Mon, 13 Jun 2016

Package zoon updated to version 0.5 with previous version 0.4.23 dated 2016-03-11

Title: Reproducible, Accessible & Shareable Species Distribution Modelling
Description: Reproducible and remixable species distribution modelling. The package reads user submitted modules from an online repository, runs full SDM workflows and returns output that is fully reproducible.
Author: Tim Lucas, Nick Golding, Tom August, Greg McInerny, Emiel van Loon
Maintainer: Tom August <tomaug@ceh.ac.uk>

Diff between zoon versions 0.4.23 dated 2016-03-11 and 0.5 dated 2016-06-13

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Package xmeta updated to version 1.1-1 with previous version 1.0-2 dated 2015-11-10

Title: A Toolbox for Multivariate Meta-Analysis
Description: A toolbox for meta-analysis. This package includes a collection of functions for (1) implementing robust multivariate meta-analysis of continuous or binary outcomes; and (2) testing and correcting of publication bias in multivariate meta-analysis settings.
Author: Yong Chen [aut, cre], Chuan Hong [aut], Haitao Chu [ctb], Yulun Liu [ctb]
Maintainer: Yong Chen <ychen.upenn@gmail.com>

Diff between xmeta versions 1.0-2 dated 2015-11-10 and 1.1-1 dated 2016-06-13

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Package xergm.common updated to version 1.7.3 with previous version 1.7.1 dated 2016-02-19

Title: Common Infrastructure for Extensions of Exponential Random Graph Models
Description: Datasets and definitions of generic functions used in dependencies of the xergm package.
Author: Philip Leifeld [aut, cre], Skyler J. Cranmer [ctb], Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>

Diff between xergm.common versions 1.7.1 dated 2016-02-19 and 1.7.3 dated 2016-06-13

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Package wmtsa updated to version 2.0-2 with previous version 2.0-1 dated 2016-05-20

Title: Wavelet Methods for Time Series Analysis
Description: Software to book Wavelet Methods for Time Series Analysis, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 2000.
Author: William Constantine [cre, aut], Donald Percival [aut]
Maintainer: William Constantine <wlbconstan@gmail.com>

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Package WikipediR updated to version 1.4.0 with previous version 1.3.0 dated 2016-01-13

Title: A MediaWiki API Wrapper
Description: A wrapper for the MediaWiki API, aimed particularly at the Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve page text, information about users or the history of pages, and elements of the category tree.
Author: Oliver Keyes [aut, cre], Brock Tilbert [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>

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Package WikidataR updated to version 1.1.0 with previous version 1.0.1 dated 2016-01-14

Title: API Client Library for 'Wikidata'
Description: An API client for the Wikidata <http://wikidata.org/> store of semantic data.
Author: Oliver Keyes [aut, cre], Christian Graul [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>

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Package VineCopula updated to version 2.0.1 with previous version 1.6-1 dated 2015-11-09

Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of vine copula models. The package includes tools for parameter estimation, model selection, simulation, goodness-of-fit tests, and visualization. Tools for estimation, selection and exploratory data analysis of bivariate copula models are also provided.
Author: Ulf Schepsmeier [aut], Jakob Stoeber [aut], Eike Christian Brechmann [aut], Benedikt Graeler [aut], Thomas Nagler [aut, cre], Tobias Erhardt [aut], Carlos Almeida [ctb], Aleksey Min [ctb, ths], Claudia Czado [ctb, ths], Mathias Hofmann [ctb], Matthias Killiches [ctb], Harry Joe [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>

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Package varhandle updated to version 2.0.0 with previous version 1.0.0 dated 2015-09-03

Title: Functions for Robust Variable Handling
Description: Variables are the fundamental parts of each programming language but handling them might be frustrating for programmers from time to time. This package contains some functions to help user (especially data explorers) to make more sense of their variables and take the most out of variables as well as their hardware. These functions are written, collected and crafted over some years of experience in statistical data analysis and for each of them there was a need. Functions in this package are suppose to be efficient and easy to use, hence they will be frequently updated to make them more convenient.
Author: Mehrad Mahmoudian [aut, cre]
Maintainer: Mehrad Mahmoudian <m.mahmoudian@gmail.com>

Diff between varhandle versions 1.0.0 dated 2015-09-03 and 2.0.0 dated 2016-06-13

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Package vaersvax updated to version 1.0.1 with previous version 1.0.0 dated 2016-04-23

Title: US Vaccine Adverse Event Reporting System (VAERS) Vaccine Data for Present
Description: US VAERS vaccine data for 01/01/2016 - 04/14/2016. If you want to explore the full VAERS data for 1990 - Present (data, symptoms, and vaccines), then check out the 'vaers' package from the URL below. The URL and BugReports below correspond to the 'vaers' package, of which 'vaersvax' is a small subset (2016 only). 'vaers' is not hosted on CRAN due to the large size of the data set. "VAERS is a national vaccine safety surveillance program co-sponsored by the US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA). VAERS is a post-marketing safety surveillance program, collecting information about adverse events (possible side effects) that occur after the administration of vaccines licensed for use in the United States." For more information about the data, visit https://vaers.hhs.gov/index. For information about vaccination/immunization hazards, visit http://www.questionuniverse.com/rethink.html/#vaccine.
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>

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Package vaersNDvax updated to version 1.0.1 with previous version 1.0.0 dated 2016-04-23

Title: Non-Domestic Vaccine Adverse Event Reporting System (VAERS) Vaccine Data for Present
Description: Non-Domestic VAERS vaccine data for 01/01/2016 - 04/14/2016. If you want to explore the full VAERS data for 1990 - Present (data, symptoms, and vaccines), then check out the 'vaersND' package from the URL below. The URL and BugReports below correspond to the 'vaersND' package, of which 'vaersNDvax' is a small subset (2016 only). 'vaersND' is not hosted on CRAN due to the large size of the data set. "VAERS is a national vaccine safety surveillance program co-sponsored by the US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA). VAERS is a post-marketing safety surveillance program, collecting information about adverse events (possible side effects) that occur after the administration of vaccines licensed for use in the United States." For more information about the data, visit https://vaers.hhs.gov/index. For information about vaccination/immunization hazards, visit http://www.questionuniverse.com/rethink.html/#vaccine.
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>

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New package units with initial version 0.1
Package: units
Version: 0.1
Title: Measurement Units of Physical Quantities for R Vectors
Authors@R: c(person("Edzer", "Pebesma", role = c("aut", "cre"), email = "edzer.pebesma@uni-muenster.de"))
Depends: R (>= 3.0.0)
Imports: utils, stats, udunits2
Suggests: knitr
VignetteBuilder: knitr
Description: Support for measurement units of physical quantities in R vectors, based on the udunits library from unidata.
License: GPL-2
URL: https://github.com/edzer/units/
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-09 12:21:19 UTC; edzer
Author: Edzer Pebesma [aut, cre]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Repository: CRAN
Date/Publication: 2016-06-09 15:19:23

More information about units at CRAN
Permanent link

Package treescape updated to version 1.9.17 with previous version 1.9.16 dated 2016-05-25

Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees. This package includes a shiny interface which can be started from R using 'treescapeServer()'.
Author: Thibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>

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Package TRAMPR updated to version 1.0-8 with previous version 1.0-7 dated 2012-03-23

Title: 'TRFLP' Analysis and Matching Package for R
Description: Matching terminal restriction fragment length polymorphism ('TRFLP') profiles between unknown samples and a database of known samples. TRAMPR facilitates analysis of many unknown profiles at once, and provides tools for working directly with electrophoresis output through to generating summaries suitable for community analyses with R's rich set of statistical functions. TRAMPR also resolves the issues of multiple 'TRFLP' profiles within a species, and shared 'TRFLP' profiles across species.
Author: Rich FitzJohn & Ian Dickie
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

Diff between TRAMPR versions 1.0-7 dated 2012-03-23 and 1.0-8 dated 2016-06-13

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Package tractor.base updated to version 3.0.2 with previous version 3.0.0 dated 2016-05-09

Title: Read, Manipulate and Visualise Magnetic Resonance Images
Description: Functions for working with magnetic resonance images. Analyze, NIfTI-1, NIfTI-2 and MGH format images can be read and written; DICOM files can only be read.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>

Diff between tractor.base versions 3.0.0 dated 2016-05-09 and 3.0.2 dated 2016-06-13

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New package tigger with initial version 0.2.5
Package: tigger
Type: Package
Version: 0.2.5
Date: 2016-06-07
Authors@R: c(person("Daniel", "Gadala-Maria", role=c("aut", "cre"), email="daniel.gadala-maria@yale.edu"), person("Jason", "Vander Heiden", role=c("ctb"), email="jason.vanderheiden@yale.edu"), person("Steven", "Kleinstein", role=c("aut", "cph"), email="steven.kleinstein@yale.edu"))
Title: R Tools for Inferring New Immunoglobulin Alleles from Rep-Seq Data
Description: Infers the V genotype of an individual from immunoglobulin (Ig) repertoire-sequencing (Rep-Seq) data, including detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences.
License: CC BY-NC-SA 4.0
URL: http://tigger.readthedocs.io
BugReports: https://bitbucket.org/kleinstein/tigger/issues
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr
Depends: R (>= 3.2.3), alakazam (>= 0.2.1), shazam (>= 0.1.2), ggplot2 (>= 2.0.0)
Imports: tidyr, dplyr, doParallel, foreach, graphics, grid, iterators, parallel, stats
Suggests: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-08 07:38:12 UTC; dgada_000
Author: Daniel Gadala-Maria [aut, cre], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Maintainer: Daniel Gadala-Maria <daniel.gadala-maria@yale.edu>
Repository: CRAN
Date/Publication: 2016-06-08 10:07:41

More information about tigger at CRAN
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Package tidyr updated to version 0.5.0 with previous version 0.4.1 dated 2016-02-05

Title: Easily Tidy Data with `spread()` and `gather()` Functions
Description: An evolution of 'reshape2'. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with 'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between tidyr versions 0.4.1 dated 2016-02-05 and 0.5.0 dated 2016-06-13

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 tidyr-0.5.0/tidyr/src/simplifyPieces.cpp           |    8 +
 tidyr-0.5.0/tidyr/tests/testthat/test-complete.R   |   11 ++
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 51 files changed, 603 insertions(+), 243 deletions(-)

More information about tidyr at CRAN
Permanent link

Package tablaxlsx updated to version 1.2.0 with previous version 1.1.0 dated 2016-05-02

Title: Write Formatted Tables in Excel Workbooks
Description: Some functions are included in this package for writing tables in Excel format suitable for distribution.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@ono.com>

Diff between tablaxlsx versions 1.1.0 dated 2016-05-02 and 1.2.0 dated 2016-06-13

 DESCRIPTION          |    8 +++---
 MD5                  |   10 +++----
 R/escribirTabla.R    |   67 +++++++++++++++++++++++++++++++--------------------
 data/estilosDGE.rda  |binary
 man/escribirTabla.Rd |   10 +++++--
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 6 files changed, 61 insertions(+), 40 deletions(-)

More information about tablaxlsx at CRAN
Permanent link

New package TANDEM with initial version 0.9.1
Package: TANDEM
Type: Package
Title: A Two-Stage Approach to Maximize Interpretability of Drug Response Models Based on Multiple Molecular Data Types
Version: 0.9.1
Date: 2016-06-02
Author: Nanne Aben
Maintainer: Nanne Aben <nanne.aben@gmail.com>
Description: A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016, in press), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.
Depends: R (>= 2.10)
Imports: glmnet
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-08 08:58:55 UTC; nanne
Repository: CRAN
Date/Publication: 2016-06-08 11:45:56

More information about TANDEM at CRAN
Permanent link

Package SPOT updated to version 1.1.0 with previous version 1.0.5543 dated 2015-04-27

Title: Sequential Parameter Optimization Toolbox
Description: The Sequential Parameter Optimization Toolbox provides a set of tools for Parameter-tuning, based on modelling techniques, DoE and statistical methods.
Author: Thomas Bartz-Beielstein [aut], Martin Zaefferer [cre, ctb], Joerg Ziegenhirt [ctb], Wolfgang Konen [ctb], Oliver Flasch [ctb], Patrick Koch [ctb], Martina Friese [ctb]
Maintainer: Martin Zaefferer <martin.zaefferer@gmx.de>

Diff between SPOT versions 1.0.5543 dated 2015-04-27 and 1.1.0 dated 2016-06-13

 DESCRIPTION                              |   28 +
 MD5                                      |  488 +++++++++++++++----------------
 NAMESPACE                                |    8 
 NEWS                                     |    6 
 R/spot.R                                 |   13 
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More information about SPOT at CRAN
Permanent link

Package SpatialPosition updated to version 1.1.1 with previous version 1.1 dated 2016-03-18

Title: Spatial Position Models
Description: Computes spatial position models: Stewart potentials, Reilly catchment areas, Huff catchment areas.
Author: Timothée Giraud [cre, aut], Hadrien Commenges [aut], Joël Boulier [ctb]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>

Diff between SpatialPosition versions 1.1 dated 2016-03-18 and 1.1.1 dated 2016-06-13

 DESCRIPTION                   |   12 +++---
 MD5                           |   60 +++++++++++++++++-----------------
 NAMESPACE                     |    1 
 NEWS                          |   10 +++++
 R/contourStewart.R            |    5 +-
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 R/rasterToContourPoly.R       |   74 ++++++++++++++++++++++++++++++++++--------
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 R/stewart.R                   |   67 ++++++++++++++++++--------------------
 build/vignette.rds            |binary
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 vignettes/SpatialPosition.Rmd |    6 +--
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More information about SpatialPosition at CRAN
Permanent link

Package sparsevar updated to version 0.0.5 with previous version 0.0.3 dated 2016-05-04

Title: A Package for Sparse VAR/VECM Estimation
Description: A wrapper for sparse VAR/VECM time series models estimation using penalties like ENET, SCAD and MCP.
Author: Simone Vazzoler [aut, cre], Lorenzo Frattarolo [aut], Monica Billio [aut]
Maintainer: Simone Vazzoler <svazzole@gmail.com>

Diff between sparsevar versions 0.0.3 dated 2016-05-04 and 0.0.5 dated 2016-06-13

 sparsevar-0.0.3/sparsevar/man/svar.Rd                                                                            |only
 sparsevar-0.0.5/sparsevar/DESCRIPTION                                                                            |   18 -
 sparsevar-0.0.5/sparsevar/MD5                                                                                    |   43 ++--
 sparsevar-0.0.5/sparsevar/NEWS.md                                                                                |only
 sparsevar-0.0.5/sparsevar/R/createSparseMatrix.R                                                                 |   19 +
 sparsevar-0.0.5/sparsevar/R/estimateVAR.R                                                                        |  103 ++++++++--
 sparsevar-0.0.5/sparsevar/R/estimateVECM.R                                                                       |    1 
 sparsevar-0.0.5/sparsevar/R/simulateVAR.R                                                                        |    6 
 sparsevar-0.0.5/sparsevar/R/sparsevar.R                                                                          |    6 
 sparsevar-0.0.5/sparsevar/README.md                                                                              |   52 ++++-
 sparsevar-0.0.5/sparsevar/build/vignette.rds                                                                     |binary
 sparsevar-0.0.5/sparsevar/inst/doc/sparsevar.R                                                                   |    2 
 sparsevar-0.0.5/sparsevar/inst/doc/sparsevar.Rmd                                                                 |   25 +-
 sparsevar-0.0.5/sparsevar/inst/doc/sparsevar.pdf                                                                 |binary
 sparsevar-0.0.5/sparsevar/man/createSparseMatrix.Rd                                                              |    5 
 sparsevar-0.0.5/sparsevar/man/estimateVAR.Rd                                                                     |   30 ++
 sparsevar-0.0.5/sparsevar/man/sparsevar.Rd                                                                       |only
 sparsevar-0.0.5/sparsevar/vignettes/sparsevar.Rmd                                                                |   25 +-
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More information about sparsevar at CRAN
Permanent link

Package spaa updated to version 0.2.2 with previous version 0.2.1 dated 2013-08-23

Title: SPecies Association Analysis
Description: Miscellaneous functions for analysing species association and niche overlap.
Author: Jinlong Zhang [aut, cre]
Maintainer: Jinlong Zhang <jinlongzhang01@gmail.com>

Diff between spaa versions 0.2.1 dated 2013-08-23 and 0.2.2 dated 2016-06-13

 DESCRIPTION                 |   13 ++++---
 MD5                         |   25 +++++++--------
 NAMESPACE                   |    3 +
 R/add.col.R                 |   34 ++++++++++----------
 R/niche.overlap.R           |   72 ++++++++++++++++++++++----------------------
 R/niche.overlap.boot.R      |    4 +-
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 R/niche.width.R             |   44 +++++++++++++-------------
 R/plotlowertri.R            |   32 +++++++++----------
 R/plotnetwork.R             |   72 ++++++++++++++++++++++----------------------
 R/sp.pair.R                 |   26 +++++++--------
 R/sub.sp.matrix.R           |   14 ++++----
 README.md                   |only
 14 files changed, 183 insertions(+), 176 deletions(-)

