of EEG data (iv) spatial or temporal Independent Component Analysis of EEG data, and (v) simulating event-related potential EEG data.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>

Diff between eegkit versions 1.0-2 dated 2015-02-17 and 1.0-3 dated 2018-05-24

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Package phmm (with last version 0.7-10) was removed from CRAN

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

2017-12-14 0.7-10

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Package EditImputeCont (with last version 1.1.0) was removed from CRAN

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

2017-11-19 1.1.0
2016-10-31 1.0.2
2016-02-19 1.0.1
2015-06-11 1.0.0

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Package biospear (with last version 1.0.1) was removed from CRAN

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

2017-08-11 1.0.1
2017-05-13 1.0.0

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Package FusedPCA (with last version 0.2) was removed from CRAN

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

2013-11-10 0.2
2013-10-09 0.1

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Package mme (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:

2014-08-29 0.1-5
2014-01-05 0.1-4

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Package mdhglm (with last version 1.6) was removed from CRAN

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

2016-09-19 1.6
2016-06-28 1.4
2016-03-17 1.2

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Package ConvCalendar (with last version 1.2) was removed from CRAN

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

2013-04-02 1.2
2010-01-20 1.1
2009-01-08 1.0

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Package ViSiElse (with last version 1.2.0) was removed from CRAN

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

2016-08-25 1.2.0
2016-03-07 1.0.1
2016-01-12 1.0.0

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Package RcmdrPlugin.BCA (with last version 0.9-8) was removed from CRAN

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2014-09-04 0.9-8
2013-12-03 0.9-7
2013-07-15 0.9-6
2013-02-28 0.9-5
2012-02-07 0.9-4
2012-01-29 0.9-3
2011-12-28 0.9-2
2011-12-22 0.9-1
2011-05-05 0.1-4
2011-03-01 0.1-3

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Package frailtyHL (with last version 2.1) was removed from CRAN

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

2018-01-23 2.1
2012-05-12 1.1
2011-02-06 1.0

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

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2018-02-04 1.0
2017-08-24 0.9

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Package rwc (with last version 1.1) was removed from CRAN

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2017-09-20 1.1
2017-09-07 1.0

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Package fuser (with last version 1.0.0) was removed from CRAN

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2017-08-17 1.0.0

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

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2013-10-12 1.0

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Package MSBVAR (with last version 0.9-3) was removed from CRAN

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2016-11-14 0.9-3
2015-02-10 0.9-2
2014-07-25 0.9-1
2014-06-02 0.9-0

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Package Bayesthresh (with last version 2.0.1) was removed from CRAN

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

2013-03-26 2.0.1

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Package DAGGER (with last version 1.4) was removed from CRAN

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

2011-08-05 1.4
2011-06-02 1.2
2011-02-19 1.1

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Package dhglm (with last version 1.7) was removed from CRAN

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

2017-05-01 1.7
2016-09-19 1.6
2015-09-18 1.5
2011-09-30 1.2

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Wed, 23 May 2018

Package riv updated to version 2.0-5 with previous version 2.0-4 dated 2013-10-03

Title: Robust Instrumental Variables Estimator
Description: Finds a robust instrumental variables estimator using a high breakdown point S-estimator of multivariate location and scatter matrix.
Author: Gabriela Cohen-Freue and Davor Cubranic, with contributions from B. Kaufmann and R.H. Zamar
Maintainer: Gabriela Cohen-Freue <gcohen@stat.ubc.ca>

Diff between riv versions 2.0-4 dated 2013-10-03 and 2.0-5 dated 2018-05-23

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Package unsystation updated to version 0.2.0 with previous version 0.1.1 dated 2016-11-03

Title: Stationarity Test Based on Unsystematic Sub-Sampling
Description: Performs a test for second-order stationarity of time series based on unsystematic sub-samples.
Author: Haeran Cho [aut, cre]
Maintainer: Haeran Cho <haeran.cho@bristol.ac.uk>

Diff between unsystation versions 0.1.1 dated 2016-11-03 and 0.2.0 dated 2018-05-23

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New package icd.data with initial version 1.0
Package: icd.data
Title: International Classifcation of Diseases (ICD) Data
Version: 1.0
Authors@R: person("Jack O. Wasey", role = c("aut", "cre", "cph"), email = "jack@jackwasey.com")
Description: Data from the United States Center for Medicare and Medicaid Services (CMS) is included in this package. There are ICD-9 and ICD-10 diagnostic and procedure codes, and lists of the chapter and sub-chapter headings and the ranges of ICD codes they encompass. There are also two sample datasets. These data are used by the 'icd' package for finding comorbidities.
Depends: R (>= 3.0.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
RoxygenNote: 6.0.1
Imports: utils
Suggests: testthat, icd
NeedsCompilation: no
Packaged: 2018-05-23 14:03:02 UTC; waseyj
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Repository: CRAN
Date/Publication: 2018-05-23 22:06:33 UTC

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New package trekfont with initial version 0.9.2
Package: trekfont
Version: 0.9.2
Title: Star Trek Fonts Collection
Description: Provides a collection of true type and open type Star Trek-themed fonts.
Authors@R: person("Matthew", "Leonawicz", email = "mfleonawicz@alaska.edu", role = c("aut", "cre"))
License: GPL-3
Encoding: UTF-8
LazyData: true
ByteCompile: true
URL: https://github.com/leonawicz/trekfont
BugReports: https://github.com/leonawicz/trekfont/issues
Depends: R (>= 2.10)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-23 15:56:54 UTC; Matt
Author: Matthew Leonawicz [aut, cre]
Maintainer: Matthew Leonawicz <mfleonawicz@alaska.edu>
Repository: CRAN
Date/Publication: 2018-05-23 22:00:18 UTC

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Package dplR updated to version 1.6.8 with previous version 1.6.7 dated 2018-01-29

Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology building, and cross dating. Read and write standard file formats used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, cph, trl], Franco Biondi [aut, cph], Filipe Campelo [aut, cph], Pierre Mérian [aut, cph], Fares Qeadan [aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb], Manfred Mudelsee [ctb], Michael Schulz [ctb], Darwin Pucha-Cofrep [aut, cph], Jakob Wernicke [aut, cph]
Maintainer: Andy Bunn <andy.bunn@wwu.edu>

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Package prodigenr updated to version 0.4.0 with previous version 0.3.0 dated 2016-07-29

Title: Research Project Directory Generator
Description: Create a project directory structure, along with typical files for that project. This allows projects to be quickly and easily created, as well as for them to be standardized. Designed specifically with scientists in mind (mainly bio-medical researchers, but likely applies to other fields).
Author: Luke Johnston [aut, cre] (<https://orcid.org/0000-0003-4169-2616>)
Maintainer: Luke Johnston <lwjohnst@gmail.com>

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Package CLME updated to version 2.0-10 with previous version 2.0-9 dated 2018-02-01

Title: Constrained Inference for Linear Mixed Effects Models
Description: Estimation and inference for linear models where some or all of the fixed-effects coefficients are subject to order restrictions. This package uses the robust residual bootstrap methodology for inference, and can handle some structure in the residual variance matrix.
Author: Casey M. Jelsema [aut, cre], Shyamal D. Peddada [aut]
Maintainer: Casey M. Jelsema <jelsema.casey@gmail.com>

Diff between CLME versions 2.0-9 dated 2018-02-01 and 2.0-10 dated 2018-05-23

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Package biolink updated to version 0.1.5 with previous version 0.1.4 dated 2018-04-20

Title: Create Hyperlinks to Biological Databases and Resources
Description: Generate urls and hyperlinks to commonly used biological databases and resources based on standard identifiers. This is primarily useful when writing dynamic reports that reference things like gene symbols in text or tables, allowing you to, for example, convert gene identifiers to hyperlinks pointing to their entry in the NCBI Gene database. Currently supports NCBI Gene, PubMed, Gene Ontology, CRAN and Bioconductor.
Author: Aaron Wolen [aut, cre]
Maintainer: Aaron Wolen <aaron@wolen.com>

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Package frailtyEM updated to version 0.8.8 with previous version 0.8.7 dated 2018-04-23

Title: Fitting Frailty Models with the EM Algorithm
Description: Contains functions for fitting shared frailty models with a semi-parametric baseline hazard with the Expectation-Maximization algorithm. Supported data formats include clustered failures with left truncation and recurrent events in gap-time or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable and the Power Variance Family are supported.
Author: Theodor Adrian Balan, Hein Putter
Maintainer: Theodor Adrian Balan <t.a.balan@lumc.nl>

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Package ukbtools updated to version 0.11.0 with previous version 0.10.1 dated 2018-02-05

Title: Manipulate and Explore UK Biobank Data
Description: A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> dataset from a UKB fileset (.tab, .r, .html), visualize primary demographic data for a sample subset, query ICD diagnoses, retrieve genetic metadata, read and write standard file formats for genetic analyses.
Author: Ken Hanscombe [aut, cre]
Maintainer: Ken Hanscombe <ken.hanscombe@gmail.com>

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Package myTAI updated to version 0.8.0 with previous version 0.7.0 dated 2018-04-11

Title: Evolutionary Transcriptomics
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2017) <doi:10.1093/bioinformatics/btx835>). The aim of this tool is to provide a transcriptome analysis environment for answering questions regarding the evolution of biological processes (Drost et al. (2016) <doi:10.1101/051565>).
Author: Hajk-Georg Drost [aut, cre] (<https://orcid.org/0000-0002-1567-306X>)
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>

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Package mratios updated to version 1.4.0 with previous version 1.3.17 dated 2012-11-02

Title: Ratios of Coefficients in the General Linear Model
Description: Performs (simultaneous) inferences for ratios of linear combinations of coefficients in the general linear model. Multiple comparisons and simultaneous confidence interval estimations can be performed for ratios of treatment means in the normal one-way layout with homogeneous and heterogeneous treatment variances, according to Dilba et al. (2007) <https://cran.r-project.org/doc/Rnews/Rnews_2007-1.pdf> and Hasler and Hothorn (2008) <doi:10.1002/bimj.200710466>. Confidence interval estimations for ratios of linear combinations of linear model parameters like in (multiple) slope ratio and parallel line assays can be carried out. Moreover, it is possible to calculate the sample sizes required in comparisons with a control based on relative margins. For the simple two-sample problem, functions for a t-test for ratio-formatted hypotheses and the corresponding confidence interval are provided assuming homogeneous or heterogeneous group variances.
Author: Gemechis Djira [aut], Mario Hasler [aut], Daniel Gerhard [aut], Frank Schaarschmidt [aut, cre]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>

Diff between mratios versions 1.3.17 dated 2012-11-02 and 1.4.0 dated 2018-05-23

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Package mleap updated to version 0.1.2 with previous version 0.1.1 dated 2018-05-10

Title: Interface to 'MLeap'
Description: A 'sparklyr' <https://spark.rstudio.com> extension that provides an interface to 'MLeap' <https://github.com/combust/mleap>, an open source library that enables exporting and serving of 'Apache Spark' pipelines.
Author: Kevin Kuo [aut, cre] (<https://orcid.org/0000-0001-7803-7901>)
Maintainer: Kevin Kuo <kevin.kuo@rstudio.com>

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Package histmdl updated to version 0.7-1 with previous version 0.6-1 dated 2016-09-28

Title: A Most Informative Histogram-Like Model
Description: Using the MDL principle, it is possible to estimate parameters for a histogram-like model. The package contains the implementation of such an estimation method.
Author: Jouke Witteveen
Maintainer: Jouke Witteveen <j.witteveen@gmail.com>

Diff between histmdl versions 0.6-1 dated 2016-09-28 and 0.7-1 dated 2018-05-23

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Package haploR updated to version 1.6.4 with previous version 1.6.2 dated 2017-10-31

Title: Query 'HaploReg' and 'RegulomeDB'
Description: A set of utilities for querying 'HaploReg' <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php> and 'RegulomeDB' <http://www.regulomedb.org> web-based tools. The package connects to 'HaploReg' or 'RegulomeDB', searches and downloads results, without opening web pages, directly from R environment. Results are stored in a data frame that can be directly used in various kinds of downstream analyses.
Author: Ilya Y. Zhbannikov [aut, cre]
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>

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Package synlik updated to version 0.1.2 with previous version 0.1.1 dated 2014-06-08

Title: Synthetic Likelihood Methods for Intractable Likelihoods
Description: Framework to perform synthetic likelihood inference for models where the likelihood function is unavailable or intractable.
Author: Matteo Fasiolo and Simon Wood
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>

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Package LS2W updated to version 1.3.4 with previous version 1.3-3 dated 2013-07-12

Title: Locally Stationary Two-Dimensional Wavelet Process Estimation Scheme
Description: Estimates two-dimensional local wavelet spectra.
Author: Idris Eckley [aut, cre], Guy Nason [aut], Sarah Taylor [ctb], Matthew Nunes [ctb]
Maintainer: Idris Eckley <i.eckley@lancaster.ac.uk>

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Package bssm updated to version 0.1.5 with previous version 0.1.4 dated 2018-02-04

Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space Models
Description: Efficient methods for Bayesian inference of state space models via particle Markov chain Monte Carlo and parallel importance sampling type weighted Markov chain Monte Carlo (Vihola, Helske, and Franks, 2017, <arXiv:1609.02541>). Gaussian, Poisson, binomial, or negative binomial observation densities and basic stochastic volatility models with Gaussian state dynamics, as well as general non-linear Gaussian models and discretised diffusion models are supported.
Author: Jouni Helske, Matti Vihola
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package vardpoor updated to version 0.10.0 with previous version 0.9.11 dated 2017-11-07

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearization of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>

Diff between vardpoor versions 0.9.11 dated 2017-11-07 and 0.10.0 dated 2018-05-23

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New package ODEsensitivity with initial version 1.1.0
Package: ODEsensitivity
Version: 1.1.0
Title: Sensitivity Analysis of Ordinary Differential Equations
Description: Performs sensitivity analysis in ordinary differential equation (ode) models. The package utilize the ode interface from 'deSolve' and connects it with the sensitivity analysis from 'sensitivity'. Additionally we add a method to run the sensitivity analysis on variables with class 'ODEnetwork'. A detailed plotting function provides outputs on the calculations.
Authors@R: c( person("Stefan", "Theers", email = "stefan.theers@tu-dortmund.de", role = "aut"), person("Frank", "Weber", email = "frank.weber@tu-dortmund.de", role = "aut"), person("Dirk", "Surmann", email = "surmann@statistik.tu-dortmund.de", role = c("ctb", "cre") , comment = c(ORCID = "0000-0003-0873-137X")) )
URL: https://github.com/surmann/ODEsensitivity
BugReports: https://github.com/surmann/ODEsensitivity/issues
License: LGPL-3
Encoding: UTF-8
Depends: R (>= 3.1.1), checkmate, deSolve, ODEnetwork (>= 1.3.0), sensitivity (>= 1.12.1)
Suggests: covr, knitr, parallel, rmarkdown, testthat
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2018-05-22 14:02:50 UTC; surmann
Author: Stefan Theers [aut], Frank Weber [aut], Dirk Surmann [ctb, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <surmann@statistik.tu-dortmund.de>
Repository: CRAN
Date/Publication: 2018-05-23 12:49:34 UTC

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Package excel.link updated to version 0.9.8-1 with previous version 0.9.7 dated 2017-05-01

Title: Convenient Data Exchange with Microsoft Excel
Description: Allows access to data in running instance of Microsoft Excel (e. g. 'xl[a1] = xl[b2]*3' and so on). Graphics can be transferred with 'xl[a1] = current.graphics()'. Additionally there are function for reading/writing 'Excel' files - 'xl.read.file'/'xl.save.file'. They are not fast but able to read/write '*.xlsb'-files and password-protected files. There is an Excel workbook with examples of calling R from Excel in the 'doc' folder. It tries to keep things as simple as possible - there are no needs in any additional installations besides R, only 'VBA' code in the Excel workbook. Microsoft Excel is required for this package.
Author: Gregory Demin <excel.link.feedback@gmail.com>. To comply CRAN policy includes source code from 'RDCOMClient' (http://www.omegahat.net/RDCOMClient) by Duncan Temple Lang <duncan@wald.ucdavis.edu>.
Maintainer: Gregory Demin <excel.link.feedback@gmail.com>

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Package adespatial updated to version 0.2-0 with previous version 0.1-1 dated 2018-01-16

Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Author: Stéphane Dray, David Bauman, Guillaume Blanchet, Daniel Borcard, Sylvie Clappe, Guillaume Guenard, Thibaut Jombart, Guillaume Larocque, Pierre Legendre, Naima Madi, Helene H Wagner
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>

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Package AdaptFitOS updated to version 0.67 with previous version 0.65 dated 2017-09-22

Title: Adaptive Semiparametric Additive Regression with Simultaneous Confidence Bands and Specification Tests
Description: Fits semiparametric additive regression models with spatially adaptive penalized splines and computes simultaneous confidence bands and associated specification (lack-of-fit) tests. Simultaneous confidence bands cover the entire curve with a prescribed level of confidence and allow us to assess the estimation uncertainty for the whole curve. In contrast to pointwise confidence bands, they permit statements about the statistical significance of certain features (e.g. bumps) in the underlying curve.The method allows for handling of spatially heterogeneous functions and their derivatives as well as heteroscedasticity in the data. See Wiesenfarth et al (2012) <doi:10.1080/01621459.2012.682809>.
Author: Manuel Wiesenfarth and Tatyana Krivobokova
Maintainer: Manuel Wiesenfarth <m.wiesenfarth@dkfz.de>

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Package gsEasy updated to version 1.3 with previous version 1.1 dated 2016-08-06

Title: Gene Set Enrichment Analysis in R
Description: R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005 <doi: 10.1073/pnas.0506580102>).
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>

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Package btb updated to version 0.1.30 with previous version 0.1.25 dated 2018-05-17