More information about spaa at CRAN
Permanent link

Package soiltexture updated to version 1.4.1 with previous version 1.3.3 dated 2015-05-26

Title: Functions for Soil Texture Plot, Classification and Transformation
Description: "The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle (classification) into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Many (> 15) texture triangles from all around the world are predefined in the package. A simple text based graphical user interface is provided: soiltexture_gui().
Author: Julien Moeys [aut, cre], Wei Shangguan [ctb], Rainer Petzold [ctb], Budiman Minasny [ctb], Bogdan Rosca [ctb], Nic Jelinski [ctb], Wiktor Zelazny [ctb], Rodolfo Marcondes Silva Souza [ctb], Jose Lucas Safanelli [ctb], Alexandre ten Caten [ctb]
Maintainer: Julien Moeys <jules_m78-soiltexture@yahoo.fr>

Diff between soiltexture versions 1.3.3 dated 2015-05-26 and 1.4.1 dated 2016-06-13

 DESCRIPTION                       |   12 +++---
 MD5                               |   68 +++++++++++++++++++-------------------
 NAMESPACE                         |   36 +++++++++++++++-----
 NEWS                              |    6 +++
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Package simsem updated to version 0.5-13 with previous version 0.5-12 dated 2016-02-29

Title: SIMulated Structural Equation Modeling
Description: Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Author: Sunthud Pornprasertmanit [aut, cre], Patrick Miller [aut], Alexander Schoemann [aut], Corbin Quick [ctb], Terry Jorgensen [ctb]
Maintainer: Sunthud Pornprasertmanit <psunthud@gmail.com>

Diff between simsem versions 0.5-12 dated 2016-02-29 and 0.5-13 dated 2016-06-13

 DESCRIPTION          |    8 +++---
 MD5                  |   14 +++++------
 R/generate.R         |    6 ++---
 R/sim.R              |   13 +++++-----
 R/summarySimResult.R |   61 +++++++++++++++++++++++++++++++++++----------------
 R/validate.R         |    7 ++++-
 man/setPopulation.Rd |    4 +--
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 8 files changed, 72 insertions(+), 43 deletions(-)

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Package SimDesign updated to version 1.0 with previous version 0.9 dated 2016-04-27

Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help safely and efficiently organize Monte Carlo simulations in R. The package controls the structure and back-end of Monte Carlo simulations by utilizing a general generate-analyse-summarise strategy. The functions provided control common simulation issues such as re-simulating non-convergent results, support parallel back-end and MPI distributed computations, save and restore temporary files, aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

Diff between SimDesign versions 0.9 dated 2016-04-27 and 1.0 dated 2016-06-13

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New package sfinx with initial version 1.7.0
Package: sfinx
Type: Package
Title: Straightforward Filtering Index for AP-MS Data Analysis (SFINX)
Version: 1.7.0
Date: 2016-06-13
Authors@R: c( person("Kevin", "Titeca", email = "sfinxinteractomics@gmail.com", role = c("aut", "cre")), person("Jan", "Tavernier", role = "ths"), person("Sven", "Eyckerman", role = "ths"))
Description: The straightforward filtering index (SFINX) identifies true positive protein interactions in a fast, user-friendly, and highly accurate way. It is not only useful for the filtering of affinity purification - mass spectrometry (AP-MS) data, but also for similar types of data resulting from other co-complex interactomics technologies, such as TAP-MS, Virotrap and BioID. SFINX can also be used via the website interface at <http://sfinx.ugent.be>.
License: Apache License 2.0
LazyData: TRUE
Depends: R (>= 3.2.3)
URL: http://sfinx.ugent.be
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-13 14:59:35 UTC; Kevin
Author: Kevin Titeca [aut, cre], Jan Tavernier [ths], Sven Eyckerman [ths]
Maintainer: Kevin Titeca <sfinxinteractomics@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-13 17:10:32

More information about sfinx at CRAN
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Package sesem updated to version 1.0.2 with previous version 1.0.1 dated 2014-03-04

Title: Spatially Explicit Structural Equation Modeling
Description: Structural equation modeling is a powerful statistical approach for the testing of networks of direct and indirect theoretical causal relationships in complex data sets with inter-correlated dependent and independent variables. Here we implement a simple method for spatially explicit structural equation modeling based on the analysis of variance co-variance matrices calculated across a range of lag distances. This method provides readily interpreted plots of the change in path coefficients across scale.
Author: Eric Lamb [aut, cre], Kerrie Mengersen [aut], Katherine Stewart [aut], Udayanga Attanayake [aut], Steven Siciliano [aut]
Maintainer: Eric Lamb <eric.lamb@usask.ca>

Diff between sesem versions 1.0.1 dated 2014-03-04 and 1.0.2 dated 2016-06-13

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More information about sesem at CRAN
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Package seqinr updated to version 3.1-5 with previous version 3.1-3 dated 2014-12-17

Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Includes also utilities for sequence data management under the ACNUC system.
Author: Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>

Diff between seqinr versions 3.1-3 dated 2014-12-17 and 3.1-5 dated 2016-06-13

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More information about seqinr at CRAN
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New package sEparaTe with initial version 0.1.0
Package: sEparaTe
Title: Maximum Likelihood Estimation and Likelihood Ratio Test Functions for Separable Variance-Covariance Structures
Version: 0.1.0
Authors@R: c( person("Ameur", "Manceur", email = "ameur.manceur@mail.mcgill.ca", role = "aut"), person("Timothy", "Schwinghamer", email = "schwinghamer@hotmail.com", role = "cre"), person("Pierre", "Dutilleul", email = "pierre.dutilleul@mcgill.ca", role = "aut") )
Maintainer: Timothy Schwinghamer <schwinghamer@hotmail.com>
Description: It combines maximum likelihood estimation of the parameters of matrix and 3rd-order tensor normal distributions with unstructured factor variance covariance matrices, two procedures, and unbiased modified likelihood ratio testing of simple and double separability for variance-covariance structures, two procedures.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2016-06-07 18:13:37 UTC; Timothy Schwinghamer
Author: Ameur Manceur [aut], Timothy Schwinghamer [cre], Pierre Dutilleul [aut]
Repository: CRAN
Date/Publication: 2016-06-08 00:59:40

More information about sEparaTe at CRAN
Permanent link

Package semTools updated to version 0.4-12 with previous version 0.4-11 dated 2016-03-01

Title: Useful Tools for Structural Equation Modeling
Description: Provides useful tools for structural equation modeling packages.
Author: Sunthud Pornprasertmanit [aut, cre], Patrick Miller [aut], Alexander Schoemann [aut], Yves Rosseel [aut], Corbin Quick [ctb], Mauricio Garnier-Villarreal [ctb], James Selig [ctb], Aaron Boulton [ctb], Kristopher Preacher [ctb], Donna Coffman [ctb], Mijke Rhemtulla [ctb], Alexander Robitzsch [ctb], Craig Enders [ctb], Ruber Arslan [ctb], Bell Clinton [ctb], Pavel Panko [ctb], Edgar Merkle [ctb], Terry Jorgensen [ctb], Steven Chesnut [ctb], Jarrett Byrnes [ctb], Jason Rights [ctb], Ylenio Longo [ctb]
Maintainer: Sunthud Pornprasertmanit <psunthud@gmail.com>

Diff between semTools versions 0.4-11 dated 2016-03-01 and 0.4-12 dated 2016-06-13

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More information about semTools at CRAN
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Package selectiveInference updated to version 1.2.0 with previous version 1.1.3 dated 2016-02-09

Title: Tools for Post-Selection Inference
Description: New tools for post-selection inference, for use with forward stepwise regression, least angle regression, the lasso, and the many means problem. The lasso function implements Gaussian, logistic and Cox survival models.
Author: Ryan Tibshirani, Rob Tibshirani, Jonathan Taylor, Joshua Loftus, Stephen Reid
Maintainer: Rob Tibshirani <tibs@stanford.edu>

Diff between selectiveInference versions 1.1.3 dated 2016-02-09 and 1.2.0 dated 2016-06-13

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More information about selectiveInference at CRAN
Permanent link

Package SciencesPo updated to version 1.4.0 with previous version 1.3.9 dated 2016-01-22

Title: A Tool Set for Analyzing Political Behavior Data
Description: Provide functions for analyzing political behavior data, including measures of political fragmentation, seat apportionment, and options for small data visualization.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>

Diff between SciencesPo versions 1.3.9 dated 2016-01-22 and 1.4.0 dated 2016-06-13

 SciencesPo-1.3.9/SciencesPo/R/DISTRIBUTIONS.R                                                                       |only
 SciencesPo-1.3.9/SciencesPo/R/Mode.R                                                                                |only
 SciencesPo-1.3.9/SciencesPo/R/SAMPLING.R                                                                            |only
 SciencesPo-1.3.9/SciencesPo/R/TABLES.R                                                                              |only
 SciencesPo-1.3.9/SciencesPo/R/aad.R                                                                                 |only
 SciencesPo-1.3.9/SciencesPo/R/bar.plot.R                                                                            |only
 SciencesPo-1.3.9/SciencesPo/R/blockRandomizedDesign.R                                                               |only
 SciencesPo-1.3.9/SciencesPo/R/bootstrap.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/butterfly.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/ci.R                                                                                  |only
 SciencesPo-1.3.9/SciencesPo/R/clear.R                                                                               |only
 SciencesPo-1.3.9/SciencesPo/R/converter.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/crosstable.R                                                                          |only
 SciencesPo-1.3.9/SciencesPo/R/cv.R                                                                                  |only
 SciencesPo-1.3.9/SciencesPo/R/database.R                                                                            |only
 SciencesPo-1.3.9/SciencesPo/R/describe.R                                                                            |only
 SciencesPo-1.3.9/SciencesPo/R/destring.R                                                                            |only
 SciencesPo-1.3.9/SciencesPo/R/detail.R                                                                              |only
 SciencesPo-1.3.9/SciencesPo/R/dot.plot.R                                                                            |only
 SciencesPo-1.3.9/SciencesPo/R/draw.norm.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/dummy.R                                                                               |only
 SciencesPo-1.3.9/SciencesPo/R/electoralTool.R                                                                       |only
 SciencesPo-1.3.9/SciencesPo/R/fade.R                                                                                |only
 SciencesPo-1.3.9/SciencesPo/R/freq.R                                                                                |only
 SciencesPo-1.3.9/SciencesPo/R/geom_foot.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/gini.simpson.R                                                                        |only
 SciencesPo-1.3.9/SciencesPo/R/has.domain.R                                                                          |only
 SciencesPo-1.3.9/SciencesPo/R/insert.row.R                                                                          |only
 SciencesPo-1.3.9/SciencesPo/R/jackknife.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/levy.flight.R                                                                         |only
 SciencesPo-1.3.9/SciencesPo/R/lm2eqn.R                                                                              |only
 SciencesPo-1.3.9/SciencesPo/R/meanFromRange.R                                                                       |only
 SciencesPo-1.3.9/SciencesPo/R/n.R                                                                                   |only
 SciencesPo-1.3.9/SciencesPo/R/normalize.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/outliers.R                                                                            |only
 SciencesPo-1.3.9/SciencesPo/R/pause.R                                                                               |only
 SciencesPo-1.3.9/SciencesPo/R/permutate.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/pie.plot.R                                                                            |only
 SciencesPo-1.3.9/SciencesPo/R/psum.R                                                                                |only
 SciencesPo-1.3.9/SciencesPo/R/randomImput.R                                                                         |only
 SciencesPo-1.3.9/SciencesPo/R/recode.R                                                                              |only
 SciencesPo-1.3.9/SciencesPo/R/rounded.R                                                                             |only
 SciencesPo-1.3.9/SciencesPo/R/safe.chars.R                                                                          |only
 SciencesPo-1.3.9/SciencesPo/R/se.R                                                                                  |only
 SciencesPo-1.3.9/SciencesPo/R/seatAllocation.R                                                                      |only
 SciencesPo-1.3.9/SciencesPo/R/stratified.R                                                                          |only
 SciencesPo-1.3.9/SciencesPo/R/sturges.R                                                                             |only
 SciencesPo-1.3.9/SciencesPo/R/svTransform.R                                                                         |only
 SciencesPo-1.3.9/SciencesPo/R/tabstat.R                                                                             |only
 SciencesPo-1.3.9/SciencesPo/R/textwrap.R                                                                            |only
 SciencesPo-1.3.9/SciencesPo/R/time.plot.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/trim.R                                                                                |only
 SciencesPo-1.3.9/SciencesPo/R/untable.R                                                                             |only
 SciencesPo-1.3.9/SciencesPo/R/voronoi.R                                                                             |only
 SciencesPo-1.3.9/SciencesPo/R/winsorize.R                                                                           |only
 SciencesPo-1.3.9/SciencesPo/R/wtd.var.R                                                                             |only
 SciencesPo-1.3.9/SciencesPo/build/SciencesPo.pdf                                                                    |only
 SciencesPo-1.3.9/SciencesPo/data/Bush.txt.gz                                                                        |only
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 SciencesPo-1.4.0/SciencesPo/DESCRIPTION                                                                             |   20 
 SciencesPo-1.4.0/SciencesPo/MD5                                                                                     |  658 ++--
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 SciencesPo-1.4.0/SciencesPo/TODO                                                                                    |    3 
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 SciencesPo-1.4.0/SciencesPo/man/LargestRemainders.Rd                                                                |only
 SciencesPo-1.4.0/SciencesPo/man/Lorenz.Rd                                                                           |only
 SciencesPo-1.4.0/SciencesPo/man/MeanFromRange.Rd                                                                    |only
 SciencesPo-1.4.0/SciencesPo/man/Normalize.Rd                                                                        |only
 SciencesPo-1.4.0/SciencesPo/man/Operations.Rd                                                                       |only
 SciencesPo-1.4.0/SciencesPo/man/Outlier.Rd                                                                          |only
 SciencesPo-1.4.0/SciencesPo/man/Palettes.Rd                                                                         |only
 SciencesPo-1.4.0/SciencesPo/man/Permutate.Rd                                                                        |only
 SciencesPo-1.4.0/SciencesPo/man/PoliticalDiversity.Rd                                                               |only
 SciencesPo-1.4.0/SciencesPo/man/PreviewTheme.Rd                                                                     |only
 SciencesPo-1.4.0/SciencesPo/man/Proportionality.Rd                                                                  |only
 SciencesPo-1.4.0/SciencesPo/man/Recode.Rd                                                                           |only
 SciencesPo-1.4.0/SciencesPo/man/Render.Rd                                                                           |only
 SciencesPo-1.4.0/SciencesPo/man/Rosenbluth.Rd                                                                       |only
 SciencesPo-1.4.0/SciencesPo/man/Safechars.Rd                                                                        |only
 SciencesPo-1.4.0/SciencesPo/man/SciencesPo-deprecated.Rd                                                            |only
 SciencesPo-1.4.0/SciencesPo/man/SciencesPo.Rd                                                                       |    8 
 SciencesPo-1.4.0/SciencesPo/man/Skewness.Rd                                                                         |only
 SciencesPo-1.4.0/SciencesPo/man/Stratify.Rd                                                                         |only
 SciencesPo-1.4.0/SciencesPo/man/TwoWay.Rd                                                                           |only
 SciencesPo-1.4.0/SciencesPo/man/Untable.Rd                                                                          |only
 SciencesPo-1.4.0/SciencesPo/man/Voronoi.Rd                                                                          |only
 SciencesPo-1.4.0/SciencesPo/man/WeightedCorrelation.Rd                                                              |only
 SciencesPo-1.4.0/SciencesPo/man/WeightedMean.Rd                                                                     |only
 SciencesPo-1.4.0/SciencesPo/man/WeightedStdz.Rd                                                                     |only
 SciencesPo-1.4.0/SciencesPo/man/WeightedVariance.Rd                                                                 |only
 SciencesPo-1.4.0/SciencesPo/man/Winsorize.Rd                                                                        |only
 SciencesPo-1.4.0/SciencesPo/man/alpha.Rd                                                                            |only
 SciencesPo-1.4.0/SciencesPo/man/baseball.Rd                                                                         |only
 SciencesPo-1.4.0/SciencesPo/man/bhodrick93.Rd                                                                       |    4 
 SciencesPo-1.4.0/SciencesPo/man/big5.Rd                                                                             |only
 SciencesPo-1.4.0/SciencesPo/man/bollen.Rd                                                                           |only
 SciencesPo-1.4.0/SciencesPo/man/bush.Rd                                                                             |only
 SciencesPo-1.4.0/SciencesPo/man/cathedrals.Rd                                                                       |    8 
 SciencesPo-1.4.0/SciencesPo/man/cgreene76.Rd                                                                        |    4 
 SciencesPo-1.4.0/SciencesPo/man/chismoke.Rd                                                                         |only
 SciencesPo-1.4.0/SciencesPo/man/color_party.Rd                                                                      |only
 SciencesPo-1.4.0/SciencesPo/man/color_pub.Rd                                                                        |only
 SciencesPo-1.4.0/SciencesPo/man/dHondt.Rd                                                                           |   29 
 SciencesPo-1.4.0/SciencesPo/man/ddirichlet.Rd                                                                       |    8 
 SciencesPo-1.4.0/SciencesPo/man/election2008.Rd                                                                     |only
 SciencesPo-1.4.0/SciencesPo/man/fill_party.Rd                                                                       |only
 SciencesPo-1.4.0/SciencesPo/man/fill_pub.Rd                                                                         |only
 SciencesPo-1.4.0/SciencesPo/man/freq.Rd                                                                             |   25 
 SciencesPo-1.4.0/SciencesPo/man/galton.Rd                                                                           |   13 
 SciencesPo-1.4.0/SciencesPo/man/geom_dumbbell.Rd                                                                    |only
 SciencesPo-1.4.0/SciencesPo/man/geom_lollipop.Rd                                                                    |only
 SciencesPo-1.4.0/SciencesPo/man/geom_spotlight.Rd                                                                   |only
 SciencesPo-1.4.0/SciencesPo/man/griliches76.Rd                                                                      |    4 
 SciencesPo-1.4.0/SciencesPo/man/ltaylor96.Rd                                                                        |    4 
 SciencesPo-1.4.0/SciencesPo/man/marriage.Rd                                                                         |    4 
 SciencesPo-1.4.0/SciencesPo/man/mishkin92.Rd                                                                        |    4 
 SciencesPo-1.4.0/SciencesPo/man/nerlove63.Rd                                                                        |    9 
 SciencesPo-1.4.0/SciencesPo/man/nin.Rd                                                                              |only
 SciencesPo-1.4.0/SciencesPo/man/paired.Rd                                                                           |    4 
 SciencesPo-1.4.0/SciencesPo/man/party_color_pal.Rd                                                                  |only
 SciencesPo-1.4.0/SciencesPo/man/pollster2008.Rd                                                                     |only
 SciencesPo-1.4.0/SciencesPo/man/print.Rd                                                                            |only
 SciencesPo-1.4.0/SciencesPo/man/pub_color_pal.Rd                                                                    |   24 
 SciencesPo-1.4.0/SciencesPo/man/pub_shape_pal.Rd                                                                    |only
 SciencesPo-1.4.0/SciencesPo/man/rdirichlet.Rd                                                                       |   15 
 SciencesPo-1.4.0/SciencesPo/man/read.zTree.Rd                                                                       |    5 
 SciencesPo-1.4.0/SciencesPo/man/religiosity.Rd                                                                      |only
 SciencesPo-1.4.0/SciencesPo/man/runExample.Rd                                                                       |   10 
 SciencesPo-1.4.0/SciencesPo/man/shape_pub.Rd                                                                        |only
 SciencesPo-1.4.0/SciencesPo/man/sheston91.Rd                                                                        |    4 
 SciencesPo-1.4.0/SciencesPo/man/stature.Rd                                                                          |only
 SciencesPo-1.4.0/SciencesPo/man/summary.Crosstable.Rd                                                               |only
 SciencesPo-1.4.0/SciencesPo/man/swatson93.Rd                                                                        |    4 
 SciencesPo-1.4.0/SciencesPo/man/theme_blank.Rd                                                                      |   11 
 SciencesPo-1.4.0/SciencesPo/man/theme_darkside.Rd                                                                   |only
 SciencesPo-1.4.0/SciencesPo/man/theme_fte.Rd                                                                        |   30 
 SciencesPo-1.4.0/SciencesPo/man/theme_pub.Rd                                                                        |   48 
 SciencesPo-1.4.0/SciencesPo/man/then.Rd                                                                             |only
 SciencesPo-1.4.0/SciencesPo/man/titanic.Rd                                                                          |    4 
 SciencesPo-1.4.0/SciencesPo/man/turnout.Rd                                                                          |    6 
 SciencesPo-1.4.0/SciencesPo/man/twins.Rd                                                                            |   12 
 SciencesPo-1.4.0/SciencesPo/man/unions.Rd                                                                           |only
 SciencesPo-1.4.0/SciencesPo/man/words.Rd                                                                            |    9 
 SciencesPo-1.4.0/SciencesPo/src/ddirichlet.c                                                                        |    1 
 SciencesPo-1.4.0/SciencesPo/src/rdirichlet.c                                                                        |   34 
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 SciencesPo-1.4.0/SciencesPo/tests/testthat/test-Atkinson.R                                                          |only
 SciencesPo-1.4.0/SciencesPo/tests/testthat/test-CV.R                                                                |only
 SciencesPo-1.4.0/SciencesPo/tests/testthat/test-Gini.R                                                              |only
 SciencesPo-1.4.0/SciencesPo/tests/testthat/test-Herfindahl.R                                                        |only
 SciencesPo-1.4.0/SciencesPo/tests/testthat/test-Proportionality.R                                                   |only
 SciencesPo-1.4.0/SciencesPo/tests/testthat/test-Rosenbluth.R                                                        |only
 SciencesPo-1.4.0/SciencesPo/tests/testthat/test-SE.R                                                                |only
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 SciencesPo-1.4.0/SciencesPo/vignettes/Indices.Rmd                                                                   |  593 +++-
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 SciencesPo-1.4.0/SciencesPo/vignettes/SciencesPo.Rmd                                                                | 1154 ++++++--
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New package SDraw with initial version 2.1.3
Package: SDraw
Type: Package
Title: Spatially Balanced Sample Draws for Spatial Objects
Version: 2.1.3
Date: 2016-06-10
Author: Trent McDonald
Maintainer: Trent McDonald <tmcdonald@west-inc.com>
Description: Routines for drawing samples, focusing on spatially balanced algorithms. Draws Halton Lattice (HAL), Balanced Acceptance Samples (BAS), Generalized Random Tesselation Stratified (GRTS), Simple Systematic Samples (SSS) and Simple Random Samples (SRS) from point, line, and polygon resources. Frames are 'SpatialPoints', 'SpatialLines', or 'SpatialPolygons' objects from package 'sp'.
License: GNU General Public License
URL: https://github.com/tmcd82070/SDraw/wiki/SDraw
BugReports: https://github.com/tmcd82070/SDraw/issues
Imports: spsurvey, utils, rgeos, graphics, methods, deldir, stats
Depends: R (>= 2.10), sp
LazyData: true
RoxygenNote: 5.0.1
Collate: 'HI.coast.r' 'WA.cities.r' 'WA.r' 'WY.r' 'SDraw-package.r' 'sdraw.SpatialPoints.r' 'sdraw.SpatialLines.r' 'sdraw.SpatialPolygons.r' 'sdraw.r' 'bas.line.r' 'bas.point.r' 'bas.polygon.r' 'extended.gcd.r' 'grts.equi.r' 'grts.line.r' 'grts.point.r' 'grts.polygon.r' 'hal.line.r' 'hal.point.r' 'hal.polygon.r' 'halton.frame.r' 'halton.indicies.CRT.r' 'halton.indicies.r' 'halton.indicies.vector.r' 'halton.lattice.polygon.r' 'halton.lattice.r' 'halton.r' 'plot.sdrawSample.R' 'primes.r' 'sss.point.r' 'sss.line.r' 'sss.polygon.r' 'srs.polygon.r' 'srs.line.r' 'srs.point.r' 'merge.lines.r' 'aprox.r' 'max.U.r' 'polygonArea.r' 'lineLength.r' 'voronoi.polygons.r' 'zzz.r'
NeedsCompilation: no
Packaged: 2016-06-10 17:51:21 UTC; tmcdonald
Repository: CRAN
Date/Publication: 2016-06-11 00:02:16