Title: Beyond the Border - Kernel Density Estimation for Urban Geography
Description: The kernelSmoothing() function allows you to square and smooth geolocated data. It calculates a classical kernel smoothing (conservative) or a geographically weighted median. There are four major call modes of the function. The first call mode is kernelSmoothing(obs, epsg, cellsize, bandwith) for a classical kernel smoothing and automatic grid. The second call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, quantiles) for a geographically weighted median and automatic grid. The third call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, centroids) for a classical kernel smoothing and user grid. The fourth call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, quantiles, centroids) for a geographically weighted median and user grid. Geographically weighted summary statistics : a framework for localised exploratory data analysis, C.Brunsdon & al., in Computers, Environment and Urban Systems C.Brunsdon & al. (2002) <doi:10.1016/S0198-9715(01)00009-6>, Statistical Analysis of Spatial and Spatio-Temporal Point Patterns, Third Edition, Diggle, pp. 83-86, (2003) <doi:10.1080/13658816.2014.937718>.
Author: Arlindo Dos Santos [cre], Francois Semecurbe [drt, aut], Auriane Renaud [ctb], Cynthia Faivre [ctb], Thierry Cornely [ctb], Farida Marouchi [ctb], Farida Marouchi [ctb]
Maintainer: Arlindo Dos Santos <Arlindo.Dos-Santos@insee.fr>

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Package monotonicity updated to version 1.1 with previous version 1.0 dated 2018-04-18

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:10.1016/0304-4076(89)90094-8> 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]
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

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Package scholar updated to version 0.1.6 with previous version 0.1.4 dated 2015-11-21

Title: Analyse Citation Data from Google Scholar
Description: Provides functions to extract citation data from Google Scholar. Convenience functions are also provided for comparing multiple scholars and predicting future h-index values.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), James Keirstead [aut], Gregory Jefferis [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package latdiag updated to version 0.2-4 with previous version 0.2-3 dated 2016-10-19

Title: Draws Diagrams Useful for Checking Latent Scales
Description: A graph proposed by Rosenbaum is useful for checking some properties of various sorts of latent scale, this program generates commands to obtain the graph using 'dot' from 'graphviz'.
Author: Michael Dewey
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>

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Package evtree updated to version 1.0-7 with previous version 1.0-6 dated 2017-12-15

Title: Evolutionary Learning of Globally Optimal Trees
Description: Commonly used classification and regression tree methods like the CART algorithm are recursive partitioning methods that build the model in a forward stepwise search. Although this approach is known to be an efficient heuristic, the results of recursive tree methods are only locally optimal, as splits are chosen to maximize homogeneity at the next step only. An alternative way to search over the parameter space of trees is to use global optimization methods like evolutionary algorithms. The 'evtree' package implements an evolutionary algorithm for learning globally optimal classification and regression trees in R. CPU and memory-intensive tasks are fully computed in C++ while the 'partykit' package is leveraged to represent the resulting trees in R, providing unified infrastructure for summaries, visualizations, and predictions.
Author: Thomas Grubinger [aut, cre], Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>>), Karl-Peter Pfeiffer [aut]
Maintainer: Thomas Grubinger <ThomasGrubinger@gmail.com>

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Package mosaic updated to version 1.2.0 with previous version 1.1.1 dated 2017-11-28

Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (<http://mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel T. Kaplan <kaplan@macalester.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>

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Tue, 22 May 2018

Package rvcheck updated to version 0.1.0 with previous version 0.0.9 dated 2017-07-10

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

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Package RSpectra updated to version 0.13-1 with previous version 0.12-0 dated 2016-06-13

Title: Solvers for Large-Scale Eigenvalue and SVD Problems
Description: R interface to the 'Spectra' library <https://spectralib.org/> for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than eigen() if k << n. This package provides the 'eigs()' function that does the similar job as in 'Matlab', 'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function to calculate the largest k singular values and corresponding singular vectors of a real matrix. The matrix to be computed on can be dense, sparse, or in the form of an operator defined by the user.
Author: Yixuan Qiu [aut, cre], Jiali Mei [aut] (Function interface of matrix operation), Gael Guennebaud [ctb] (Eigenvalue solvers from the 'Eigen' library), Jitse Niesen [ctb] (Eigenvalue solvers from the 'Eigen' library)
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

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Package templates updated to version 0.3.0 with previous version 0.2.0 dated 2017-06-22

Title: A System for Working with Templates
Description: Provides tools to work with template code and text in R. It aims to provide a simple substitution mechanism for R-expressions inside these templates. Templates can be written in other languages like 'SQL', can simply be represented by characters in R, or can themselves be R-expressions or functions.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>

Diff between templates versions 0.2.0 dated 2017-06-22 and 0.3.0 dated 2018-05-22

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New package rvalues with initial version 0.6.3
Package: rvalues
Type: Package
Title: R-Values for Ranking in High-Dimensional Settings
Version: 0.6.3
Date: 2018-5-21
Authors@R: c(person("Nicholas", "Henderson", email = "nhender5@jhmi.edu", role = "cre"), person("Michael", "Newton", email = "newton@stat.wisc.edu", role = "aut"))
Maintainer: Nicholas Henderson <nhender5@jhmi.edu>
Imports: graphics, stats, utils
Description: A collection of functions for computing "r-values" from various kinds of user input such as MCMC output or a list of effect size estimates and associated standard errors. Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units.
License: GPL-2
LazyData: yes
NeedsCompilation: yes
Packaged: 2018-05-21 16:01:36 UTC; nhenders
Author: Nicholas Henderson [cre], Michael Newton [aut]
X-CRAN-Comment: Archived on 2018-01-30 as maintainer address bounced when asked to correct memory-access errors.
Repository: CRAN
Date/Publication: 2018-05-22 21:04:42 UTC

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Package rsparkling updated to version 0.2.4 with previous version 0.2.3 dated 2018-03-08

Title: R Interface for H2O Sparkling Water
Description: An extension package for 'sparklyr' that provides an R interface to H2O Sparkling Water machine learning library (see <https://github.com/h2oai/sparkling-water> for more information).
Author: Navdeep Gill [aut, cre], Erin LeDell [aut], Michal Malohlava [aut], Jakub Hava [aut], JJ Allaire [aut], H2O.ai [cph], RStudio [cph]
Maintainer: Navdeep Gill <navdeep@h2o.ai>

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Package RcppThread updated to version 0.3.0 with previous version 0.2.0 dated 2018-04-23

Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely be interrupted from R.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>

Diff between RcppThread versions 0.2.0 dated 2018-04-23 and 0.3.0 dated 2018-05-22

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Package mosaicCore updated to version 0.5.0 with previous version 0.4.2 dated 2017-11-28

Title: Common Utilities for Other MOSAIC-Family Packages
Description: Common utilities used in other MOSAIC-family packages are collected here.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel T. Kaplan <kaplan@macalester.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>

Diff between mosaicCore versions 0.4.2 dated 2017-11-28 and 0.5.0 dated 2018-05-22

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Package ICtest updated to version 0.3-1 with previous version 0.3 dated 2017-06-27

Title: Estimating and Testing the Number of Interesting Components in Linear Dimension Reduction
Description: For different linear dimension reduction methods like principal components analysis (PCA), independent components analysis (ICA) and supervised linear dimension reduction tests and estimates for the number of interesting components (ICs) are provided.
Author: Klaus Nordhausen, Hannu Oja, David E. Tyler, Joni Virta
Maintainer: Klaus Nordhausen <klaus.nordhausen@tuwien.ac.at>

Diff between ICtest versions 0.3 dated 2017-06-27 and 0.3-1 dated 2018-05-22

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Package ggformula updated to version 0.7.0 with previous version 0.6.2 dated 2018-02-06

Title: Formula Interface to the Grammar of Graphics
Description: Provides a formula interface to 'ggplot2' graphics.
Author: Daniel Kaplan [aut], Randall Pruim [aut, cre]
Maintainer: Randall Pruim <rpruim@calvin.edu>

Diff between ggformula versions 0.6.2 dated 2018-02-06 and 0.7.0 dated 2018-05-22

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Package DALEX updated to version 0.2.2 with previous version 0.2.0 dated 2018-04-05

Title: Descriptive mAchine Learning EXplanations
Description: Machine Learning (ML) models are widely used and have various applications in classification or regression. Models created with boosting, bagging, stacking or similar techniques are often used due to their high performance, but such black-box models usually lack of interpretability. 'DALEX' package contains various explainers that help to understand the link between input variables and model output. The single_variable() explainer extracts conditional response of a model as a function of a single selected variable. It is a wrapper over packages 'pdp' and 'ALEPlot'. The single_prediction() explainer attributes arts of model prediction to articular variables used in the model. It is a wrapper over 'breakDown' package. The variable_dropout() explainer assess variable importance based on consecutive permutations. All these explainers can be plotted with generic plot() function and compared across different models.
Author: Przemyslaw Biecek [aut, cre]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

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Package Mega2R updated to version 1.0.3 with previous version 1.0.2 dated 2018-04-03

Title: Accessing and Processing a 'Mega2' Genetic Database
Description: Uses as input genetic data that have been reformatted and stored in a 'SQLite' database; this database is initially created by the standalone 'mega2' C++ program (available freely from <https://watson.hgen.pitt.edu/register/>). Loads and manipulates data frames containing genotype, phenotype, and family information from the input 'SQLite' database, and decompresses needed subsets of the genotype data, on the fly, in a memory efficient manner. We have also created several more functions that illustrate how to use the data frames as well as perform useful tasks: these permit one to run the 'pedgene' package to carry out gene-based association tests on family data using selected marker subsets, to run the 'SKAT' package to carry out gene-based association tests using selected marker subsets, to output the 'Mega2R' data as a VCF file and related files (for phenotype and family data), and to convert the data frames into 'GenABEL' gwaa.data-class objects.
Author: Robert V. Baron [aut], Daniel E. Weeks [aut, cre], University of Pittsburgh [cph]
Maintainer: Daniel E. Weeks <weeks@pitt.edu>

Diff between Mega2R versions 1.0.2 dated 2018-04-03 and 1.0.3 dated 2018-05-22

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Package C50 updated to version 0.1.2 with previous version 0.1.1 dated 2017-12-01

Title: C5.0 Decision Trees and Rule-Based Models
Description: C5.0 decision trees and rule-based models for pattern recognition that extend the work of Quinlan (1993, ISBN:1-55860-238-0).
Author: Max Kuhn [aut, cre], Steve Weston [ctb], Mark Culp [ctb], Nathan Coulter [ctb], Ross Quinlan [aut] (Author of imported C code), RuleQuest Research [cph] (Copyright holder of imported C code), Rulequest Research Pty Ltd. [cph] (Copyright holder of imported C code)
Maintainer: Max Kuhn <mxkuhn@gmail.com>

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New package antaresViz with initial version 0.13.0
Package: antaresViz
Type: Package
Title: Antares Visualizations
Version: 0.13.0
Date: 2018-05-03
Authors@R: c( person("Jalal-Edine", "ZAWAM", , "jalal-edine.zawam@rte-france.com", role = c("aut", "cre")), person("Francois", "Guillem", , "francois.guillem@rte-france.com", role = "aut"), person("Benoit", "Thieurmel", email = "benoit.thieurmel@datastorm.fr", role = "aut"), person(given = "Titouan", family = "Robert", email = "titouan.robert@datastorm.fr", role = "aut"), person("Baptiste", "SEGUINOT", , "baptiste.seguinot@rte-france.com", role = "ctb"), person("RTE", role = "cph") )
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>
Description: Visualize results generated by Antares, a powerful software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://antares.rte-france.com>). This package provides functions that create interactive charts to help Antares users visually explore the results of their simulations. You can see the results of several ANTARES studies here : <http://bpnumerique.rte-france.com/>.
URL: https://github.com/rte-antares-rpackage/antaresViz
BugReports: https://github.com/rte-antares-rpackage/antaresViz/issues
License: GPL (>= 2) | file LICENSE
LazyData: TRUE
Encoding: UTF-8
Depends: antaresRead (>= 2.0.0), antaresProcessing (>= 0.13.0), spMaps (>= 0.2)
Imports: dygraphs (>= 1.1.1), shiny (>= 0.13.0), plotly (>= 4.5.6), htmltools, htmlwidgets (>= 0.7.0), manipulateWidget (>= 0.9.0), leaflet (>= 1.1.0), sp, rgeos, raster, webshot, data.table, methods, lubridate, geojsonio, graphics, stats, leaflet.minicharts (>= 0.5.3), assertthat, rAmCharts, utils
RoxygenNote: 6.0.1
Suggests: testthat, covr, rhdf5 (>= 2.20.2), rbokeh, knitr, visNetwork
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-05-15 08:30:53 UTC; jalazawa
Author: Jalal-Edine ZAWAM [aut, cre], Francois Guillem [aut], Benoit Thieurmel [aut], Titouan Robert [aut], Baptiste SEGUINOT [ctb], RTE [cph]
Repository: CRAN
Date/Publication: 2018-05-22 20:50:29 UTC

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Package kmi updated to version 0.5.4 with previous version 0.5.3 dated 2017-09-26

Title: Kaplan-Meier Multiple Imputation for the Analysis of Cumulative Incidence Functions in the Competing Risks Setting
Description: Performs a Kaplan-Meier multiple imputation to recover the missing potential censoring information from competing risks events, so that standard right-censored methods could be applied to the imputed data sets to perform analyses of the cumulative incidence functions (Allignol and Beyersmann, 2010 <doi:10.1093/biostatistics/kxq018>).
Author: Arthur Allignol <arthur.allignol@gmail.com>
Maintainer: Arthur Allignol <arthur.allignol@gmail.com>

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Package Cprob updated to version 1.4.1 with previous version 1.4 dated 2017-09-25

Title: The Conditional Probability Function of a Competing Event
Description: Permits to estimate the conditional probability function of a competing event, and to fit, using the temporal process regression or the pseudo-value approach, a proportional-odds model to the conditional probability function (or other models by specifying another link function). See <doi:10.1111/j.1467-9876.2010.00729.x>.
Author: Arthur Allignol
Maintainer: Arthur Allignol <arthur.allignol@gmail.com>

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Package codebook updated to version 0.5.9 with previous version 0.5.8 dated 2018-03-21

Title: Automatic Codebooks from Survey Metadata Encoded in Attributes
Description: Easily automate the following tasks to describe data frames: computing reliabilities (internal consistencies, retest, multilevel) for psychological scales, summarise the distributions of scales and items graphically and using descriptive statistics, combine this information with metadata (such as item labels and labelled values) that is derived from R attributes. To do so, the package relies on 'rmarkdown' partials, so you can generate HTML, PDF, and Word documents. Codebooks are also available as tables (CSV, Excel, etc.).
Author: Ruben Arslan [aut, cre]
Maintainer: Ruben Arslan <ruben.arslan@gmail.com>

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Package AppliedPredictiveModeling updated to version 1.1-7 with previous version 1.1-6 dated 2014-07-25

Title: Functions and Data Sets for 'Applied Predictive Modeling'
Description: A few functions and several data set for the Springer book 'Applied Predictive Modeling'.
Author: Max Kuhn, Kjell Johnson
Maintainer: Max Kuhn <mxkuhn@gmail.com>

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Package sValues updated to version 0.1.5 with previous version 0.1.4 dated 2015-12-22

Title: Measures of the Sturdiness of Regression Coefficients
Description: Implements the s-values proposed by Ed. Leamer. It provides a context-minimal approach for sensitivity analysis using extreme bounds to assess the sturdiness of regression coefficients.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>

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Package regnet updated to version 0.3.0 with previous version 0.2.0 dated 2017-10-14

Title: Network-Based Regularization for Generalized Linear Models
Description: Network-based regularization has achieved success in variable selection for high-dimensional biological data due to its ability to incorporate correlations among genomic features. This package provides procedures of network-based variable selection for generalized linear models. Two recent additions are the robust network regularization for the survival response and the network regularization for continuous response. Functions for other regularization methods will be included in the forthcoming upgraded versions.
Author: Jie Ren, Luann C. Jung, Yinhao Du, Cen Wu, Yu Jiang, Junhao Liu
Maintainer: Jie Ren <jieren@ksu.edu>

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Package devEMF updated to version 3.6-1 with previous version 3.6 dated 2017-07-24

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

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Package aprof updated to version 0.4.1 with previous version 0.3.9 dated 2017-12-04

Title: Amdahl's Profiler, Directed Optimization Made Easy
Description: Assists the evaluation of whether and where to focus code optimization, using Amdahl's law and visual aids based on line profiling. Amdahl's profiler organizes profiling output files (including memory profiling) in a visually appealing way. It is meant to help to balance development vs. execution time by helping to identify the most promising sections of code to optimize and projecting potential gains. The package is an addition to R's standard profiling tools and is not a wrapper for them.
Author: Marco D. Visser
Maintainer: Marco D. Visser <marco.d.visser@gmail.com>

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Package philentropy updated to version 0.2.0 with previous version 0.1.0 dated 2018-04-10

Title: Similarity and Distance Quantification Between Probability Functions
Description: Computes 46 optimized distance and similarity measures for comparing probability functions. These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.
Author: Hajk-Georg Drost [aut, cre] (<https://orcid.org/0000-0002-1567-306X>>)
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>

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Package margins updated to version 0.3.23 with previous version 0.3.20 dated 2018-04-24

Title: Marginal Effects for Model Objects
Description: An R port of Stata's 'margins' command, which can be used to calculate marginal (or partial) effects from model objects.
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>>), Jeffrey Arnold [ctb], Vincent Arel-Bundock [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

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Package cAIC4 updated to version 0.4 with previous version 0.3 dated 2018-03-21

Title: Conditional Akaike Information Criterion for 'lme4'
Description: Provides functions for the estimation of the conditional Akaike information in generalized mixed-effect models fitted with (g)lmer() from 'lme4'.
Author: Benjamin Saefken and David Ruegamer, with contributions from Sonja Greven and Thomas Kneib
Maintainer: David Ruegamer <david.ruegamer@gmail.com>

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Package nauf (with last version 1.1.0) was removed from CRAN

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

2017-06-14 1.1.0
2017-05-27 1.0.1
2017-05-09 1.0.0

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Package Datasmith (with last version 1.0-1) was removed from CRAN

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2017-01-06 1.0-1

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Package smdata updated to version 1.2 with previous version 1.1 dated 2013-09-10