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Package samplingVarEst updated to version 1.0-2 with previous version 1.0-1 dated 2016-01-03

Title: Sampling Variance Estimation
Description: Functions to calculate some point estimators and estimating their variance under unequal probability sampling without replacement. Single and two stage sampling designs are considered. Some approximations for the second order inclusion probabilities are also available (sample and population based). A variety of Jackknife variance estimators are implemented.
Author: Emilio Lopez Escobar [aut, cre, cph] <emilio@numerika.mx>, Ernesto Barrios Zamudio [ctb] <ebarrios@itam.mx>, Juan Francisco Munoz Rosas [ctb] <jfmunoz@go.ugr.es>
Maintainer: Emilio Lopez Escobar <emilio@numerika.mx>

Diff between samplingVarEst versions 1.0-1 dated 2016-01-03 and 1.0-2 dated 2016-06-13

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New package rwty with initial version 1.0.0
Package: rwty
Type: Package
Title: R We There Yet? Visualizing MCMC Convergence in Phylogenetics
Version: 1.0.0
Author: Dan Warren <dan.l.warren@gmail.com>, Anthony Geneva <anthony.geneva@gmail.com>, Rob Lanfear <rob.lanfear@gmail.com>
Maintainer: Dan Warren <dan.l.warren@gmail.com>
Description: Implements various tests, visualizations, and metrics for diagnosing convergence of MCMC chains in phylogenetics. It implements and automates many of the functions of the AWTY package in the R environment.
License: GPL-2
Depends: R (>= 3.0.1), ape, ggplot2,
Imports: reshape2, phangorn, coda, viridis, grid, plyr, ggdendro, GGally, parallel,
Suggests: knitr,
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-10 22:09:29 UTC; dwarren
Repository: CRAN
Date/Publication: 2016-06-11 09:29:05

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Package RWeka updated to version 0.4-29 with previous version 0.4-28 dated 2016-06-04

Title: R/Weka Interface
Description: An R interface to Weka (Version 3.9.0). Weka is a collection of machine learning algorithms for data mining tasks written in Java, containing tools for data pre-processing, classification, regression, clustering, association rules, and visualization. Package 'RWeka' contains the interface code, the Weka jar is in a separate package 'RWekajars'. For more information on Weka see <http://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre], Christian Buchta [ctb], Torsten Hothorn [ctb], Alexandros Karatzoglou [ctb], David Meyer [ctb], Achim Zeileis [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between RWeka versions 0.4-28 dated 2016-06-04 and 0.4-29 dated 2016-06-13

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Package rts updated to version 1.0-11 with previous version 1.0-10 dated 2015-08-03

Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between rts versions 1.0-10 dated 2015-08-03 and 1.0-11 dated 2016-06-13

 DESCRIPTION       |   12 ++++++------
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Package rtkore updated to version 1.1.0 with previous version 1.0.1 dated 2015-11-24

Title: STK++ Core Library Integration to R using Rcpp
Description: STK++ (http://www.stkpp.org) is a collection of C++ classes for statistics, clustering, linear algebra, arrays (with an Eigen-like API), regression, dimension reduction, etc. The integration of the library to R is using Rcpp. The rtkore package includes the header files from the STK++ core library. All files contain only templated classes and/or inlined functions. STK++ is licensed under the GNU LGPL version 2 or later. rtkore (the stkpp integration into R) is licensed under the GNU GPL version 2 or later. See file LICENSE.note for details.
Author: Serge Iovleff [aut, cre], Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff <serge.iovleff@stkpp.org>

Diff between rtkore versions 1.0.1 dated 2015-11-24 and 1.1.0 dated 2016-06-13

 rtkore-1.0.1/rtkore/.Rinstignore                                                     |only
 rtkore-1.1.0/rtkore/DESCRIPTION                                                      |   18 
 rtkore-1.1.0/rtkore/LICENSE.note                                                     |    2 
 rtkore-1.1.0/rtkore/MD5                                                              |  384 +++++-----
 rtkore-1.1.0/rtkore/build/vignette.rds                                               |binary
 rtkore-1.1.0/rtkore/inst/NEWS.Rd                                                     |   10 
 rtkore-1.1.0/rtkore/inst/doc/rtkpp-introduction.pdf                                  |binary
 rtkore-1.1.0/rtkore/inst/include/Algebra.h                                           |    2 
 rtkore-1.1.0/rtkore/inst/include/Analysis.h                                          |    2 
 rtkore-1.1.0/rtkore/inst/include/Arrays.h                                            |    2 
 rtkore-1.1.0/rtkore/inst/include/DManager.h                                          |    7 
 rtkore-1.1.0/rtkore/inst/include/STKernel.h                                          |    2 
 rtkore-1.1.0/rtkore/inst/include/STKpp.h                                             |    6 
 rtkore-1.1.0/rtkore/inst/include/STatistiK.h                                         |    4 
 rtkore-1.1.0/rtkore/inst/include/Sdk.h                                               |    2 
 rtkore-1.1.0/rtkore/inst/include/StatModels.h                                        |    6 
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 rtkore-1.1.0/rtkore/inst/projects/Algebra/include/STK_Qr.h                           |    2 
 rtkore-1.1.0/rtkore/inst/projects/Algebra/include/STK_Svd.h                          |    2 
 rtkore-1.1.0/rtkore/inst/projects/Algebra/include/STK_SymEigen.h                     |    2 
 rtkore-1.1.0/rtkore/inst/projects/Algebra/include/STK_WeightedSvd.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Algebra/include/STK_lapack_MultiLeastSquare.h      |    2 
 rtkore-1.1.0/rtkore/inst/projects/Algebra/include/STK_lapack_Qr.h                    |    2 
 rtkore-1.1.0/rtkore/inst/projects/Algebra/include/STK_lapack_Svd.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/Algebra/include/STK_lapack_SymEigen.h              |    2 
 rtkore-1.1.0/rtkore/inst/projects/Algebra/include/STK_lapack_Util.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_Algo.h                        |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_Algo_FindZero.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_Const_Math.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_Const_Sequences.h             |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_Funct_Util.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_Funct_betaRatio.h             |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_Funct_gamma.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_Funct_gammaRatio.h            |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_Funct_raw.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_IFunction.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/Analysis/include/STK_ISerie.h                      |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_AllocatorBase.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array1D.h                       |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array2D.h                       |    4 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array2DDiagonal.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array2DLowerTriangular.h        |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array2DNumber.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array2DPoint.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array2DSquare.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array2DUpperTriangular.h        |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array2DVector.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Array2D_Functors.h              |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ArrayBase.h                     |    5 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ArrayBaseApplier.h              |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ArrayBaseAssign.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ArrayBaseInitializer.h          |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Arrays_Util.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_CAllocator.h                    |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_CArray.h                        |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_CArrayNumber.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_CArrayPoint.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_CArraySquare.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_CArrayVector.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Const_Arrays.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Display.h                       |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ExprBase.h                      |   28 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ExprBaseDot.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ExprBaseFunctors.h              |   10 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ExprBaseProduct.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ExprBaseVisitor.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_IArray1D.h                      |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_IArray2D.h                      |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_IArray2DBase.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ICArray.h                       |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ITContainer.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ITContainer1D.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_ITContainer2D.h                 |    7 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Iterators.h                     |only
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_SparseMatrix.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/STK_Traits.h                        |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/operators/STK_BinaryOperators.h     |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/operators/STK_DiagonalOperator.h    |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/operators/STK_DotOperators.h        |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/operators/STK_SlicingOperators.h    |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/operators/STK_TransposeOperator.h   |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/operators/STK_UnaryOperators.h      |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/products/STK_ArrayByArrayProduct.h  |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/products/STK_ArrayByVectorProduct.h |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/products/STK_ProductDispatcher.h    |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/products/STK_ProductOperators.h     |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/products/STK_ProductRaw.h           |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/visitors/STK_SlicingVisitors.h      |    8 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/visitors/STK_VisitorSelector.h      |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/visitors/STK_Visitors.h             |    2 
 rtkore-1.1.0/rtkore/inst/projects/Arrays/include/visitors/STK_VisitorsImpl.h         |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_CsvToArray.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_DManager_Util.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_DataBridge.h                  |  191 ++++
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_DataFrame.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_DataFrameToArray2D.h          |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_DataHandler.h                 |   16 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_DataHandlerBase.h             |   21 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_ExportToCsv.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_IDataBridge.h                 |   16 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_IDataHandler.h                |    4 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_IPage.h                       |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_IVariable.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_ImportFromCsv.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_Import_Util.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_List1D.h                      |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_ReadWriteCsv.h                |    2 
 rtkore-1.1.0/rtkore/inst/projects/DManager/include/STK_Variable.h                    |    2 
 rtkore-1.1.0/rtkore/inst/projects/Rtkpp/include/STK_RMatrix.h                        |   15 
 rtkore-1.1.0/rtkore/inst/projects/Rtkpp/include/STK_RVector.h                        |    3 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Arithmetic.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Char.h                        |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Chrono.h                      |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Constants.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Exceptions.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Functors.h                    |  194 ++---
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Integer.h                     |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Misc.h                        |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Proxy.h                       |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Range.h                       |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Real.h                        |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_Stream.h                      |    2 
 rtkore-1.1.0/rtkore/inst/projects/STKernel/include/STK_String.h                      |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Kernel_Exponential.h         |   35 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Kernel_Gaussian.h            |   37 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Kernel_Hamming.h             |only
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Kernel_IKernelBase.h         |   87 +-
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Kernel_Linear.h              |   37 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Kernel_Polynomial.h          |   38 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Kernel_RationalQuadratic.h   |   37 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Kernel_Util.h                |   36 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Bernoulli.h              |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Beta.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Binomial.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Categorical.h            |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Cauchy.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_ChiSquared.h             |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Exponential.h            |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_FisherSnedecor.h         |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Gamma.h                  |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Geometric.h              |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_HyperGeometric.h         |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_ILawBase.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_IUnivLaw.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_LogNormal.h              |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Logistic.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_NegativeBinomial.h       |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Normal.h                 |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Poisson.h                |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Student.h                |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Uniform.h                |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_UniformDiscrete.h        |   16 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Util.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Law_Weibull.h                |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_MultiLaw_IMultiLaw.h         |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_MultiLaw_JointBernoulli.h    |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_MultiLaw_JointCauchy.h       |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_MultiLaw_JointGamma.h        |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_MultiLaw_JointNormal.h       |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_MultiLaw_Normal.h            |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_RandBase.h                   |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Stat_Bivariate.h             |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Stat_BivariateRealReal.h     |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Stat_Factor.h                |only
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Stat_Functors.h              |  230 ++---
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Stat_Multivariate.h          |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Stat_MultivariateReal.h      |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Stat_Online.h                |   23 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Stat_Transform.h             |    2 
 rtkore-1.1.0/rtkore/inst/projects/STatistiK/include/STK_Stat_UnivariateReal.h        |   58 +
 rtkore-1.1.0/rtkore/inst/projects/Sdk/include/STK_IRecursiveTemplate.h               |    2 
 rtkore-1.1.0/rtkore/inst/projects/Sdk/include/STK_IRunner.h                          |    2 
 rtkore-1.1.0/rtkore/inst/projects/Sdk/include/STK_Macros.h                           |    2 
 rtkore-1.1.0/rtkore/inst/projects/Sdk/include/STK_MetaTemplate.h                     |    2 
 rtkore-1.1.0/rtkore/inst/projects/Sdk/include/STK_StaticAssert.h                     |    4 
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_BernoulliModel.h            |    2 
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_GaussianModel.h             |   38 
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_IGaussianModel.h            |   37 
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_IMultiStatModel.h           |  192 ++---
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_IStatModel.h                |   64 -
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_IStatModelBase.h            |   22 
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_IUnivStatModel.h            |    2 
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_ModelBernoulli_pj.h         |only
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_ModelDiagGaussian_muj_sj.h  |only
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_ModelGamma_aj_bj.h          |only
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_Model_Util.h                |   42 -
 rtkore-1.1.0/rtkore/inst/projects/StatModels/include/STK_PenCriterion.h              |    2 
 rtkore-1.1.0/rtkore/man/rtkore-package.Rd                                            |    2 
 rtkore-1.1.0/rtkore/man/rtkoreFlags.Rd                                               |    2 
 197 files changed, 1270 insertions(+), 1018 deletions(-)