Title: Data to Accompany Smithson & Merkle, 2013
Description: Contains data files to accompany Smithson & Merkle (2013), Generalized Linear Models for Categorical and Continuous Limited Dependent Variables.
Author: Ed Merkle and Michael Smithson
Maintainer: Ed Merkle <merklee@missouri.edu>

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Package qut updated to version 2.1 with previous version 2.0 dated 2018-01-29

Title: Quantile Universal Threshold
Description: Thresholding based tests for null hypothesis of the form A beta =c, and the Quantile Universal Threshold (QUT) for GLM-lasso and Square-root lasso to obtain a sparse model with a good compromise between high true positive rate and low false discovery rate.
Author: Jairo Diaz-Rodriguez, Sylvain Sardy, Caroline Giacobino, Nick Hengartner.
Maintainer: Jairo Diaz-Rodriguez<jairo.diaz@unige.ch>

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Package ggstatsplot updated to version 0.0.3 with previous version 0.0.2 dated 2018-04-28

Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests (parametric, non-parametric, or robust) included in the plots themselves. It is targeted primarily at behavioral sciences community to provide a one-line code to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms) or categorical (pie charts) data.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package FastPCS updated to version 0.1.3 with previous version 0.1.2 dated 2015-01-07

Title: FastPCS Robust Fit of Multivariate Location and Scatter
Description: The FastPCS algorithm of Vakili and Schmitt (2014) <doi:10.1016/j.csda.2013.07.021> for robust estimation of multivariate location and scatter and multivariate outliers detection.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili <vakili.kaveh.email@gmail.com>

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Package FastHCS updated to version 0.0.6 with previous version 0.0.5 dated 2015-05-19

Title: FastHCS Robust Algorithm for Principal Component Analysis
Description: The FastHCS algorithm of Schmitt and Vakili (2014) <doi:10.1007/s11222-015-9602-5> for high-dimensional, robust PCA modelling and associated outlier detection and diagnostic tools.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili <vakili.kaveh.email@gmail.com>

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Package dbhydroR updated to version 0.2-5 with previous version 0.2-4 dated 2017-10-30

Title: 'DBHYDRO' Hydrologic and Water Quality Data
Description: Client for programmatic access to the South Florida Water Management District's 'DBHYDRO' database at <https://www.sfwmd.gov/science-data/dbhydro>, with functions for accessing hydrologic and water quality data.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>>)
Maintainer: Joseph Stachelek <stachel2@msu.edu>

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Package cartogram updated to version 0.0.3 with previous version 0.0.2 dated 2016-09-28

Title: Create Cartograms with R
Description: Construct continuous and non-contiguous area cartograms.
Author: Sebastian Jeworutzki [aut, cre] (<https://orcid.org/0000-0002-2671-5253>>), Timothee Giraud [ctb], Nicolas Lambert [ctb], Roger Bivand [cph], Edzer Pebesma [cph], Jakub Nowosad [ctb] (<https://orcid.org/0000-0002-1057-3721>>)
Maintainer: Sebastian Jeworutzki <sebastian.jeworutzki@ruhr-uni-bochum.de>

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Package Rraven updated to version 1.0.3 with previous version 1.0.2 dated 2018-03-11

Title: Connecting R and 'Raven' Sound Analysis Software
Description: A tool to exchange data between R and 'Raven' sound analysis software <http://www.birds.cornell.edu/brp/raven/RavenOverview.html> (Cornell Lab of Ornithology). Functions work on data formats compatible with the R package 'warbleR'.
Author: Marcelo Araya-Salas
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>

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Package microPop updated to version 1.4 with previous version 1.3 dated 2017-08-04

Title: Modelling Microbial Populations
Description: Modelling interacting microbial populations - example applications include human gut microbiota, rumen microbiota and phytoplankton. Solves a system of ordinary differential equations to simulate microbial growth and resource uptake over time.
Author: Helen Kettle [aut, cre]
Maintainer: Helen Kettle <Helen.Kettle@bioss.ac.uk>

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Package lavaan updated to version 0.6-1 with previous version 0.5-23.1097 dated 2017-02-24

Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre], Daniel Oberski [ctb], Jarrett Byrnes [ctb], Leonard Vanbrabant [ctb], Victoria Savalei [ctb], Ed Merkle [ctb], Michael Hallquist [ctb], Mijke Rhemtulla [ctb], Myrsini Katsikatsou [ctb], Mariska Barendse [ctb], Michael Chow [ctb], Terrence D. Jorgensen [ctb]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>

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Package gjam updated to version 2.2.2 with previous version 2.2.1 dated 2018-03-29

Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi.org/10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>

Diff between gjam versions 2.2.1 dated 2018-03-29 and 2.2.2 dated 2018-05-22

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New package rsinaica with initial version 0.5.0
Package: rsinaica
Type: Package
Title: Download Data from Mexico's Air Quality Information System
Version: 0.5.0
Authors@R: c(person("Diego", "Valle-Jones", email = "diego@diegovalle.net", role = c("aut", "cre")))
Description: Easy-to-use functions for downloading air quality data from the Mexican National Air Quality Information System (SINAICA). Allows you to query pollution and meteorological parameters from more than a hundred monitoring stations located throughout Mexico. See <http://sinaica.inecc.gob.mx> for more information.
License: MIT + file LICENSE
URL: https://hoyodesmog.diegovalle.net/rsinaica/, https://github.com/diegovalle/rsinaica
BugReports: https://github.com/diegovalle/rsinaica/issues
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 3.2)
Suggests: aire.zmvm, testthat, covr, knitr, rmarkdown, ggplot2, maps, mapproj, sp, ggmap, gstat, zoo, tidyr
Imports: jsonlite, httr, stringr, dplyr, lubridate
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-20 17:44:59 UTC; diego
Author: Diego Valle-Jones [aut, cre]
Maintainer: Diego Valle-Jones <diego@diegovalle.net>
Repository: CRAN
Date/Publication: 2018-05-22 13:01:50 UTC

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Package openair updated to version 2.4-2 with previous version 2.4-0 dated 2018-05-09

Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically hourly time series and both monitoring data and dispersion model output can be analysed. Many functions can also be applied to other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre], Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>

Diff between openair versions 2.4-0 dated 2018-05-09 and 2.4-2 dated 2018-05-22

 DESCRIPTION        |    8 +--
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Package ODEnetwork updated to version 1.3.1 with previous version 1.3.0 dated 2018-05-14

Title: Network of Differential Equations
Description: Simulates a network of ordinary differential equations of order two. The package provides an easy interface to construct networks. In addition you are able to define different external triggers to manipulate the trajectory. The method is described by Surmann, Ligges, and Weihs (2014) <doi:10.1109/ENERGYCON.2014.6850482>.
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>>)
Maintainer: Dirk Surmann <surmann@statistik.tu-dortmund.de>

Diff between ODEnetwork versions 1.3.0 dated 2018-05-14 and 1.3.1 dated 2018-05-22

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New package spMaps with initial version 0.3
Package: spMaps
Type: Package
Title: Europe SpatialPolygonsDataFrame Builder
Version: 0.3
Date: 2018-05-03
Authors@R: c( person("Jalal-Edine", "ZAWAM", email = "jalal-edine.zawam@rte-france.com", role = c("aut", "cre")), person("Benoit", "Thieurmel", email = "benoit.thieurmel@datastorm.fr", role = "aut"), person("RTE", role = "cph") )
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>
Description: Build custom Europe SpatialPolygonsDataFrame, if you don't know what is a SpatialPolygonsDataFrame see SpatialPolygons() in 'sp', by example for mapLayout() in 'antaresViz'. Antares is a powerful software developed by RTE to simulate and study electric power systems (more information about 'Antares' here: <https://antares.rte-france.com>).
URL: https://github.com/rte-antares-rpackage/antaresMaps
BugReports: https://github.com/rte-antares-rpackage/antaresMaps/issues
License: GPL (>= 2) | file LICENSE
LazyData: TRUE
Encoding: UTF-8
Depends: R (>= 2.10), sp, raster, rgeos
RoxygenNote: 6.0.1
Suggests: testthat, covr, antaresViz
NeedsCompilation: no
Packaged: 2018-05-15 07:04:00 UTC; jalazawa
Author: Jalal-Edine ZAWAM [aut, cre], Benoit Thieurmel [aut], RTE [cph]
Repository: CRAN
Date/Publication: 2018-05-22 12:22:28 UTC

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Package spatsurv updated to version 1.2 with previous version 1.1 dated 2017-03-23

Title: Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models
Description: Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models.
Author: Benjamin M. Taylor and Barry S. Rowlingson Additional contributions Ziyu Zheng
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>

Diff between spatsurv versions 1.1 dated 2017-03-23 and 1.2 dated 2018-05-22

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New package solrad with initial version 0.99.0
Package: solrad
Title: Calculating Solar Radiation and Related Variables Based on Location, Time and Topographical Conditions
Description: For surface energy models and estimation of solar positions and components with varying topography, time and locations. The functions calculate solar top-of-atmosphere, open, diffuse and direct components, atmospheric transmittance and diffuse factors, day length, sunrise and sunset, solar azimuth, zenith, altitude, incidence, and hour angles, earth declination angle, equation of time, and solar constant. Details about the methods and equations are explained in Seyednasrollah, Bijan, Mukesh Kumar, and Timothy E. Link. 'On the role of vegetation density on net snow cover radiation at the forest floor.' Journal of Geophysical Research: Atmospheres 118.15 (2013): 8359-8374, <doi:10.1002/jgrd.50575>.
Version: 0.99.0
Date: 2018-05-18
Author: Bijan Seyednasrollah
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>
Depends: R (>= 2.1.1)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
URL: https://github.com/bnasr/solrad/
BugReports: https://github.com/bnasr/solrad/issues
NeedsCompilation: no
Packaged: 2018-05-18 22:34:38 UTC; bijan
Repository: CRAN
Date/Publication: 2018-05-22 12:04:12 UTC

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New package PetfindeR with initial version 1.1.3
Package: PetfindeR
Type: Package
Title: 'Petfinder' API Wrapper
Version: 1.1.3
Author: Aaron Schlegel
Maintainer: Aaron Schlegel <aaron@aaronschlegel.com>
Description: Wrapper of the 'Petfinder API' <https://www.petfinder.com/developers/api-docs> that implements methods for interacting with and extracting data from the 'Petfinder' database. The 'Petfinder REST API' allows access to the 'Petfinder' database, one of the largest online, searchable databases of adoptable animals and animal welfare organizations across North America.
Encoding: UTF-8
LazyData: true
Imports: dplyr, httr, jsonlite, plyr
RoxygenNote: 6.0.1
License: MIT + file LICENSE
URL: https://github.com/aschleg/PetfindeR
VignetteBuilder: knitr
Suggests: R6, httptest, testthat, knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-05-19 12:58:56 UTC; aaronschlegel
Repository: CRAN
Date/Publication: 2018-05-22 12:23:55 UTC

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New package MaskJointDensity with initial version 1.0
Package: MaskJointDensity
Type: Package
Title: Masking, Unmasking and Restoring Confidential Data
Version: 1.0
Date: 2018-05-05
Author: Yan-Xia Lin [aut, cre], Luke Mazur [aut, cre], Jordan Morris [ctb]
Maintainer: Luke Mazur <lm810@uowmail.edu.au>
Description: Three key functionalities are present. It is able to mask confidential data using multiplicative noise. It is able to unmask this data while still preserving confidentiality. It is able to calculate the numerical joint density function of the original data from the unmasked data, as well as obtaining a sample from the marginal density functions of the unmasked data. The final results are a reasonable approximation to the original data for the purposes of analysis (Lin et al. (2018) <http://www.tdp.cat/issues16/abs.a271a17.php>).
License: GPL-2
Imports: ks,np,plyr,parallel,MASS
Packaged: 2018-05-17 12:28:14 UTC; lmm
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-05-22 12:13:25 UTC

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Package lgcp updated to version 1.5 with previous version 1.4 dated 2017-04-12

Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle. Additional code contributions from Edzer Pebesma, Dominic Schumacher.
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>

Diff between lgcp versions 1.4 dated 2017-04-12 and 1.5 dated 2018-05-22

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Package intRegGOF updated to version 0.85-5 with previous version 0.85-1 dated 2011-11-17

Title: Integrated Regression Goodness of Fit
Description: Performs Goodness of Fit for regression models using Integrated Regression method. Works for several different fitting techniques.
Author: Jorge Luis Ojeda Cabrera <jojeda@unizar.es>
Maintainer: Jorge Luis Ojeda Cabrera <jojeda@unizar.es>

Diff between intRegGOF versions 0.85-1 dated 2011-11-17 and 0.85-5 dated 2018-05-22

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New package interlineaR with initial version 1.0
Package: interlineaR
Type: Package
Title: Importing Interlinearized Corpora and Dictionaries as Produced by Descriptive Linguistics Software
Version: 1.0
Date: 2018-05-18
Authors@R: person("Sylvain", "Loiseau", email = "sylvain.loiseau@univ-paris13.fr", role = c("aut", "cre"))
Description: Interlinearized glossed texts (IGT) are used in descriptive linguistics for representing a morphological analysis of a text through a morpheme-by-morpheme gloss. 'InterlineaR' provide a set of functions that targets several popular formats of IGT ('SIL Toolbox', 'EMELD XML') and that turns an IGT into a set of data frames following a relational model (the tables represent the different linguistic units: texts, sentences, word, morphems). The same pieces of software ('SIL FLEX', 'SIL Toolbox') typically produce dictionaries of the morphemes used in the glosses. 'InterlineaR' provide a function for turning the LIFT XML dictionary format into a set of data frames following a relational model in order to represent the dictionary entries, the sense(s) attached to the entries, the example(s) attached to senses, etc.
License: BSD_3_clause + file LICENSE
Depends: R (>= 2.14), xml2, reshape2
LazyData: true
URL: https://github.com/sylvainloiseau/interlineaR
Collate: read.emeld.R read.lift.R interlineaR-package.R read.toolbox.R read.pangloss.R dataset.R lift.specifications.R common.R
BuildResaveData: xz
Encoding: UTF-8
RoxygenNote: 6.0.1
Suggests: kableExtra, knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-05-19 06:35:56 UTC; sloiseau
Author: Sylvain Loiseau [aut, cre]
Maintainer: Sylvain Loiseau <sylvain.loiseau@univ-paris13.fr>
Repository: CRAN
Date/Publication: 2018-05-22 12:17:37 UTC

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New package IATanalytics with initial version 0.1.0
Package: IATanalytics
Type: Package
Title: Compute Effect Sizes and Reliability for Implicit Association Test (IAT) Data
Version: 0.1.0
Author: Daniel Storage [aut, cre]
Maintainer: Daniel Storage <research@danielstorage.com>
Description: Quickly score raw data outputted from an Implicit Association Test (IAT; Greenwald, McGhee, & Schwartz, 1998) <doi:10.1037/0022-3514.74.6.1464>. IAT scores are calculated as specified by Greenwald, Nosek, and Banaji (2003) <doi:10.1037/0022-3514.85.2.197>. The output of this function is a data frame that consists of four rows containing the following information: (1) the overall IAT effect size for the participant's dataset, (2) the effect size calculated for odd trials only, (3) the effect size calculated for even trials only, and (4) the proportion of trials with reaction times under 300ms (which is important for exclusion purposes). Items (2) and (3) allow for a measure of the internal consistency of the IAT. Specifically, you can use the subsetted IAT effect sizes for odd and even trials to calculate Cronbach's alpha across participants in the sample. The input function consists of three arguments. First, indicate the name of the dataset to be analyzed. This is the only required input. Second, indicate the number of trials in your entire IAT (the default is set to 220, which is typical for most IATs). Last, indicate whether congruent trials (e.g., flowers and pleasant) or incongruent trials (e.g., guns and pleasant) were presented first for this participant (the default is set to congruent). Data files should consist of six columns organized in order as follows: Block (0-6), trial (0-19 for training blocks, 0-39 for test blocks), category (dependent on your IAT), the type of item within that category (dependent on your IAT), a dummy variable indicating whether the participant was correct or incorrect on that trial (0=correct, 1=incorrect), and the participant’s reaction time (in milliseconds). A sample dataset (titled 'sampledata') is included in this package to practice with.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: stats
NeedsCompilation: no
Packaged: 2018-05-18 19:32:40 UTC; Sabby
Repository: CRAN
Date/Publication: 2018-05-22 12:01:43 UTC

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New package droptest with initial version 0.1.0
Package: droptest
Title: Simulates LOX/GOX Drop Testing
Version: 0.1.0
Authors@R: person("Chad", "Ross", email = "chad.ross@gmail.com", role = c("aut", "cre"))
Author: Chad Ross [aut, cre]
Maintainer: Chad Ross <chad.ross@gmail.com>
Description: Generates simulated data representing the LOX/GOX drop testing process (also known as impact testing). A simulated process allows for accelerated study of test behavior. Functions are provided to simulate trials, test series, and groups of test series. Functions for creating plots specific to this process are also included. Test attributes and criteria can be set arbitrarily. This work is not endorsed by or affiliated with NASA. See "ASTM G86-17, Standard Test Method for Determining Ignition Sensitivity of Materials to Mechanical Impact in Ambient Liquid Oxygen and Pressurized Liquid and Gaseous Oxygen Environments" <doi:10.1520/G0086-17>.
Depends: R (>= 3.4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: data.table
URL: https://github.com/chadr/droptest
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-19 16:45:35 UTC; Chad
Repository: CRAN
Date/Publication: 2018-05-22 12:39:22 UTC

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Package rebmix updated to version 2.10.2 with previous version 2.10.1 dated 2018-04-07

Title: Finite Mixture Modeling, Clustering & Classification
Description: R functions for random univariate and multivariate finite mixture model generation, estimation, clustering and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, binomial, Poisson, Dirac or circular von Mises parametric families.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>

Diff between rebmix versions 2.10.1 dated 2018-04-07 and 2.10.2 dated 2018-05-22

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Package rcarbon updated to version 1.1.2 with previous version 1.1.1 dated 2018-04-28