More information about rtkore at CRAN
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Package RSpectra updated to version 0.12-0 with previous version 0.11-0 dated 2016-02-29

Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: R interface to the 'Spectra' library <http://yixuan.cos.name/spectra/> 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 which 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. Matrices can be given in either dense or sparse form.
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>

Diff between RSpectra versions 0.11-0 dated 2016-02-29 and 0.12-0 dated 2016-06-13

 DESCRIPTION                                      |   10 +-
 MD5                                              |   78 +++++++++++-----------
 NAMESPACE                                        |    1 
 R/00_eigs.R                                      |   76 +++++++++------------
 R/10_eigs_real_gen.R                             |   34 ++++-----
 R/20_eigs_real_sym.R                             |   32 ++++-----
 R/30_svds.R                                      |   81 +++++++++++++++++++----
 R/40_svds_real_gen.R                             |   32 +++++----
 R/50_svds_real_sym.R                             |   22 ++----
 README.md                                        |   13 +++
 build                                            |only
 inst/NEWS.Rd                                     |   15 +++-
 inst/doc                                         |only
 inst/include/RMatOp/ComplexShift.h               |    6 -
 inst/include/RMatOp/ComplexShift_matrix.h        |   10 +-
 inst/include/RMatOp/ComplexShift_sparseMatrix.h  |   12 +--
 inst/include/RMatOp/MatProd.h                    |    8 +-
 inst/include/RMatOp/MatProd_function.h           |   43 +++++++-----
 inst/include/RMatOp/MatProd_matrix.h             |   22 +++---
 inst/include/RMatOp/MatProd_sparseMatrix.h       |   10 +-
 inst/include/RMatOp/MatProd_sym_matrix.h         |   18 ++---
 inst/include/RMatOp/MatProd_sym_sparseMatrix.h   |   14 +--
 inst/include/RMatOp/RealShift.h                  |    6 -
 inst/include/RMatOp/RealShift_matrix.h           |   10 +-
 inst/include/RMatOp/RealShift_sparseMatrix.h     |   10 +-
 inst/include/RMatOp/RealShift_sym_matrix.h       |   10 +-
 inst/include/RMatOp/RealShift_sym_sparseMatrix.h |   14 +--
 inst/include/RMatOp/SVDOp.h                      |   32 ++++-----
 inst/include/Spectra/SymEigsSolver.h             |    4 -
 inst/include/SpectraC.h                          |   60 ++++++++---------
 man/eigs.Rd                                      |   20 ++---
 man/svds.Rd                                      |   64 +++++++++++++++++-
 src/eigs_gen.cpp                                 |   18 ++---
 src/eigs_sym.cpp                                 |   16 ++--
 src/matops.cpp                                   |   15 ++--
 src/matops.h                                     |    8 +-
 src/matops_c.h                                   |   20 ++---
 src/register_routines.c                          |    3 
 src/svds.cpp                                     |   11 +--
 vignettes                                        |only
 40 files changed, 503 insertions(+), 355 deletions(-)

More information about RSpectra at CRAN
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Package RSentiment updated to version 2.0 with previous version 1.0.4 dated 2016-05-04

Title: Analyse Sentiment of English Sentences
Description: Analyses sentiment of a sentence in English and assigns score to it. It can classify sentences to the following categories of sentiments:- Positive, Negative, very Positive, very negative, Neutral or Sarcasm. For a vector of sentences, it counts the number of sentences in each category of sentiment.In calculating the score, negation and various degrees of adjectives are taken into consideration. It deals only with English sentences.
Author: Subhasree Bose <subhasree10.7@gmail.com> with contributons from Saptarsi Goswami.
Maintainer: Subhasree Bose <subhasree10.7@gmail.com>

Diff between RSentiment versions 1.0.4 dated 2016-05-04 and 2.0 dated 2016-06-13

 DESCRIPTION                |    8 +-
 MD5                        |   14 +--
 R/test.R                   |   18 +++-
 build/vignette.rds         |binary
 inst/doc/introduction.R    |   12 +--
 inst/doc/introduction.Rmd  |    4 -
 inst/doc/introduction.html |  171 ++++++++++++++++++++++-----------------------
 vignettes/introduction.Rmd |    4 -
 8 files changed, 122 insertions(+), 109 deletions(-)

More information about RSentiment at CRAN
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New package Rsampling with initial version 0.1.1
Package: Rsampling
Title: Ports the Workflow of "Resampling Stats" Add-in to R
Version: 0.1.1
Authors@R: c( person("Paulo", "Prado", , "prado@ib.usp.br", role = c("aut", "cre")), person("Andr\'e", "Chalom", , "andrechalom@gmail.com", role = c("aut")), person("Alexandre", "Oliveira", , "adalardo@usp.br", role = c("aut")) )
Description: Resampling Stats (http://www.resample.com) is an add-in for running randomization tests in Excel worksheets. The workflow is (1) to define a statistic of interest that can be calculated from a data table, (2) to randomize rows ad/or columns of a data table to simulate a null hypothesis and (3) and to score the value of the statistic from many randomizations. The relative frequency distribution of the statistic in the simulations is then used to infer the probability of the observed value be generated by the null process (probability of Type I error). This package intends to translate this logic for R for teaching purposes. Keeping the original workflow is favored over performance.
Depends: R (>= 3.0.0)
Imports: graphics, stats, utils
License: GPL-2
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-06-07 03:50:26 UTC; chalom
Author: Paulo Prado [aut, cre], Andr'e Chalom [aut], Alexandre Oliveira [aut]
Maintainer: Paulo Prado <prado@ib.usp.br>
Repository: CRAN
Date/Publication: 2016-06-07 14:46:12

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New package rpn with initial version 1.0
Package: rpn
Type: Package
Title: Converter and Interpreter for Reverse Polish Notation Expressions
Description: Pure R implementation of a simple (Reverse) Polish Notation (RPN) interpreter and converter.
Version: 1.0
Date: 2016-06-06
Authors@R: c(person("Jakob", "Bossek", email = "j.bossek@gmail.com", role = c("aut", "cre")))
Maintainer: Jakob Bossek <j.bossek@gmail.com>
URL: https://github.com/jakobbossek/rpn
BugReports: https://github.com/jakobbossek/rpn/issues
License: BSD_2_clause + file LICENSE
Depends: BBmisc (>= 1.6), checkmate (>= 1.1),
Suggests: testthat
ByteCompile: yes
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-07 13:53:54 UTC; jboss
Author: Jakob Bossek [aut, cre]
Repository: CRAN
Date/Publication: 2016-06-07 16:36:19

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Package rpart.plot updated to version 2.0.0 with previous version 1.5.3 dated 2015-10-01

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

Diff between rpart.plot versions 1.5.3 dated 2015-10-01 and 2.0.0 dated 2016-06-13

 rpart.plot-1.5.3/rpart.plot/.Rinstignore                      |only
 rpart.plot-2.0.0/rpart.plot/DESCRIPTION                       |    6 
 rpart.plot-2.0.0/rpart.plot/MD5                               |   47 
 rpart.plot-2.0.0/rpart.plot/NAMESPACE                         |    7 
 rpart.plot-2.0.0/rpart.plot/NEWS                              |   28 
 rpart.plot-2.0.0/rpart.plot/R/as.char.R                       |only
 rpart.plot-2.0.0/rpart.plot/R/check.index.R                   |only
 rpart.plot-2.0.0/rpart.plot/R/describe.col.R                  |only
 rpart.plot-2.0.0/rpart.plot/R/layout.R                        |    7 
 rpart.plot-2.0.0/rpart.plot/R/lib.R                           | 1216 +++++++---
 rpart.plot-2.0.0/rpart.plot/R/lib.rpart.plot.R                |only
 rpart.plot-2.0.0/rpart.plot/R/node.labs.R                     |  126 -
 rpart.plot-2.0.0/rpart.plot/R/palette.R                       |only
 rpart.plot-2.0.0/rpart.plot/R/prp.R                           |  183 +
 rpart.plot-2.0.0/rpart.plot/R/rounded.rect.R                  |   13 
 rpart.plot-2.0.0/rpart.plot/R/snip.R                          |   34 
 rpart.plot-2.0.0/rpart.plot/R/yes.no.R                        |  141 -
 rpart.plot-2.0.0/rpart.plot/inst/doc/index.html               |    2 
 rpart.plot-2.0.0/rpart.plot/inst/doc/prp.pdf                  |binary
 rpart.plot-2.0.0/rpart.plot/inst/slowtests/make.bat           |    2 
 rpart.plot-2.0.0/rpart.plot/inst/slowtests/test.imports.R     |only
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 rpart.plot-2.0.0/rpart.plot/inst/slowtests/test.palette.R     |only
 rpart.plot-2.0.0/rpart.plot/inst/slowtests/test.prp.R         |  130 -
 rpart.plot-2.0.0/rpart.plot/inst/slowtests/test.prp.Rout.save |  544 +++-
 rpart.plot-2.0.0/rpart.plot/inst/slowtests/user-manual-figs.R |  133 -
 rpart.plot-2.0.0/rpart.plot/man/prp.Rd                        |  223 +
 rpart.plot-2.0.0/rpart.plot/man/ptitanic.Rd                   |    2 
 rpart.plot-2.0.0/rpart.plot/man/rpart.plot.Rd                 |  538 ++--
 rpart.plot-2.0.0/rpart.plot/man/rpart.plot.version1.Rd        |only
 30 files changed, 2337 insertions(+), 1045 deletions(-)

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Package rgho updated to version 0.1.0 with previous version 0.0.1 dated 2016-03-19

Title: Access WHO Global Health Observatory Data from R
Description: Access WHO Global Health Observatory data from R via the Athena web service, an application program interface providing a simple query interface to the World Health Organization's data and statistics content.
Author: Antoine Filipovic-Pierucci [aut,cre]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>

Diff between rgho versions 0.0.1 dated 2016-03-19 and 0.1.0 dated 2016-06-13

 DESCRIPTION              |    6 -
 MD5                      |   21 +++---
 NEWS.md                  |only
 R/get_attrs.R            |    2 
 R/get_data.R             |   11 ++-
 R/get_gho.R              |   33 ++++++++--
 README.md                |    7 --
 build/vignette.rds       |binary
 inst/doc/codes-gho.html  |  153 +++++++++++++++++++++++++++++++++++++++--------
 inst/doc/dimensions.html |   19 +++--
 inst/doc/intro.html      |  126 ++++++++++++++++++--------------------
 man/get_gho_.Rd          |    8 +-
 12 files changed, 262 insertions(+), 124 deletions(-)

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New package RmarineHeatWaves with initial version 0.13.1
Package: RmarineHeatWaves
Version: 0.13.1
Date: 2016-06-09
Title: Detect Marine Heat Waves and Marine Cold Spells
Type: Package
Authors@R: c(person("Albertus J.", "Smit", role = c("aut", "cre"), email = "albertus.smit@gmail.com", comment = "R implementation."), person("Eric C. J.", "Oliver", role = "aut", comment = "The brain behind the Python implementation."), person("Robert W.", "Schlegel", role = "ctb", comment = "Graphical and data summaries."))
Maintainer: Albertus J. Smit <albertus.smit@gmail.com>
Depends: R (>= 2.10)
Imports: stats, utils, ggplot2 (>= 2.0.0), zoo, lubridate, tidyr, plyr, raster, dplyr, magrittr, grid, lazyeval
Description: Applies the Hobday et al. (2016) <DOI:10.1016/j.pocean.2015.12.014> marine heat wave definition to an input time series of daily temperature. It outputs properties of all detected marine heat waves (and marine cold spells). The package provides data of observed SST records for three historical MHWs: the 2011 Western Australia event, the 2012 Northwest Atlantic event and the 2003 Mediterranean event.
License: MIT + file LICENSE
URL: https://github.com/ajsmit/RmarineHeatWaves
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-09 12:46:09 UTC; ajsmit
Author: Albertus J. Smit [aut, cre] (R implementation.), Eric C. J. Oliver [aut] (The brain behind the Python implementation.), Robert W. Schlegel [ctb] (Graphical and data summaries.)
Repository: CRAN
Date/Publication: 2016-06-09 15:19:19

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New package RFinfer with initial version 0.2.0
Package: RFinfer
Type: Package
Title: Inference for Random Forests
Version: 0.2.0
Date: 2016-06-09
Author: Cole Brokamp
Maintainer: Cole Brokamp <cole.brokamp@gmail.com>
Description: A set of add on tools for the 'randomForest' package.
Depends: R (>= 3.1.2), randomForest (>= 4.6-12)
Imports: Matrix, party, pbapply
License: GPL
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, ggplot2, nhanesA
VignetteBuilder: knitr
URL: https://github.com/cole-brokamp/RFinfer
BugReports: https://github.com/cole-brokamp/RFinfer/issues
NeedsCompilation: no
Packaged: 2016-06-10 16:03:35 UTC; cole
Repository: CRAN
Date/Publication: 2016-06-10 18:27:02

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Package remote updated to version 1.2.0 with previous version 1.0.0 dated 2015-06-12

Title: Empirical Orthogonal Teleconnections in R
Description: Empirical orthogonal teleconnections in R. 'remote' is short for 'R(-based) EMpirical Orthogonal TEleconnections'. It implements a collection of functions to facilitate empirical orthogonal teleconnection analysis. Empirical Orthogonal Teleconnections (EOTs) denote a regression based approach to decompose spatio-temporal fields into a set of independent orthogonal patterns. They are quite similar to Empirical Orthogonal Functions (EOFs) with EOTs producing less abstract results. In contrast to EOFs, which are orthogonal in both space and time, EOT analysis produces patterns that are orthogonal in either space or time.
Author: Tim Appelhans, Florian Detsch, Thomas Nauss
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>