Title: Calibration and Analysis of Radiocarbon Dates
Description: Enables the calibration and analysis of radiocarbon dates, often but not exclusively for the purposes of archaeological research. It includes functions not only for basic calibration, uncalibration, and plotting of one or more dates, but also a statistical framework for building demographic and related longitudinal inferences from aggregate radiocarbon date lists, including: Monte-Carlo simulation test (Timpson et al 2014 <doi:10.1016/j.jas.2014.08.011>), random mark permutation test (Crema et al 2016 <doi:10.1371/journal.pone.0154809>) and spatial permutation tests (Crema, Bevan, and Shennan 2017 <doi:10.1016/j.jas.2017.09.007>).
Author: Andrew Bevan [aut], Enrico Crema [aut, cre], Fabio Silva [ctb]
Maintainer: Enrico Crema <enrico.crema@gmail.com>

Diff between rcarbon versions 1.1.1 dated 2018-04-28 and 1.1.2 dated 2018-05-22

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Package prediction updated to version 0.3.6 with previous version 0.3.2 dated 2018-04-12

Title: Tidy, Type-Safe 'prediction()' Methods
Description: A one-function package containing 'prediction()', a type-safe alternative to 'predict()' that always returns a data frame. The package currently supports common model types (e.g., "lm", "glm") from the 'stats' package, as well as numerous other model classes from other add-on packages. See the README or main package documentation page for a complete listing.
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>>), Carl Ganz [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

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Package ore updated to version 1.6.1 with previous version 1.6.0 dated 2017-04-13

Title: An R Interface to the Onigmo Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling regular expressions, based on the Onigmo library. Offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>

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Package miniGUI updated to version 0.8-1 with previous version 0.8.0 dated 2012-09-04

Title: Tcl/Tk Quick and Simple Function GUI
Description: Quick and simple Tcl/Tk Graphical User Interface to call functions. Also comprises a very simple experimental GUI framework.
Author: Jorge Luis Ojeda Cabrera <jojeda@unizar.es>
Maintainer: Jorge Luis Ojeda Cabrera <jojeda@unizar.es>

Diff between miniGUI versions 0.8.0 dated 2012-09-04 and 0.8-1 dated 2018-05-22

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Package mapplots updated to version 1.5.1 with previous version 1.5 dated 2014-10-30

Title: Data Visualisation on Maps
Description: Create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data. The package was developed for displaying fisheries data but most functions can be used for more generic data visualisation.
Author: Hans Gerritsen
Maintainer: Hans Gerritsen <hans.gerritsen@marine.ie>

Diff between mapplots versions 1.5 dated 2014-10-30 and 1.5.1 dated 2018-05-22

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Package liftLRD updated to version 1.0-7 with previous version 1.0-6 dated 2017-09-11

Title: Wavelet Lifting Estimators of the Hurst Exponent for Regularly and Irregularly Sampled Time Series
Description: Implementations of Hurst exponent estimators based on the relationship between wavelet lifting scales and wavelet energy.
Author: Marina Knight [aut], Guy Nason [ctb], Matt Nunes [aut, cre]
Maintainer: Matt Nunes <m.nunes@lancaster.ac.uk>

Diff between liftLRD versions 1.0-6 dated 2017-09-11 and 1.0-7 dated 2018-05-22

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Package cruts updated to version 0.4 with previous version 0.3 dated 2016-05-12

Title: Interface to Climatic Research Unit Time-Series Version 3.21 Data
Description: Functions for reading in and manipulating CRU TS3.21: Climatic Research Unit (CRU) Time-Series (TS) Version 3.21 data.
Author: Benjamin M. Taylor Additional contributions Bikash Parida
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>

Diff between cruts versions 0.3 dated 2016-05-12 and 0.4 dated 2018-05-22

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Package cranly updated to version 0.2 with previous version 0.1 dated 2018-03-28

Title: Package Directives and Collaboration Networks in CRAN
Description: Provides core visualisations and summaries for the CRAN package database. The package provides comprehensive methods for cleaning up and organising the information in the CRAN package database, for building package directives networks (depends, imports, suggests, enhances, linking to) and collaboration networks, producing package dependence trees, and for computing useful summaries and producing interactive visualisations from the resulting networks. The package also provides functions to coerce the networks to 'igraph' <https://CRAN.R-project.org/package=igraph> objects for further analyses and modelling.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>>)
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>

Diff between cranly versions 0.1 dated 2018-03-28 and 0.2 dated 2018-05-22

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Package ziphsmm updated to version 2.0.6 with previous version 2.0.5 dated 2018-04-29

Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly minimizing the negative log likelihood function using the gradient descent algorithm. Multiple starting values should be used to avoid local minima.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun (Jack) Xu <zekunxu@gmail.com>

Diff between ziphsmm versions 2.0.5 dated 2018-04-29 and 2.0.6 dated 2018-05-22

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Package srvyr updated to version 0.3.3 with previous version 0.3.2 dated 2018-05-06

Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre], Thomas Lumley [ctb]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>

Diff between srvyr versions 0.3.2 dated 2018-05-06 and 0.3.3 dated 2018-05-22

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Package processmapR updated to version 0.3.1 with previous version 0.3.0 dated 2018-03-28

Title: Construct Process Maps Using Event Data
Description: Visualize of process maps based on event logs, in the form of directed graphs. Part of the 'bupaR' framework.
Author: Gert Janssenswillen [aut, cre], Benoît Depaire [ctb], Felix Mannhardt [ctb], Thijs Beuving [ctb]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>

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Package prioritizrdata updated to version 0.2.2 with previous version 0.2.1 dated 2017-11-12

Title: Conservation Planning Data Sets
Description: Conservation planning data sets for learning how to use the 'prioritizr' package <https://CRAN.R-project.org/package=prioritizr>.
Author: Jeffrey O Hanson [aut], Richard Schuster [aut, cre], Nina Morrell [aut], Matthew Strimas-Mackey [aut], Matthew E Watts [aut], Peter Arcese [aut], Joeseph Bennett [aut], Hugh P Possingham [aut]
Maintainer: Richard Schuster <mail@richard-schuster.com>

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Package FinePop updated to version 1.5.0 with previous version 1.4.1 dated 2017-11-19

Title: Fine-Scale Population Analysis
Description: Statistical tool set for population genetics. The package provides following functions: 1) empirical Bayes estimator of Fst and other measures of genetic differentiation, 2) regression analysis of environmental effects on genetic differentiation using bootstrap method, 3) interfaces to read and manipulate 'GENEPOP' format data files and allele/haplotype frequency format files.
Author: Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada
Maintainer: Reiichiro Nakamichi <nakamichi@affrc.go.jp>

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Package bmixture updated to version 1.1 with previous version 0.8 dated 2018-04-27

Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation for finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the recent improvements in Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <https://doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <https://doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi <https://orcid.org/0000-0001-9538-0648>
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>

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More information about bmixture at CRAN
Permanent link

Package BIS updated to version 0.2.1 with previous version 0.2.0 dated 2018-04-09

Title: Programmatic Access to Bank for International Settlements Data
Description: Provides an interface to data provided by the Bank for International Settlements <https://www.bis.org>, allowing for programmatic retrieval of a large quantity of (central) banking data.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>

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Package BIFIEsurvey updated to version 2.5-44 with previous version 2.4-9 dated 2018-04-09

Title: Tools for Survey Statistics in Educational Assessment
Description: Contains tools for survey statistics (especially in educational assessment) for datasets with replication designs (jackknife, bootstrap, replicate weights; see Kolenikov, 2010). Descriptive statistics, linear and logistic regression, path models for manifest variables with measurement error correction and two-level hierarchical regressions for weighted samples are included. Statistical inference can be conducted for multiply imputed datasets and nested multiply imputed datasets. This package is developed by BIFIE (Federal Institute for Educational Research, Innovation and Development of the Austrian School System; Salzburg, Austria).
Author: BIFIE
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between BIFIEsurvey versions 2.4-9 dated 2018-04-09 and 2.5-44 dated 2018-05-22

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Permanent link

Package ALA4R updated to version 1.6.0 with previous version 1.5.6 dated 2017-02-18

Title: Atlas of Living Australia (ALA) Data and Resources in R
Description: The Atlas of Living Australia (ALA) provides tools to enable users of biodiversity information to find, access, combine and visualise data on Australian plants and animals; these have been made available from <http://ala.org.au/>. ALA4R provides a subset of the tools to be directly used within R. It enables the R community to directly access data and resources hosted by the ALA.
Author: Peggy Newman [aut, cre], Ben Raymond [aut], Jeremy VanDerWal [aut], Lee Belbin [aut], Michael Sumner [ctb], Tom August [ctb], John Baumgartner [ctb]
Maintainer: Peggy Newman <peggy.newman@csiro.au>

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Package quadprogXT updated to version 0.0.3 with previous version 0.0.2 dated 2018-02-04

Title: Quadratic Programming with Absolute Value Constraints
Description: Extends the quadprog package to solve quadratic programs with absolute value constraints and absolute values in the objective function.
Author: Bob Harlow [aut, cre]
Maintainer: Bob Harlow <rharlow86@gmail.com>

Diff between quadprogXT versions 0.0.2 dated 2018-02-04 and 0.0.3 dated 2018-05-22

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More information about quadprogXT at CRAN
Permanent link