Diff between remote versions 1.0.0 dated 2015-06-12 and 1.2.0 dated 2016-06-13

 DESCRIPTION              |   34 ++--
 MD5                      |   84 +++++------
 NAMESPACE                |   23 ++-
 R/anomalize.R            |    4 
 R/deseason.R             |  110 ++++++++++----
 R/eot.R                  |  208 +++++++++++++--------------
 R/longtermMeans.R        |only
 R/nXplain.R              |    2 
 R/plot.R                 |  350 +++++++++++++++++++++++++----------------------
 R/predict.R              |    3 
 R/remote-package.R       |    6 
 R/subset.R               |   11 -
 R/writeEot.R             |   17 +-
 README.md                |   12 +
 data/australiaGPCP.RData |binary
 data/pacificSST.RData    |binary
 data/vdendool.RData      |binary
 inst/CITATION            |   42 ++---
 man/EotCycle.Rd          |   10 -
 man/EotMode-class.Rd     |    2 
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 man/anomalize.Rd         |    6 
 man/australiaGPCP.Rd     |    8 -
 man/calcVar.Rd           |    4 
 man/covWeight.Rd         |    4 
 man/cutStack.Rd          |    7 
 man/deg2rad.Rd           |    3 
 man/denoise.Rd           |   14 -
 man/deseason.Rd          |   32 ++--
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 man/geoWeight.Rd         |    4 
 man/getWeights.Rd        |    5 
 man/lagalize.Rd          |    3 
 man/longtermMeans.Rd     |only
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 man/predict.Rd           |   17 +-
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 44 files changed, 666 insertions(+), 553 deletions(-)

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New package resampledata with initial version 0.1.0
Package: resampledata
Type: Package
Title: Data Sets for Mathematical Statistics with Resampling in R
Version: 0.1.0
Authors@R: c( person("Laura", "Chihara", email = "lchihara@carleton.edu", role = "aut"), person("Tim", "Hesterberg", email = "TimHesterberg@gmail.com", role = "aut"), person("Albert Y.", "Kim", email = "albert.ys.kim@gmail.com", role = "cre") )
Suggests: resample (>= 0.4)
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Description: Package to load data sets from "Mathematical Statistics with Resampling in R" (2011) by Laura Chihara and Tim Hesterberg.
Depends: R (>= 2.10)
License: CC0
LazyData: TRUE
RoxygenNote: 5.0.1
URL: https://github.com/rudeboybert/resampledata
BugReports: https://github.com/rudeboybert/resampledata/issues
NeedsCompilation: no
Packaged: 2016-06-13 12:20:40 UTC; aykim
Author: Laura Chihara [aut], Tim Hesterberg [aut], Albert Y. Kim [cre]
Repository: CRAN
Date/Publication: 2016-06-13 15:01:57

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Package regsem updated to version 0.1.3 with previous version 0.1.2 dated 2016-04-18

Title: Performs Regularization on Structural Equation Models
Description: Uses both ridge and lasso penalties (and extensions) to penalize specific parameters in structural equation models. The package offers additional cost functions, cross validation, and other extensions beyond traditional SEM.
Author: Ross Jacobucci[aut,cre]
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>

Diff between regsem versions 0.1.2 dated 2016-04-18 and 0.1.3 dated 2016-06-13

 DESCRIPTION            |   10 
 MD5                    |   65 -
 NAMESPACE              |   41 -
 R/RAMmult.R            |   56 -
 R/RcppExports.R        |  104 +-
 R/cv_regsem.R          |  314 ++++----
 R/extractMatrices.R    |  590 ++++++++--------
 R/fiml_calc.R          |  132 ++-
 R/fit_fun.R            |  140 +--
 R/fit_indices.R        |  357 +++++-----
 R/grad_fun.R           |  192 ++---
 R/grad_ram.R           |  192 ++---
 R/grad_ram_wMean.R     |  194 ++---
 R/hess_ram.R           |  112 +--
 R/hess_ramParallel.R   |  138 +--
 R/hessian.R            |   60 -
 R/hessian_parallel.R   |   80 +-
 R/multi_optim.R        |  464 ++++++-------
 R/optim_rj.R           |  128 +--
 R/ram_calc.R           |  154 ++--
 R/regsem.R             | 1718 +++++++++++++++++++++++++------------------------
 R/ret_hess.R           |   16 
 R/summary.R            |   46 -
 R/trace.R              |    8 
 README.md              |only
 man/cv_regsem.Rd       |  184 ++---
 man/extractMatrices.Rd |   57 -
 man/fit_indices.Rd     |   64 -
 man/multi_optim.Rd     |  206 ++---
 man/rcpp_RAMmult.Rd    |   62 -
 man/rcpp_fit_fun.Rd    |   50 -
 man/rcpp_grad_ram.Rd   |   76 +-
 man/regsem.Rd          |  308 ++++----
 man/summary.regsem.Rd  |   34 
 34 files changed, 3253 insertions(+), 3099 deletions(-)

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Package recmap updated to version 0.4.0 with previous version 0.3.0 dated 2016-05-30

Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2 construction heuristic (see 'citation("recmap")' for details). This algorithm draws maps according to a given statistical value (e. g. election results, population or epidemiological data). The basic idea of the RecMap algorithm is that each map region (e. g. different countries) is represented by a rectangle. The area of each rectangle represents the statistical value given as input (maintain zero cartographic error). Documentation about 'RecMap' is provided by a vignette included in this package and a 'RecMap gallery' site at <http://cartodraw.science/recmap/gallery>.
Author: Christian Panse
Maintainer: Christian Panse <Christian.Panse@gmail.com>

Diff between recmap versions 0.3.0 dated 2016-05-30 and 0.4.0 dated 2016-06-13

 DESCRIPTION                         |    6 
 MD5                                 |   27 -
 NAMESPACE                           |    1 
 R/recmap.R                          |    9 
 README.md                           |   30 -
 inst/NEWS.Rd                        |   30 +
 inst/doc/recmap.R                   |   77 ++-
 inst/doc/recmap.Rmd                 |   96 +++-
 inst/doc/recmap.html                |   74 ++-
 man/recmap.Rd                       |   84 ++--
 src/Rrecmap.cpp                     |  107 +++--
 src/recmap.h                        |  749 ++++++++++++++++++------------------
 tests/testthat/test-topoloy_error.R |only
 vignettes/recmap.Rmd                |   96 +++-
 vignettes/recmap.bib                |   29 +
 15 files changed, 836 insertions(+), 579 deletions(-)

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New package read.dbc with initial version 1.0.3
Package: read.dbc
Title: Read Data Stored in DBC (Compressed DBF) Files
Description: Functions for reading and decompressing the DBC (compressed DBF) files. Please note that this is the file format used by the Brazilian Ministry of Health (DATASUS) to publish healthcare datasets. It is not related to the FoxPro or CANdb DBC file formats.
Version: 1.0.3
Depends: R (>= 3.3.0)
Imports: foreign
Authors@R: person("Daniela", "Petruzalek", email = "daniela.petruzalek@gmail.com", role = c("aut", "cre"))
Maintainer: Daniela Petruzalek <daniela.petruzalek@gmail.com>
URL: https://github.com/danicat/read.dbc
BugReports: https://github.com/danicat/read.dbc/issues
Copyright: 2016 Daniela Petruzalek
License: AGPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1.9000
NeedsCompilation: yes
Packaged: 2016-06-07 18:35:45 UTC; dani
Author: Daniela Petruzalek [aut, cre]
Repository: CRAN
Date/Publication: 2016-06-08 01:00:30

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New package rdefra with initial version 0.1
Package: rdefra
Type: Package
Title: Interact with the UK AIR Pollution Database from DEFRA
Version: 0.1
Date: 2016-06-09
Author: Claudia Vitolo [aut, cre], Andrew Russell [aut], Allan Tucker [aut]
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
URL: https://github.com/kehraProject/r_rdefra
BugReports: https://github.com/kehraProject/r_rdefra/issues
Description: Get data from DEFRA's UK-AIR website. It basically scraps the HTML content.
Depends: R (>= 2.10)
Imports: RCurl, XML, plyr
Encoding: UTF-8
License: GPL-3
Repository: CRAN
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-10 06:54:59 UTC; claudia
Date/Publication: 2016-06-10 09:53:36

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New package rcqp with initial version 0.4
Package: rcqp
Type: Package
Title: Interface to the Corpus Query Protocol
Version: 0.4
Date: 2016-06-10
Author: Bernard Desgraupes <bernard.desgraupes@u-paris10.fr>, Sylvain Loiseau <sylvain.loiseau@univ-paris13.fr>
Maintainer: Bernard Desgraupes <bernard.desgraupes@u-paris10.fr>
Depends: R (>= 1.8.0), plyr
Suggests: reshape
Description: Implements Corpus Query Protocol functions based on the CWB software. Rely on CWB (GPL v2), PCRE (BSD licence), glib2 (LGPL).
License: GPL-2 | file LICENCE
LazyLoad: yes
URL: http://www.r-project.org
Collate: main.R zzz.R s3.R
Encoding: latin1
SystemRequirements: GNU make, pcre (>= 7), glib2 (>= 2)
OS_type: unix
NeedsCompilation: yes
Packaged: 2016-06-10 13:36:24 UTC; bernardo
Repository: CRAN
Date/Publication: 2016-06-12 19:08:49

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Package Rcplex updated to version 0.3-3 with previous version 0.3-2 dated 2014-07-01

Title: R Interface to CPLEX
Description: R interface to CPLEX solvers for linear, quadratic, and (linear and quadratic) mixed integer programs. Support for quadratically constrained programming is available. See the file "INSTALL" for details on how to install the Rcplex package in Linux/Unix-like and Windows systems. Support for sparse matrices is provided by an S3-style class "simple_triplet_matrix" from package slam and by objects from the Matrix package class hierarchy.
Author: Hector Corrada Bravo [aut], Kurt Hornik [ctb], Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>

Diff between Rcplex versions 0.3-2 dated 2014-07-01 and 0.3-3 dated 2016-06-13

 DESCRIPTION              |   27 +++++++++++++++------------
 MD5                      |   19 ++++++++++---------
 NAMESPACE                |    3 ++-
 R/quadratic_constraint.R |   12 +++++++-----
 inst/INSTALL             |   46 +++++++++++++++++++++++++++++-----------------
 inst/NEWS                |    5 +++++
 inst/README              |   24 +++++++++++++-----------
 man/Rcplex.Rd            |    4 ++--
 man/Rcplex_solve_QCP.Rd  |only
 src/Makevars.win         |    9 +++++++--
 src/Rcplex_QCP.c         |   24 ++++++++++++------------
 11 files changed, 102 insertions(+), 71 deletions(-)

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New package rccmisc with initial version 0.3.7
Package: rccmisc
Type: Package
Title: Miscellaneous R Functions for Swedish Regional Cancer Centers
Version: 0.3.7
Date: 2016-06-08
Author: Erik Bulow
Maintainer: Erik Bulow <erik.bulow@rccvast.se>
Description: Functions either required by other Swedish Regional Cancer Center packages or standalone functions outside the scope of other packages.
License: GPL-2
Imports: dplyr
Suggests: checkpoint, testthat, R.rsp, rvest, xml2
BugReports: https://bitbucket.com/cancercentrum/rccmisc/issues
LazyLoad: TRUE
VignetteBuilder: R.rsp
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-08 08:16:20 UTC; erikbulow
Repository: CRAN
Date/Publication: 2016-06-08 10:40:43

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New package Rbent with initial version 0.1.0
Package: Rbent
Type: Package
Title: Robust Bent Line Regression
Version: 0.1.0
Authors@R: c( person("Feipeng", "Zhang", email = "zhangfp108@gmail.com", role = "cre"), person("Qunhua", "Li", email = "qunhua.li@psu.edu", role = "aut"))
Maintainer: Feipeng Zhang <zhangfp108@gmail.com>
Description: An implementation of robust bent line regression. It can fit the bent line regression and test the existence of change point, for the paper, "Feipeng Zhang and Qunhua Li (2016). Robust bent line regression, submitted."
License: GPL (>= 2.0)
LazyData: TRUE
RoxygenNote: 5.0.1
Depends: R (>= 3.1.0), Rfit
URL: http://arxiv.org/abs/1606.02234
NeedsCompilation: no
Packaged: 2016-06-08 02:04:42 UTC; Frank2015
Author: Feipeng Zhang [cre], Qunhua Li [aut]
Repository: CRAN
Date/Publication: 2016-06-08 05:46:58

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Package quickpsy updated to version 0.1.3 with previous version 0.1.2 dated 2015-11-30

Title: Fits Psychometric Functions for Multiple Groups
Description: Quickly fits and plots psychometric functions (normal, logistic, Weibull or any or any function defined by the user) for multiple groups.
Author: Linares Daniel [aut, cre], López-Moliner Joan [aut]
Maintainer: Linares Daniel <danilinares@gmail.com>

Diff between quickpsy versions 0.1.2 dated 2015-11-30 and 0.1.3 dated 2016-06-13

 quickpsy-0.1.2/quickpsy/R/one_bootstrap.R           |only
 quickpsy-0.1.2/quickpsy/README.md                   |only
 quickpsy-0.1.3/quickpsy/DESCRIPTION                 |   10 +-
 quickpsy-0.1.3/quickpsy/MD5                         |   85 +++++++++++++-------
 quickpsy-0.1.3/quickpsy/NAMESPACE                   |   20 ++++
 quickpsy-0.1.3/quickpsy/R/aic.R                     |only
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Permanent link

Package quantreg updated to version 5.26 with previous version 5.24 dated 2016-05-13

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

Diff between quantreg versions 5.24 dated 2016-05-13 and 5.26 dated 2016-06-13

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Package qrng updated to version 0.0-3 with previous version 0.0-2 dated 2015-05-05

Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in high dimensions.
Author: Marius Hofert [aut, cre], Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>

Diff between qrng versions 0.0-2 dated 2015-05-05 and 0.0-3 dated 2016-06-13

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Permanent link

New package quadmesh with initial version 0.1.0
Package: quadmesh
Type: Package
Title: Quadrangle Mesh
Version: 0.1.0
Authors@R: person("Michael D.","Sumner", role = c("aut", "cre"), email = "mdsumner@gmail.com")
Description: Gridded data need not be regular, quadmesh creates a mesh from rasters. Future versions may be more general.
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Imports: dplyr, raster
Suggests: datasets
NeedsCompilation: no
Packaged: 2016-06-11 18:43:32 UTC; mdsumner
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-12 17:35:22

More information about quadmesh at CRAN
Permanent link

Package QCEWAS updated to version 1.0-7 with previous version 1.0-6 dated 2016-05-24

Title: Fast & Easy Quality Control of EWAS Results Files
Description: Tools for (automated and manual) quality control of the results of Epigenome-Wide Association Studies.
Author: Peter J. van der Most, Leanne K. Kupers, Ilja M. Nolte
Maintainer: Peter J. van der Most <p.j.van.der.most@umcg.nl>

Diff between QCEWAS versions 1.0-6 dated 2016-05-24 and 1.0-7 dated 2016-06-13

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Package poppr updated to version 2.2.0 with previous version 2.1.1 dated 2016-03-15

Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut], Javier F. Tabima [aut], Sydney E. Everhart [ctb, dtc], Jonah C. Brooks [aut], Stacy A. Krueger-Hadfield [ctb], Erik Sotka [ctb], Brian J. Knaus [ctb], Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>

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Package pmc updated to version 1.0.2 with previous version 1.0.1 dated 2015-09-14

Title: Phylogenetic Monte Carlo
Description: Monte Carlo based model choice for applied phylogenetics of continuous traits. Method described in Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. doi:10.1111/j.1558-5646.2011.01574.x.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>

Diff between pmc versions 1.0.1 dated 2015-09-14 and 1.0.2 dated 2016-06-13

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Package plyr updated to version 1.8.4 with previous version 1.8.3 dated 2015-06-12

Title: Tools for Splitting, Applying and Combining Data
Description: A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of 'plyr' has been generously supported by 'Becton Dickinson'.
Author: Hadley Wickham [aut, cre]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between plyr versions 1.8.3 dated 2015-06-12 and 1.8.4 dated 2016-06-13

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Package plfMA updated to version 1.0.3 with previous version 1.0.2 dated 2016-01-25

Title: A GUI to View, Design and Export Various Graphs of Data
Description: Provides a graphical user interface for viewing and designing various types of graphs of the data. The graphs can be saved in different formats of an image.
Author: Dhammapal Bharne, Vaibhav Vindal
Maintainer: Dhammapal Bharne <dhammapalb@uohyd.ac.in>

Diff between plfMA versions 1.0.2 dated 2016-01-25 and 1.0.3 dated 2016-06-13

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Package PharmacoGx updated to version 1.1.6 with previous version 1.1.5 dated 2016-05-17

Title: Analysis of Large-Scale Pharmacogenomic Data
Description: Contains a set of functions to perform large-scale analysis of pharmacogenomic data.
Author: Petr Smirnov, Zhaleh Safikhani, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>

Diff between PharmacoGx versions 1.1.5 dated 2016-05-17 and 1.1.6 dated 2016-06-13

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New package platetools with initial version 0.0.1
Package: platetools
Title: Tools and Plots for Multi-Well Plates
Version: 0.0.1
Authors@R: person("Scott", "Warchal", email = "s.warchal@sms.ed.ac.uk", role = c("aut", "cre"))
Description: Collection of functions for working with multi-well microtitre plates, mainly 96, 384 and 1536 well plates.
Depends: R (>= 3.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, ggplot2, plyr, lazyeval, raster, RColorBrewer, MASS, viridis
Suggests: testthat
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-10 14:21:55 UTC; scott
Author: Scott Warchal [aut, cre]
Maintainer: Scott Warchal <s.warchal@sms.ed.ac.uk>
Repository: CRAN
Date/Publication: 2016-06-10 18:27:03

More information about platetools at CRAN
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New package PARSE with initial version 0.1.0
Package: PARSE
Type: Package
Title: Model-Based Clustering with Regularization Methods for High-Dimensional Data
Version: 0.1.0
Date: 2016-06-10
Author: Lulu Wang, Wen Zhou, Jennifer Hoeting
Maintainer: Lulu Wang <wanglulu@stat.colostate.edu>
Description: Model-based clustering and identifying informative features based on regularization methods. The package includes three regularization methods - PAirwise Reciprocal fuSE (PARSE) penalty proposed by Wang, Zhou and Hoeting (2016), the adaptive L1 penalty (APL1) and the adaptive pairwise fusion penalty (APFP). Heatmaps are included to shown the identification of informative features.
License: CC0
LazyData: TRUE
Depends: R (>= 3.0.0)
Imports: stats, mvtnorm, gplots, foreach, doParallel, grDevices, utils
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-10 19:42:13 UTC; luluwang
Repository: CRAN
Date/Publication: 2016-06-11 09:42:05

More information about PARSE at CRAN
Permanent link

Package ncvreg updated to version 3.6-0 with previous version 3.5-2 dated 2016-04-08

Title: Regularization Paths for SCAD and MCP Penalized Regression Models
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>

Diff between ncvreg versions 3.5-2 dated 2016-04-08 and 3.6-0 dated 2016-06-13

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More information about ncvreg at CRAN
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Package MXM updated to version 0.8.8 with previous version 0.8.7 dated 2016-05-23

Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying 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.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Athineou, Michail Tsagris, Giorgos Borboudakis, Anna Roumpelaki
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>

Diff between MXM versions 0.8.7 dated 2016-05-23 and 0.8.8 dated 2016-06-13

 DESCRIPTION            |    8 ++++----
 MD5                    |   42 ++++++++++++++++++++++--------------------
 NAMESPACE              |    4 ++--
 R/MMPC.temporal.R      |    4 ++--
 R/SES.temporal.R       |    4 ++--
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 R/bic.glm.fsreg.R      |   18 ++++++++++--------
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More information about MXM at CRAN
Permanent link

Package mvinfluence updated to version 0.8 with previous version 0.6 dated 2012-12-21

Title: Influence Measures and Diagnostic Plots for Multivariate Linear Models
Description: Computes regression deletion diagnostics for multivariate linear models and provides some associated diagnostic plots. The diagnostic measures include hat-values (leverages), generalized Cook's distance, and generalized squared 'studentized' residuals. Several types of plots to detect influential observations are provided.
Author: Michael Friendly
Maintainer: Michael Friendly <friendly@yorku.ca>

Diff between mvinfluence versions 0.6 dated 2012-12-21 and 0.8 dated 2016-06-13

 DESCRIPTION                |   20 +++++++++++---------
 MD5                        |   22 +++++++++++++---------
 NAMESPACE                  |   37 ++++++++++++++++++++++++++++++++++++-
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New package multipanelfigure with initial version 0.8.2
Package: multipanelfigure
Type: Package
Title: Infrastructure to Assemble Multi-Panel Figures (from Grobs)
Version: 0.8.2
Date: 2016-06-12
Author: Johannes Graumann [cre, aut], Richard Cotton [ctb]
Maintainer: Johannes Graumann <jog2030@qatar-med.cornell.edu>
Authors@R: c(person("Johannes", "Graumann", email = "jog2030@qatar-med.cornell.edu", role = c("cre", "aut")), person("Richard","Cotton", email = "richierocks@gmail.com", role = c("ctb")))
Description: Tools to create a layout for figures made of multiple panels, and to fill the panels with base, lattice and ggplot2 plots, grobs, and PNG, JPEG, and TIFF images.
Imports: assertive.base (>= 0.0-5), assertive.files (>= 0.0-2), assertive.numbers (>= 0.0-1), assertive.properties (>= 0.0-2), assertive.types (>= 0.0-2), ggplot2 (>= 2.1.0), grid, gridGraphics (>= 0.1-5), gtable (>= 0.2.0), jpeg (>= 0.1-8), magrittr (>= 1.5), png (>= 0.1-7), rsvg (<= 0.5), stats, tiff (>= 0.1-5), utils
Suggests: grDevices, lattice (>= 0.20-33), roxygen2 (>= 5.0.1), VennDiagram (>= 1.6.16)
License: GPL (>= 3)
RoxygenNote: 5.0.1
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-06-12 08:43:22 UTC; rjc2003
Repository: CRAN
Date/Publication: 2016-06-12 17:23:00

More information about multipanelfigure at CRAN
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New package multiDimBio with initial version 1.0.1
Package: multiDimBio
Type: Package
Title: Multivariate Analysis and Visualization for Biological Data
Version: 1.0.1
Date: 2016-06-08
Author: Samuel V. Scarpino
Maintainer: Samuel V. Scarpino <scarpino@utexas.edu>
Description: Code to support a systems biology research program from inception through publication. The methods focus on dimension reduction approaches to detect patterns in complex, multivariate experimental data and places an emphasis on informative visualizations. The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques. As a result, we encourage suggested additions to the package, both methodological and graphical.
License: GPL (>= 3.0)
LazyLoad: yes
Imports: ggplot2 (>= 0.9.3.1), lme4 (>= 1.0-5), pcaMethods (>= 1.48.0), misc3d (>= 0.8-4), MASS (>= 7.3-29), RColorBrewer(>= 1.0-5), gridGraphics (>= 0.1-5)
NeedsCompilation: no
Packaged: 2016-06-08 13:58:08 UTC; scarpino
Repository: CRAN
Date/Publication: 2016-06-08 17:14:57

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Package MplusAutomation updated to version 0.6-4 with previous version 0.6-3 dated 2014-10-10

Title: Automating Mplus Model Estimation and Interpretation
Description: Leverages the R language to automate latent variable model estimation and interpretation using Mplus, a powerful latent variable modeling program developed by Muthen and Muthen (www.statmodel.com). Specifically, this package provides routines for creating related groups of models, running batches of models, and extracting and tabulating model parameters and fit statistics.
Author: Michael Hallquist [aut, cre], Joshua Wiley [aut]
Maintainer: Michael Hallquist <michael.hallquist@gmail.com>

Diff between MplusAutomation versions 0.6-3 dated 2014-10-10 and 0.6-4 dated 2016-06-13

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 man/graphModel.Rd                   |    3 
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 man/lookupValue.Rd                  |    7 
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More information about MplusAutomation at CRAN
Permanent link

Package move updated to version 2.0.0 with previous version 1.6.541 dated 2016-02-08

Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in movebank.org as well as tools to visualize and statistically analyze animal movement data, among others functions to calculate dynamic Brownian Bridge Movement Models. Move helps addressing movement ecology questions.
Author: Bart Kranstauber <bart.kranstauber@ieu.uzh.ch>, Marco Smolla <marco.smolla@postgrad.manchester.ac.uk>
Maintainer: Bart Kranstauber <bart.kranstauber@ieu.uzh.ch>

Diff between move versions 1.6.541 dated 2016-02-08 and 2.0.0 dated 2016-06-13

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 move-2.0.0/move/R/distance.R                              |    6 -
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Permanent link

Package mousetrap updated to version 1.1.0 with previous version 1.0.0 dated 2016-03-19

Title: Process and Analyze Mouse-Tracking Data
Description: Mouse-tracking, the analysis of mouse movements in computerized experiments, is a method that is becoming increasingly popular in the cognitive sciences. The mousetrap package offers functions for importing, preprocessing, analyzing, aggregating, and visualizing mouse-tracking data.
Author: Pascal J. Kieslich [aut, cre], Felix Henninger [aut]
Maintainer: Pascal J. Kieslich <kieslich@psychologie.uni-mannheim.de>

Diff between mousetrap versions 1.0.0 dated 2016-03-19 and 1.1.0 dated 2016-06-13

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More information about mousetrap at CRAN
Permanent link

Package morse updated to version 2.2.0 with previous version 2.1.1 dated 2015-12-21

Title: MOdelling Tools for Reproduction and Survival Data in Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the mathematical and statistical modelling of bioassay data. They use advanced and innovative methods for a valuable quantitative environmental risk assessment.
Author: Marie Laure Delignette-Muller [aut], Philippe Ruiz [aut], Sandrine Charles [aut], Wandrille Duchemin [ctb], Christelle Lopes [ctb], Guillaume Kon- Kam-king [ctb], Philippe Veber [aut]
Maintainer: Philippe Veber <philippe.veber@univ-lyon1.fr>

Diff between morse versions 2.1.1 dated 2015-12-21 and 2.2.0 dated 2016-06-13

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Permanent link

Package MonetDBLite updated to version 0.3.0 with previous version 0.2.2 dated 2016-04-23

Title: In-Process Version of MonetDB for R
Description: An in-process version of MonetDB, a relational database focused on analytical tasks. Similar to SQLite, the database runs entirely inside the R shell, with the main difference that queries complete much faster thanks to MonetDB's columnar architecture.
Author: Hannes Muehleisen [aut, cre], Anthony Damico [aut], Mark Raasveldt [ctb], Thomas Lumley [ctb], MonetDB Development Team [ctb]
Maintainer: Hannes Muehleisen <hannes@cwi.nl>

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More information about MonetDBLite at CRAN
Permanent link

Package MicSim updated to version 1.0.12 with previous version 1.0.11 dated 2016-02-08

Title: Performing Continuous-Time Microsimulation
Description: This entry-level toolkit allows performing continuous-time microsimulation for a wide range of demographic applications. Individual life-courses are specified by a continuous-time multi-state model.
Author: Sabine Zinn
Maintainer: Sabine Zinn <sabine.zinn@lifbi.de>

Diff between MicSim versions 1.0.11 dated 2016-02-08 and 1.0.12 dated 2016-06-13

 DESCRIPTION           |    8 ++++----
 MD5                   |    8 ++++----
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Package MGSDA updated to version 1.4 with previous version 1.3 dated 2016-05-12

Title: Multi-Group Sparse Discriminant Analysis
Description: Implements Multi-Group Sparse Discriminant Analysis proposal of I.Gaynanova, J.Booth and M.Wells (2015), Simultaneous sparse estimation of canonical vectors in the p>>N setting, JASA, to appear,[DOI:10.1080/01621459.2015.1034318].
Author: Irina Gaynanova
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>

Diff between MGSDA versions 1.3 dated 2016-05-12 and 1.4 dated 2016-06-13

 DESCRIPTION          |   10 +--
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New package mcglm with initial version 0.3.0
Package: mcglm
Type: Package
Title: Multivariate Covariance Generalized Linear Models
Version: 0.3.0
Date: 2016-06-06
Author: Wagner Hugo Bonat [aut, cre], Walmes Marques Zeviani [ctb], Fernando de Pol Mayer [ctb]
Maintainer: Wagner Hugo Bonat <wbonat@ufpr.br>
Authors@R: c(person(c("Wagner","Hugo"), "Bonat", role = c("aut", "cre"), email = "wbonat@ufpr.br"), person(c("Walmes","Marques"), "Zeviani", role = "ctb"), person(c("Fernando", "de Pol"), "Mayer", role = "ctb"))
Description: Fitting multivariate covariance generalized linear models (McGLMs) to data. McGLMs is a general framework for non-normal multivariate data analysis, designed to handle multivariate response variables, along with a wide range of temporal and spatial correlation structures defined in terms of a covariance link function combined with a matrix linear predictor involving known matrices. The models take non-normality into account in the conventional way by means of a variance function, and the mean structure is modelled by means of a link function and a linear predictor. The models are fitted using an efficient Newton scoring algorithm based on quasi-likelihood and Pearson estimating functions, using only second-moment assumptions. This provides a unified approach to a wide variety of different types of response variables and covariance structures, including multivariate extensions of repeated measures, time series, longitudinal, spatial and spatio-temporal structures. The package offers a user-friendly interface for fitting McGLMs similar to the glm() R function.
Depends: R (>= 3.2.1)
Suggests: testthat, plyr, lattice, latticeExtra, knitr, rmarkdown, MASS, mvtnorm, tweedie, devtools
Imports: stats, Matrix, assertthat, graphics
License: GPL-3 | file LICENSE
LazyData: TRUE
URL: https://github.com/wbonat/mcglm
BugReports: https://github.com/wbonat/mcglm/issues
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-09 14:10:09 UTC; fernando
Repository: CRAN
Date/Publication: 2016-06-09 20:23:56

More information about mcglm at CRAN
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Package matrixpls updated to version 1.0.0 with previous version 0.7.0 dated 2016-02-01

Title: Matrix-Based Partial Least Squares Estimation
Description: Partial Least Squares Path Modeling algorithm and related algorithms. The algorithm implementations aim for computational efficiency using matrix algebra and covariance data. The package is designed toward Monte Carlo simulations and includes functions to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö <mikko.ronkko@aalto.fi>

Diff between matrixpls versions 0.7.0 dated 2016-02-01 and 1.0.0 dated 2016-06-13

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Permanent link

Package marima updated to version 1.5 with previous version 1.4 dated 2016-04-18

Title: Multivariate ARIMA and ARIMA-X Analysis
Description: Multivariate arima and arima-x estimation using Spliid's algorithm (marima) and simulation (marima.sim).
Author: Henrik Spliid
Maintainer: Henrik Spliid <hspl@dtu.dk>

Diff between marima versions 1.4 dated 2016-04-18 and 1.5 dated 2016-06-13

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More information about marima at CRAN
Permanent link

Package mapview updated to version 1.1.0 with previous version 1.0.0 dated 2015-12-15

Title: Interactive Viewing of Spatial Objects in R
Description: Methods to view spatial objects interactively.
Author: Tim Appelhans [cre, aut], Florian Detsch [aut], Christoph Reudenbach [aut], Stefan Woellauer [aut], Spaska Forteva [ctb], Thomas Nauss [ctb], Edzer Pebesma [ctb], Kenton Russell [ctb], Environmental Informatics Marburg [ctb]
Maintainer: Tim Appelhans <admin@environmentalinformatics-marburg.de>

Diff between mapview versions 1.0.0 dated 2015-12-15 and 1.1.0 dated 2016-06-13

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More information about mapview at CRAN
Permanent link

New package manhattanly with initial version 0.1.0
Package: manhattanly
Type: Package
Title: Interactive Q-Q and Manhattan Plots Using 'plotly.js'
Version: 0.1.0
Date: 2016-06-07
LazyData: true
Authors@R: c(person("Sahir", "Bhatnagar", email = "sahir.bhatnagar@gmail.com", role = c("aut", "cre"), comment = "http://sahirbhatnagar.com/"))
Description: Create interactive Q-Q and manhattan plots that are usable from the R console, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a point to show details or drag a rectangle to zoom. A manhattan plot is a popular graphical method for visualizing results from high-dimensional data analysis such as a (epi)genome wide association study (GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter plot against their genomic position. Manhattan plots are used for visualizing potential regions of interest in the genome that are associated with a phenotype. Interactive manhattan plots allow the inspection of specific value (e.g. rs number or gene name) by hovering the mouse over a cell, as well as zooming into a region of the genome (e.g. a chromosome) by dragging a rectangle around the relevant area. This work is based on the 'qqman' package by Stephen Turner and the 'plotly.js' engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq' functions in the 'qqman' package, with the advantage of including extra annotation information and interactive web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
Depends: R (>= 3.0.0)
Imports: stats, magrittr (>= 1.0.1), plotly (>= 3.6.0), ggplot2
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
License: MIT + file LICENSE
URL: https://github.com/sahirbhatnagar/manhattanly/, http://sahirbhatnagar.com/manhattanly/
BugReports: https://github.com/sahirbhatnagar/manhattanly/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-08 15:32:04 UTC; sahir
Author: Sahir Bhatnagar [aut, cre] (http://sahirbhatnagar.com/)
Maintainer: Sahir Bhatnagar <sahir.bhatnagar@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-08 17:52:18