Package qmethod updated to version 1.5.4 with previous version 1.5.2 dated 2017-03-21

Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology, used to identify distinct perspectives existing within a group. This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see <http://qmethod.org>). A single function runs the full analysis. Each step can be run separately using the corresponding functions: for automatic flagging of Q-sorts (manual flagging is optional), for statement scores, for distinguishing and consensus statements, and for general characteristics of the factors. Additional functions are available to import and export data, to print and plot, to import raw data from individual *.CSV files, and to make printable cards. The package also offers functions to print Q cards and to generate Q distributions for study administration. The package uses principal components and it allows manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix. See further details in the package documentation, and in the web pages below, which include a cookbook, guidelines for more advanced analysis (how to perform manual flagging or change the sign of factors), data management, and a beta graphical user interface for online and offline use.
Author: Aiora Zabala [aut, cre] (Main author, <https://orcid.org/0000-0001-8534-3325>>), Maximilian Held [aut] (Author of additional data management functions)
Maintainer: Aiora Zabala <aiora.zabala@gmail.com>

Diff between qmethod versions 1.5.2 dated 2017-03-21 and 1.5.4 dated 2018-05-22

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Package genotypeR updated to version 0.0.1.8 with previous version 0.0.1.7 dated 2018-05-13

Title: SNP Genotype Marker Design and Analysis
Description: We implement a common genotyping workflow with a standardized software interface. 'genotypeR' designs genotyping markers from vcf files, outputs markers for multiplexing suitability on various platforms (Sequenom and Illumina GoldenGate), and provides various QA/QC and analysis functions. We developed this package to analyze data in Stevison LS, SA Sefick, CA Rushton, and RM Graze. 2017. Invited Review: Recombination rate plasticity: revealing mechanisms by design. Philosophical Transactions Royal Society London B Biol Sci 372:1-14. <DOI:10.1098/rstb.2016.0459>, and have published it here Sefick, S.A., M.A. Castronova, and L.S. Stevison. 2017. GENOTYPER: An integrated R packages for single nuleotide polymorphism genotype marker design and data analysis. Methods in Ecology and Evolution 9: 1318-1323. <DOI: 10.1111/2041-210X.12965>.
Author: Stephen Alfred Sefick [aut, cre], Magdelena A Castronova [aut], Laurie S Stevison [aut]
Maintainer: Stephen Alfred Sefick <ssefick@gmail.com>

Diff between genotypeR versions 0.0.1.7 dated 2018-05-13 and 0.0.1.8 dated 2018-05-22

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Mon, 21 May 2018

Package momentuHMM updated to version 1.4.1 with previous version 1.4.0 dated 2018-02-27

Title: Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. These include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2017) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock, Theo Michelot
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>

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Package MCMCvis updated to version 0.11.0 with previous version 0.10.2 dated 2018-05-02

Title: Tools to Visualize, Manipulate, and Summarize MCMC Output
Description: Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with JAGS, Stan, or other MCMC samplers.
Author: Casey Youngflesh [aut, cre] (<https://orcid.org/0000-0001-6343-3311>>), Christian Che-Castaldo [ctb], Tyler Hardy [ctb]
Maintainer: Casey Youngflesh <caseyyoungflesh@gmail.com>

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Package tabularaster updated to version 0.5.0 with previous version 0.4.0 dated 2017-12-10

Title: Tidy Tools for 'Raster' Data
Description: Facilities to work with vector and raster data in efficient repeatable and systematic work flow. Missing functionality in existing packages is included here to allow extraction from raster data with 'simple features' and 'Spatial' types and to make extraction consistent and straightforward. Extract cell numbers from raster data and return the cells, values and weights as a data frame rather than as lists of matrices or vectors. The functions here allow spatial data to be used without special handling for the format currently in use.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

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Package nlmixr updated to version 0.9.1-2 with previous version 0.9.1-0 dated 2018-05-19

Title: Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'RxODE' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut], Yuan Xiong [aut], Rik Schoemaker [aut], Justin Wilkins [aut], Mirjam Trame [aut], Teun Post [aut], Robert Leary [ctb], Wenping Wang [aut, cre], Hadley Wickham [ctb], Dirk Eddelbuettel [cph], David Ardia [cph], Katharine Mullen [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>

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Package imager updated to version 0.41.0 with previous version 0.40.2 dated 2017-04-24

Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.
Author: Simon Barthelme [aut, cre], David Tschumperle [ctb], Jan Wijffels [ctb], Haz Edine Assemlal [ctb]
Maintainer: Simon Barthelme <simon.barthelme@gipsa-lab.fr>

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Package HEMDAG updated to version 2.1.3 with previous version 2.1.2 dated 2018-05-07

Title: Hierarchical Ensemble Methods for Directed Acyclic Graphs
Description: An implementation of Hierarchical Ensemble Methods for Directed Acyclic Graphs (DAGs). The 'HEMDAG' package can be used to enhance the predictions of virtually any flat learning methods, by taking into account the hierarchical nature of the classes of a bio-ontology. 'HEMDAG' is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but it can be also safely applied to tree-structured taxonomies (as FunCat), since trees are DAGs. 'HEMDAG' scale nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).
Author: Marco Notaro [aut, cre] and Giorgio Valentini [aut] (AnacletoLab, Dipartimento di Informatica, Universita' degli Studi di Milano)
Maintainer: Marco Notaro <marco.notaro@unimi.it>

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Package clubSandwich updated to version 0.3.2 with previous version 0.3.1 dated 2018-04-04

Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections
Description: Provides several cluster-robust variance estimators (i.e., sandwich estimators) for ordinary and weighted least squares linear regression models, including the bias-reduced linearization estimator introduced by Bell and McCaffrey (2002) <http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf> and developed further by Pustejovsky and Tipton (2017) <DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating the variance- covariance matrix and for testing single- and multiple- contrast hypotheses based on Wald test statistics. Tests of single regression coefficients use Satterthwaite or saddle-point corrections. Tests of multiple- contrast hypotheses use an approximation to Hotelling's T-squared distribution. Methods are provided for a variety of fitted models, including lm() and mlm objects, glm(), ivreg (from package 'AER'), plm() (from package 'plm'), gls() and lme() (from 'nlme'), robu() (from 'robumeta'), and rma.uni() and rma.mv() (from 'metafor').
Author: James Pustejovsky [aut, cre]
Maintainer: James Pustejovsky <jepusto@gmail.com>

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Package SARP.compo updated to version 0.0.7 with previous version 0.0.3 dated 2018-01-12

Title: Network-based Interpretation of Changes in Compositional Data
Description: Provides a set of functions to interpret changes in compositional data based on a network representation of all pairwise ratio comparisons: computation of all pairwise ratio, construction of a p-value matrix of all pairwise tests of these ratios between conditions, conversion of this matrix to a network.
Author: Emmanuel Curis [aut, cre]
Maintainer: Emmanuel Curis <emmanuel.curis@parisdescartes.fr>

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Package openEBGM updated to version 0.6.0 with previous version 0.5.0 dated 2018-04-02

Title: EBGM Scores for Mining Large Contingency Tables
Description: An implementation of DuMouchel's (1999) <doi:10.1080/00031305.1999.10474456> Bayesian data mining method for the market basket problem. Calculates Empirical Bayes Geometric Mean (EBGM) and quantile scores from the posterior distribution using the Gamma-Poisson Shrinker (GPS) model to find unusually large cell counts in large, sparse contingency tables. Can be used to find unusually high reporting rates of adverse events associated with products. In general, can be used to mine any database where the co-occurrence of two variables or items is of interest. Also calculates relative and proportional reporting ratios. Builds on the work of the 'PhViD' package, from which much of the code is derived. Some of the added features include stratification to adjust for confounding variables and data squashing to improve computational efficiency. Now includes an implementation of the EM algorithm for hyperparameter estimation loosely derived from the 'mederrRank' package.
Author: John Ihrie [cre, aut], Travis Canida [aut], Ismaïl Ahmed [ctb] (author of 'PhViD' package (derived code)), Antoine Poncet [ctb] (author of 'PhViD'), Sergio Venturini [ctb] (author of 'mederrRank' package (derived code)), Jessica Myers [ctb] (author of 'mederrRank')
Maintainer: John Ihrie <John.Ihrie@fda.hhs.gov>

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Package EFAutilities updated to version 1.2.2 with previous version 1.2.1 dated 2017-12-09

Title: Utility Functions for Exploratory Factor Analysis
Description: A number of utility function for exploratory factor analysis are included in this package. In particular, it computes standard errors for parameter estimates and factor correlations under a variety of conditions.
Author: Guangjian Zhang, Ge Jiang, Minami Hattori, Lauren Trichtinger
Maintainer: Guangjian Zhang <gzhang3@nd.edu>

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Package easycsv updated to version 1.0.8 with previous version 1.0.7 dated 2018-01-23

Title: Load Multiple 'csv' and 'txt' Tables
Description: Allows users to easily read multiple comma separated tables and create a data frame under the same name. Is able to read multiple comma separated tables from a local directory, a zip file or a zip file on a remote directory.
Author: Dror Bogin [aut, cre]
Maintainer: Dror Bogin <dror.bogin@gmail.com>

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