More information about manhattanly at CRAN
Permanent link

New package macleish with initial version 0.3.0
Package: macleish
Type: Package
Title: Retrieve Data from MacLeish Field Station
Version: 0.3.0
Date: 2016-06-08
Authors@R: c( person("Ben", "Baumer", email = "ben.baumer@gmail.com", role = c("aut", "cre")), person("Rose", "Goueth", role = "aut"), person("Wencong", "Li", email = "liwencong1995@gmail.com", role = "aut"), person("Weijia", "Zhang", email = "wzhang23@smith.edu", role = "aut"), person("Nicholas", "Li", email = "nhorton@amherst.edu", role = "aut") )
Description: Download data from the Ada and Archibald MacLeish Field Station in Whately, MA. The Ada and Archibald MacLeish Field Station is a 260-acre patchwork of forest and farmland located in West Whately, MA that provides opportunities for faculty and students to pursue environmental research, outdoor education, and low-impact recreation (see <http://www.smith.edu/ceeds/macleish.php> for more information). This package contains weather data over several years, and spatial data on various man-made and natural structures.
License: CC0
LazyData: TRUE
Imports: dplyr, DBI, lubridate, readr
Depends: R (>= 2.10), etl
Suggests: ggplot2, RSQLite, broom, knitr, ggmap, leaflet, rmarkdown, clifro, testthat
Enhances: sp, rgdal, rgeos
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-09 12:56:47 UTC; bbaumer
Author: Ben Baumer [aut, cre], Rose Goueth [aut], Wencong Li [aut], Weijia Zhang [aut], Nicholas Li [aut]
Maintainer: Ben Baumer <ben.baumer@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-09 15:19:17

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Package machQA updated to version 0.1.2 with previous version 0.1.1 dated 2016-06-06

Title: QA Machina Indicators
Description: Performs QA on Machina (see <https://machi.na/> for more information) algebraic indicators 'sma' (simple moving average), 'wavg' (weighted average),'xavg' (exponential moving average), 'hma' (Hull moving average), 'adma' (adaptive moving average), 'tsi' (true strength index), 'rsi' (relative strength index), 'gauss' (Gaussian elimination), 'momo' (momentum), 't3' (triple exponential moving average), 'macd' (moving average convergence divergence).
Author: Norton Tim [aut, cre]
Maintainer: Norton Tim <tnorton@machi.na>

Diff between machQA versions 0.1.1 dated 2016-06-06 and 0.1.2 dated 2016-06-13

 DESCRIPTION  |   12 +++++-------
 MD5          |    6 +++---
 R/machQA.R   |   29 ++++++++++++++++++++++-------
 R/versions.R |    2 ++
 4 files changed, 32 insertions(+), 17 deletions(-)

More information about machQA at CRAN
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New package LTRCtrees with initial version 0.1.0
Package: LTRCtrees
Type: Package
Title: Survival Trees to Fit Left-Truncated and Right-Censored Survival Data
Version: 0.1.0
Description: Recursive partition algorithms designed for fitting survival tree with left-truncated and right censored (LTRC) data. Such LTRC trees can also be used to fit survival tree with time-varying covariates.
Authors@R: c( person("Wei", "Fu", email = "weifu.scott@gmail.com", role = c("aut", "cre")), person("Jeffrey", "Simonoff", role = "aut") )
Imports: partykit, rpart, survival
Suggests: Formula, rpart.plot, knitr, rmarkdown
Depends: R (>= 3.2.0)
License: GPL-3
LazyData: TRUE
Author: Wei Fu [aut, cre], Jeffrey Simonoff [aut]
Maintainer: Wei Fu <weifu.scott@gmail.com>
VignetteBuilder: knitr, rmarkdown
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-12 01:48:02 UTC; wfu
Repository: CRAN
Date/Publication: 2016-06-12 17:23:02

More information about LTRCtrees at CRAN
Permanent link

Package lifecontingencies updated to version 1.2 with previous version 1.1.12 dated 2016-05-12

Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table, actuarial tables (also multiple decrement tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J. Owens [ctb], Christophe Dutang [ctb], Ernesto Schirmacher[ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>

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Package lazyeval updated to version 0.2.0 with previous version 0.1.10 dated 2015-01-02

Title: Lazy (Non-Standard) Evaluation
Description: An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package kSamples updated to version 1.2-4 with previous version 1.2-3 dated 2016-02-17

Title: K-Sample Rank Tests and their Combinations
Description: Compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples. Also analyzed are 2 x t contingency tables and their blocked combinations using the Kruskal-Wallis criterion. Steel's test is inverted to provide simultaneous confidence bounds for shift parameters. A plotting function compares tail probabilities obtained under asymptotic approximation with those obtained via simulation or exact calculations.
Author: Fritz Scholz [aut, cre], Angie Zhu [aut]
Maintainer: Fritz Scholz <fscholz@u.washington.edu>

Diff between kSamples versions 1.2-3 dated 2016-02-17 and 1.2-4 dated 2016-06-13

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New package kehra with initial version 0.1
Package: kehra
Type: Package
Title: Collect, Assemble and Model Air Pollution, Weather and Health Data
Version: 0.1
Date: 2016-06-09
Author: Claudia Vitolo [aut, cre], Allan Tucker [aut], Andrew Russell [aut]
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
URL: https://github.com/kehraProject/r_kehra
BugReports: https://github.com/kehraProject/r_kehra/issues
Description: Collection of utility functions used in the KEHRA project (see http://www.brunel.ac.uk/ife/britishcouncil). It refers to the multidimensional analysis of air pollution, weather and health data.
Depends: R (>= 2.14.0)
Imports: Hmisc, raster, reshape2, stringr, sp, xts, zoo
License: GPL-3
Repository: CRAN
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-10 11:07:52 UTC; claudia
Date/Publication: 2016-06-10 13:48:43

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New package jtGWAS with initial version 1.1
Package: jtGWAS
Type: Package
Title: Efficient Jonckheere-Terpstra Test Statistics
Version: 1.1
Date: 2016-06-10
Author: Jiaxing Lin, Alexander Sibley, Ivo Shterev, and Kouros Owzar
Maintainer: Jiaxing Lin <jiaxing.lin@duke.edu>
Description: The core of this 'Rcpp' based package is a function to compute standardized Jonckheere-Terpstra test statistics for large numbers of dependent and independent variables, e.g., genome-wide analysis. It implements 'OpenMP', allowing the option of computing on multiple threads. Supporting functions are also provided to calculate p-values and summarize results.
License: GPL (>= 2)
URL: https://bitbucket.org/impactp01/jtgwas
Imports: Rcpp (>= 0.12.3)
LinkingTo: Rcpp
Suggests: knitr
VignetteBuilder: knitr
BuildVignettes: yes
NeedsCompilation: yes
Packaged: 2016-06-10 17:11:09 UTC; jl354
Repository: CRAN
Date/Publication: 2016-06-10 23:14:19

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New package jsonvalidate with initial version 1.0.0
Package: jsonvalidate
Title: Validate 'JSON'
Version: 1.0.0
Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"), email = "rich.fitzjohn@gmail.com"), person("Mathias", "Buus", role = "cph"))
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Description: Uses the node library 'is-my-json-valid' to validate 'JSON' against a 'JSON' schema.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/ropenscilabs/jsonvalidate
BugReports: https://github.com/ropenscilabs/jsonvalidate/issues
Imports: V8
Suggests: knitr, rmarkdown, testthat
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-13 08:22:07 UTC; rich
Author: Rich FitzJohn [aut, cre], Mathias Buus [cph]
Repository: CRAN
Date/Publication: 2016-06-13 13:07:03

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New package JointModel with initial version 1.0
Package: JointModel
Title: Semiparametric Joint Models for Longitudinal and Counting Processes
Version: 1.0
Date: 2016-06-01
Author: Sehee Kim <seheek@umich.edu>
Maintainer: Sehee Kim <seheek@umich.edu>
Description: Joint fit of a semiparametric regression model for longitudinal responses and a semiparametric transformation model for time-to-event data.
Depends: R (>= 3.2.0), lme4, survival, splines, statmod
License: GPL-3
LazyData: TRUE
NeedsCompilation: no
Repository: CRAN
Packaged: 2016-06-08 18:35:05 UTC; seheek
Date/Publication: 2016-06-09 05:49:19

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Package jmotif updated to version 1.0.2.900 with previous version 1.0.2 dated 2015-12-08

Title: Time Series Analysis Toolkit Based on Symbolic Aggregate Dicretization, i.e. SAX
Description: Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly), and characteristic pattern discovery along with interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>

Diff between jmotif versions 1.0.2 dated 2015-12-08 and 1.0.2.900 dated 2016-06-13

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Package itsadug updated to version 2.2 with previous version 2.1 dated 2016-05-28

Title: Interpreting Time Series and Autocorrelated Data Using GAMMs
Description: GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999) as implemented in the R package 'mgcv' (Wood, S.N., 2006; 2011) is a nonlinear regression analysis which is particularly useful for time course data such as EEG, pupil dilation, gaze data (eye tracking), and articulography recordings, but also for behavioral data such as reaction times and response data. As time course measures are sensitive to autocorrelation problems, GAMMs implements methods to reduce the autocorrelation problems. This package includes functions for the evaluation of GAMM models (e.g., model comparisons, determining regions of significance, inspection of autocorrelational structure in residuals) and interpreting of GAMMs (e.g., visualization of complex interactions, and contrasts).
Author: Jacolien van Rij [aut, cre], Martijn Wieling [aut], R. Harald Baayen [aut], Hedderik van Rijn [ctb]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>

Diff between itsadug versions 2.1 dated 2016-05-28 and 2.2 dated 2016-06-13

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Package install.load updated to version 1.1.1 with previous version 1.0.4 dated 2016-02-03

Title: Check, Install and Load CRAN & USGS GRAN Packages
Description: Checks the local R library(ies) to see if the required package(s) is/are installed or not. If the package(s) is/are not installed, then the package(s) will be installed along with the required dependency(ies). This function pulls source or binary packages from the Rstudio-sponsored CRAN mirror and/or the USGS GRAN Repository. Lastly, the chosen package(s) is/are loaded.
Author: maloneypatr [aut, cre] (Author of original install_load function, see http://stackoverflow.com/questions/15155814/ check-if-r-package-is-installed-then-load-library), Irucka Embry [aut, ctb]
Maintainer: Irucka Embry <iembry@ecoccs.com>

Diff between install.load versions 1.0.4 dated 2016-02-03 and 1.1.1 dated 2016-06-13

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Package inflection updated to version 1.2 with previous version 1.1 dated 2013-04-04

Title: Finds the Inflection Point of a Curve
Description: Implementation of methods Extremum Surface Estimator and Extremum Distance Estimator for identifying the inflection point of a convex/concave curve.
Author: Demetris T. Christopoulos
Maintainer: Demetris T. Christopoulos <dchristop@econ.uoa.gr>

Diff between inflection versions 1.1 dated 2013-04-04 and 1.2 dated 2016-06-13

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Package imputeMulti updated to version 0.5.2 with previous version 0.4.6 dated 2016-05-26

Title: Imputation Methods for Multivariate Multinomial Data
Description: Implements imputation methods using EM and Data Augmentation for multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>

Diff between imputeMulti versions 0.4.6 dated 2016-05-26 and 0.5.2 dated 2016-06-13

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Package iemiscdata updated to version 0.5.2 with previous version 0.5.1 dated 2016-05-30

Title: Irucka Embry's Miscellaneous Data Collection
Description: Miscellaneous data sets [Environmental/Water Resources Engineering].
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>

Diff between iemiscdata versions 0.5.1 dated 2016-05-30 and 0.5.2 dated 2016-06-13

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Package iemisc updated to version 0.9.0 with previous version 0.6.2 dated 2016-05-30

Title: Irucka Embry's Miscellaneous Functions
Description: A collection of Irucka Embry's miscellaneous functions (Engineering Economics, Environmental/Water Resources Engineering, Geometry, Statistics, GNU Octave length functions, etc.).
Author: Irucka Embry [aut, cre], Felix Andrews [aut, ctb] (zoo), Hans Werner Borchers [aut, ctb] (pracma), Samit Basu [aut, ctb] (FreeMat)
Maintainer: Irucka Embry <iembry@ecoccs.com>

Diff between iemisc versions 0.6.2 dated 2016-05-30 and 0.9.0 dated 2016-06-13

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New package ibm with initial version 0.1.0
Package: ibm
Version: 0.1.0
Authors@R: c( person("Ricardo", "Oliveros-Ramos", email="ricardo.oliveros@gmail.com", role=c("aut", "cre")))
Title: Individual Based Models in R
Description: Implementation of some (simple) Individual Based Models and methods to create new ones, particularly for population dynamics models (reproduction, mortality and movement). The basic operations for the simulations are implemented in Rcpp for speed.
Depends: R (>= 2.15)
Imports: Rcpp (>= 0.11.5), stats, graphics
License: GPL-2
URL: http://roliveros-ramos.github.io/ibm
BugReports: https://github.com/roliveros-ramos/ibm/issues
LinkingTo: Rcpp
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-06-09 22:27:39 UTC; Ricardo
Author: Ricardo Oliveros-Ramos [aut, cre]
Maintainer: Ricardo Oliveros-Ramos <ricardo.oliveros@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-10 08:36:50

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New package hypothesisr with initial version 0.1.0
Package: hypothesisr
Type: Package
Title: Wrapper for the 'Hypothes.is' API
Version: 0.1.0
Authors@R: person("Matthew", "Lincoln", email = "matthew.d.lincoln@gmail.com", role = c("aut", "cre"))
Description: Interact with the API for the web annotation service 'Hypothes.is' (See <http://hypothes.is> for more information.) Allows users to download data about public annotations, and create, retrieve, update, and delete their own annotations.
Imports: dplyr, httr, jsonlite
License: MIT + file LICENSE
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: testthat
URL: https://github.com/mdlincoln/hypothesisr
BugReports: https://github.com/mdlincoln/hypothesisr/issues
NeedsCompilation: no
Packaged: 2016-06-10 16:45:19 UTC; admin
Author: Matthew Lincoln [aut, cre]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-12 17:41:30

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New package hsm with initial version 0.1
Package: hsm
Type: Package
Title: A Path-Based BCD for Proximal Function of Latent Group Lasso
Description: Implementation of the block coordinate descent procedure for solving the proximal function of latent group Lasso, highlighted by decomposing a DAG into several non-overlapping path graphs, and getting closed-form solution for each path graph. The procedure was introduced as Algorithm 4 in Yan and Bien (2015) <https://arxiv.org/abs/1512.01631> "Hierarchical Sparse Modeling: A Choice of Two Regularizers", and the closed-form solution for each path graph is solved in Algorithm 3 of that paper.
Version: 0.1
Author: Xiaohan Yan <xy257@cornell.edu>, Jacob Bien
Depends: R (>= 3.2.1)
Suggests: knitr
License: GPL-3
LazyData: TRUE
Maintainer: Xiaohan Yan <xy257@cornell.edu>
VignetteBuilder: knitr
RoxygenNote: 5.0.1
URL: https://arxiv.org/abs/1512.01631
NeedsCompilation: yes
Packaged: 2016-06-09 05:06:25 UTC; xiaohanyan
Repository: CRAN
Date/Publication: 2016-06-09 07:56:49

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Package heemod updated to version 0.3.2 with previous version 0.3.1 dated 2016-04-04

Title: Models for Health Economic Evaluation
Description: Health Economic Evaluation Modelling. Markov models (homogeneous and non-homogeneous) for health economic evaluation. Model comparison, sensitivity and probabilistic analysis.
Author: Kevin Zarca [aut], Antoine Filipovic-Pierucci [aut,cre]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>

Diff between heemod versions 0.3.1 dated 2016-04-04 and 0.3.2 dated 2016-06-13

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New package hierformR with initial version 0.1.0
Package: hierformR
Type: Package
Title: Analysis of Dynamics Hierarchy Formation
Version: 0.1.0
Authors@R: c(person("James P.", "Curley", role = c("aut", "cre"), email = "jc3181@columbia.edu"), person("Ivan D.", "Chase", role = "aut", email = "ivan.chase@stonybrook.edu"))
Maintainer: James P. Curley <jc3181@columbia.edu>
Description: Determine paths and states that social networks develop over time to form social hierarchies. Based upon algorithms described in W. Brent Lindquist & Ivan D. Chase (2009) <DOI:10.1007/s11538-008-9371-9>.
Depends: R (>= 3.1.0)
Imports: igraph, utils
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.0
NeedsCompilation: no
Packaged: 2016-06-10 15:31:26 UTC; James Curley
Author: James P. Curley [aut, cre], Ivan D. Chase [aut]
Repository: CRAN
Date/Publication: 2016-06-10 18:27:00

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New package HDDesign with initial version 1.1
Package: HDDesign
Version: 1.1
Date: 2016-06-10
Title: Sample Size Calculation for High Dimensional Classification Study
Author: Meihua Wu <meihuawu@umich.edu>, Brisa N. Sanchez <brisa@umich.edu>, Peter X.K. Song <pxsong@umich.edu>, Raymond Luu <raluu@umich.edu>, Wen Wang <wangwen@umich.edu>
Maintainer: Brisa N. Sanchez <brisa@umich.edu>
Description: Determine the sample size requirement to achieve the target probability of correct classification (PCC) for studies employing high-dimensional features. The package implements functions to 1) determine the asymptotic feasibility of the classification problem; 2) compute the upper bounds of the PCC for any linear classifier; 3) estimate the PCC of three design methods given design assumptions; 4) determine the sample size requirement to achieve the target PCC for three design methods.
License: GPL-2
Packaged: 2016-06-11 01:01:05 UTC; jiangwenjiaowa
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2016-06-11 09:37:25

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Package googleway updated to version 1.0.0 with previous version 0.2.0 dated 2016-05-30

Title: Retrieves Data from Google Maps APIs
Description: Retrieves data from six Google Maps APIs: directions, distances, elevation, geocode, reverse geocode and timezone. Also able to decode encoded location data.
Author: David Cooley [aut, cre], Paulo Barcelos [ctb] (Author of c++ decode_pl)
Maintainer: David Cooley <dcooley@symbolix.com.au>

Diff between googleway versions 0.2.0 dated 2016-05-30 and 1.0.0 dated 2016-06-13

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New package grex with initial version 1.1
Package: grex
Type: Package
Title: Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Version: 1.1
Author: Nan Xiao <nanx@uchicago.edu>, Gao Wang <gaow@uchicago.edu>
Maintainer: Nan Xiao <nanx@uchicago.edu>
Description: Convert the 'Ensembl' gene identifiers from Genotype-Tissue Expression (GTEx) data to identifiers in other annotation systems, including 'Entrez', 'HGNC', and 'UniProt'.
License: GPL
LazyData: TRUE
VignetteBuilder: knitr
URL: http://nanx.me/grex/
BugReports: https://github.com/road2stat/grex/issues
Depends: R (>= 3.0.2)
Suggests: knitr, rmarkdown
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-12 20:51:10 UTC; jimmy
Repository: CRAN
Date/Publication: 2016-06-13 07:30:16

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Package gofCopula updated to version 0.1-3 with previous version 0.1-2 dated 2016-01-27

Title: Goodness-of-Fit Tests for Copulae
Description: Several GoF tests for Copulae are provided. A new hybrid test is implemented which supports all of the individual tests. Estimation methods for the margins are provided. All the tests support parameter estimation and predefined values. The parameters are estimated by pseudo maximum likelihood but if it fails the estimation switches automatically to inversion of Kendall's tau.
Author: Ostap Okhrin <ostap.okhrin@tu-dresden.de>, Simon Trimborn <simon.trimborn@wiwi.hu-berlin.de>, Shulin Zhang <slzhang@swufe.edu.cn>, Qian M. Zhou <qmzhou@sfu.ca>
Maintainer: Simon Trimborn <simon.trimborn@wiwi.hu-berlin.de>

Diff between gofCopula versions 0.1-2 dated 2016-01-27 and 0.1-3 dated 2016-06-13

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Package GHap updated to version 1.2.1 with previous version 1.2.0 dated 2016-05-03

Title: Genome-Wide Haplotyping
Description: Haplotype calling from phased SNP data.
Author: Yuri Tani Utsunomiya, Marco Milanesi
Maintainer: Yuri Tani Utsunomiya <ytutsunomiya@gmail.com>

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New package githubinstall with initial version 0.0.1
Package: githubinstall
Type: Package
Version: 0.0.1
Date: 2016-06-10
Title: An Easy Way to Install R Packages on GitHub
Description: Provides an easy way to install packages on GitHub.
Authors@R: c( person("Koji", "Makiyama", email = "hoxo.smile@gmail.com", role = c("cre", "aut")), person("Atsushi", "Hayakawa", role = "ctb"), person("Shinya", "Uryu", role = "ctb"), person("Hiroaki", "Yutani", role = "ctb"))
URL: https://github.com/hoxo-m/githubinstall
BugReports: https://github.com/hoxo-m/githubinstall/issues
License: MIT + file LICENSE
Imports: data.table, ghit, httr, jsonlite, stringr, utils
RoxygenNote: 5.0.1
Suggests: testthat, ggplot2, lubridate, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-11 09:34:28 UTC; kmakiyam
Author: Koji Makiyama [cre, aut], Atsushi Hayakawa [ctb], Shinya Uryu [ctb], Hiroaki Yutani [ctb]
Maintainer: Koji Makiyama <hoxo.smile@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-12 17:35:25

More information about githubinstall at CRAN
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Package ggRandomForests updated to version 2.0.0 with previous version 1.2.1 dated 2015-12-12

Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the 'randomForest' or 'randomForestSRC' package for survival, regression and classification forests and 'ggplot2' package plotting.
Author: John Ehrlinger <john.ehrlinger@gmail.com>
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>

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Package GenCAT updated to version 1.0.3 with previous version 1.0.2 dated 2016-02-17

Title: Genetic Class Association Testing
Description: Implementation of the genetic class level association testing (GenCAT) method from SNP level association data. Refer to: "Qian J, Nunez S, Reed E, Reilly MP, Foulkes AS (2016) <DOI:10.1371/journal.pone.0148218> A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci. PLoS ONE 11(2): e0148218".
Author: Eric Reed, Sara Nunez, Jing Qian, Andrea Foulkes
Maintainer: Eric Reed <reeder@bu.edu>

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Package GA updated to version 3.0.2 with previous version 3.0.1 dated 2016-05-16

Title: Genetic Algorithms
Description: An R package for optimisation using genetic algorithms. The package provides a flexible general-purpose set of tools for implementing genetic algorithms search in both the continuous and discrete case, whether constrained or not. Users can easily define their own objective function depending on the problem at hand. Several genetic operators are available and can be combined to explore the best settings for the current task. Furthermore, users can define new genetic operators and easily evaluate their performances. Local search using general-purpose optimisation algorithms can be applied stochastically to exploit interesting regions. GAs can be run sequentially or in parallel, using an explicit master-slave parallelisation or a coarse-grain islands approach.
Author: Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>

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Package ezknitr updated to version 0.4 with previous version 0.3.1 dated 2016-01-06

Title: Avoid the Typical Working Directory Pain When Using 'knitr'
Description: An extension of 'knitr' that adds flexibility in several ways. One common source of frustration with 'knitr' is that it assumes the directory where the source file lives should be the working directory, which is often not true. 'ezknitr' addresses this problem by giving you complete control over where all the inputs and outputs are, and adds several other convenient features to make rendering markdown/HTML documents easier.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

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Package ezec updated to version 1.0.0 with previous version 0.1.0 dated 2015-11-30

Title: Easy Interface to Effective Concentration Calculations
Description: Because fungicide resistance is an important phenotypic trait for fungi and oomycetes, it is necessary to have a standardized method of statistically analyzing the Effective Concentration (EC) values. This package is designed for those who are not terribly familiar with R to be able to analyze and plot an entire set of isolates using the 'drc' package.
Author: Zhian N. Kamvar [cre, aut], Niklaus J. Grunwald [ths, ctb]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>

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New package extraDistr with initial version 1.7.0
Package: extraDistr
Type: Package
Title: Additional Univariate and Multivariate Distributions
Version: 1.7.0
Date: 2016-06-10
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>
Description: Density, distribution function, quantile function and random generation for a number of univariate and multivariate distributions.
License: GPL-2
LazyData: TRUE
LinkingTo: Rcpp
Imports: Rcpp
Suggests: testthat
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-06-11 13:10:22 UTC; tymek
Repository: CRAN
Date/Publication: 2016-06-11 22:26:50

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New package etl with initial version 0.3.1
Package: etl
Type: Package
Title: Extract-Transfer-Load Framework for Medium Data
Version: 0.3.1
Date: 2016-06-07
Authors@R: c( person("Ben", "Baumer", email = "ben.baumer@gmail.com", role = c("aut", "cre")), person("Carson", "Sievert", email = "cpsievert1@gmail.com", role = "ctb"))
Maintainer: Ben Baumer <ben.baumer@gmail.com>
Description: A framework for loading medium-sized data from the Internet to a local or remote relational database management system. This package itself doesn't do much more than provide a toy example and set up the method structure. Packages that depend on this package will facilitate the construction and maintenance of their respective databases.
License: CC0
LazyData: TRUE
Imports: DBI, datasets, methods, utils
Depends: R (>= 2.10), dplyr
Suggests: knitr, RSQLite, RPostgreSQL, RMySQL, testthat
URL: http://github.com/beanumber/etl
BugReports: https://github.com/beanumber/etl/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-08 01:42:33 UTC; bbaumer
Author: Ben Baumer [aut, cre], Carson Sievert [ctb]
Repository: CRAN
Date/Publication: 2016-06-08 05:47:00

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New package engsoccerdata with initial version 0.1.5
Title: English and European Soccer Results 1871-2016
Type: Package
Package: engsoccerdata
Version: 0.1.5
Date: 2016-06-11
Author: James Curley
Maintainer: James Curley <jc3181@columbia.edu>
Description: Analyzing English & European soccer results data from 1871-2016.
Depends: R (>= 2.10)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Suggests:
RoxygenNote: 5.0.1
Imports: dplyr, magrittr, tidyr, utils
NeedsCompilation: no
Packaged: 2016-06-11 12:46:31 UTC; curley1
Repository: CRAN
Date/Publication: 2016-06-12 17:35:23

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New package dynr with initial version 0.1.7
Package: dynr
Date: 2016-06-07
Title: Dynamic Modeling in R
Authors@R: c(person("Lu", "Ou", role=c("aut", "cre"), email="lzo114@psu.edu"), person(c("Michael", "D."), "Hunter", role="aut"), person("Sy-Miin", "Chow", role="aut"))
Author: Lu Ou [aut, cre], Michael D. Hunter [aut], Sy-Miin Chow [aut]
Maintainer: Lu Ou <lzo114@psu.edu>
Depends: R (>= 3.0.0), methods, ggplot2
Imports: numDeriv, xtable, latex2exp, grid, reshape2, plyr
Suggests: testthat, roxygen2 (>= 3.1)
Description: Dynamic modeling of all kinds in R. These include models of processes in discrete time or continuous time. They also include processes that are linear or nonlinear. Latent variables can be continuous (e.g. state space models) or discrete (e.g. regime-switching models). The general approach involves maximum likelihood estimation of single- and multi-subject models of latent time series with the extended Kalman filter and Kim filter. The user provides recipes and data which are combined into a model that is then cooked to obtain free parameter estimates.
SystemRequirements: GNU make
NeedsCompilation: yes
License: Apache License (== 2.0)
LazyLoad: yes
LazyData: yes
Collate: 'dynrData.R' 'dynrRecipe.R' 'dynrModelInternal.R' 'dynrModel.R' 'dynrCook.R' 'dynrPlot.R' 'dynrFuncAddress.R' 'dynrVersion.R' 'dataDoc.R'
Version: 0.1.7
Packaged: 2016-06-07 18:33:18 UTC; mhunter
Repository: CRAN
Date/Publication: 2016-06-09 20:41:13

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Package dvn updated to version 0.3.5 with previous version 0.3.3 dated 2013-12-02

Title: Access to Dataverse 3 APIs
Description: Provides access to Dataverse version 3 APIs, enabling access to archived data (and metadata), and the ability to create and manipulate studies in a user's dataverse(s). For Dataverse server versions >= 4.0, please use the dataverse package <https://github.com/IQSS/dataverse-client-r> instead.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

Diff between dvn versions 0.3.3 dated 2013-12-02 and 0.3.5 dated 2016-06-13

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Package docopt updated to version 0.4.5 with previous version 0.4.3.3 dated 2015-05-04

Title: Command-Line Interface Specification Language
Description: Define a command-line interface by just giving it a description in the specific format.
Author: Edwin de Jonge (edwindjonge@gmail.com)
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>

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Package dlsem updated to version 1.0.3 with previous version 1.0.1 dated 2016-05-24

Title: Distributed-Lag Structural Equation Modelling
Description: Fit distributed-lag structural equation models and perform path analysis at different time lags.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>

Diff between dlsem versions 1.0.1 dated 2016-05-24 and 1.0.3 dated 2016-06-13

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Package DLMtool updated to version 3.2 with previous version 3.1 dated 2016-02-27

Title: Data-Limited Methods Toolkit
Description: Simulation testing and implementation of data-limited fishery stock assessment methods.
Author: Tom Carruthers and Adrian Hordyk
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>

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New package DiffusionRimp with initial version 0.1.0
Package: DiffusionRimp
Version: 0.1.0
Title: Inference and Analysis for Diffusion Processes via Data Imputation and Method of Lines
Description: Tools for performing inference and analysis using a data-imputation scheme and the method of lines.
Authors@R: c(person("Etienne A.D.", "Pienaar", email = "etiennead@gmail.com",role = c("aut", "cre")), person("Melvin M.", "Varughese", email = "melvin.varughese@uct.ac.za",role = c("ctb")))
URL: https://github.com/eta21
BugReports: https://github.com/eta21/DiffusionRimp/issues
MailingList: Please send questions and comments to etiennead@gmail.com.
Depends: R (>= 3.2.1)
Imports: Rcpp, RcppArmadillo, rgl, colorspace
LinkingTo: Rcpp, RcppArmadillo
Suggests: DiffusionRgqd, DiffusionRjgqd, knitr, coda, Quandl, R.rsp
License: GPL (>= 2)
VignetteBuilder: knitr, R.rsp
NeedsCompilation: yes
Packaged: 2016-06-07 17:24:57 UTC; Etienne
Author: Etienne A.D. Pienaar [aut, cre], Melvin M. Varughese [ctb]
Maintainer: Etienne A.D. Pienaar <etiennead@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-08 05:47:01

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New package DCG with initial version 0.9.2
Package: DCG
Type: Package
Title: Data Cloud Geometry (DCG): Using Random Walks to Find Community Structure in Social Network Analysis
Version: 0.9.2
Date: 2016-05-09
Authors@R: c(person("Chen", "Chen", role = "aut"), person("Jian", "Jin", email = "jinjian.pku@gmail.com", role = c("aut", "cre")), person("Brianne", "Beisner", role = "aut"), person("Brenda", "McCowan", role = c("aut", "cph")), person("Hsieh", "Fushing", role = c("aut", "cph")))
Depends: R (>= 2.14.0)
Description: Data cloud geometry (DCG) applies random walks in finding community structures for social networks.
License: GPL (>= 2)
Copyright: Fushing Lab & McCowan Lab, University of California, Davis
Imports: stats
LazyData: TRUE
Suggests: testthat, knitr, rmarkdown, devtools, lattice, png
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-07 20:59:41 UTC; JianJin
Author: Chen Chen [aut], Jian Jin [aut, cre], Brianne Beisner [aut], Brenda McCowan [aut, cph], Hsieh Fushing [aut, cph]
Maintainer: Jian Jin <jinjian.pku@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-08 05:47:08

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Package CUB updated to version 0.1 with previous version 0.0 dated 2015-11-07

Title: A Class of Mixture Models for Ordinal Data
Description: Estimate and test models for ordinal data concerning the family of CUB models and their extensions (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions).
Author: Maria Iannario <maria.iannario@unina.it>, Domenico Piccolo <domenico.piccolo@unina.it>, Rosaria Simone <rosaria.simone@unina.it>
Maintainer: Rosaria Simone <rosaria.simone@unina.it>

Diff between CUB versions 0.0 dated 2015-11-07 and 0.1 dated 2016-06-13

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New package dam with initial version 0.0.1
Package: dam
Title: Data Analysis Metabolomics
Version: 0.0.1
Authors@R: person("Slavik", "Koval", email = "slakov@gmail.com", role = c("aut", "cre"))
Description: A collection of functions which aim to assist common computational workflow for analysis of matabolomic data..
Depends: R (>= 3.2.3)
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1.9000
NeedsCompilation: no
Packaged: 2016-06-09 12:36:30 UTC; slakov
Author: Slavik Koval [aut, cre]
Maintainer: Slavik Koval <slakov@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-09 15:19:21

More information about dam at CRAN
Permanent link

New package countytimezones with initial version 0.1.0
Package: countytimezones
Type: Package
Title: Convert from UTC to Local Time for United States Counties
Version: 0.1.0
Date: 2016-06-10
Authors@R: c(person("Brooke", "Anderson", email = "brooke.anderson@colostate.edu", role = c("aut", "cre")))
Description: Inputs date-times in Coordinated Universal Time (UTC) and converts to a local date-time and local date for US counties, based on each county's Federal Information Processing Standard (FIPS) code. This work was supported in part by grants from the National Institute of Environmental Health Sciences (R00ES022631) and the National Science Foundation (1331399).
URL: https://github.com/geanders/countytimezones
BugReports: https://github.com/geanders/countytimezones/issues
License: GPL-2
LazyData: TRUE
Imports: dplyr (>= 0.4.3), lubridate (>= 1.5.6)
RoxygenNote: 5.0.1
Depends: R (>= 2.10)
Suggests: choroplethr (>= 3.5.2), choroplethrMaps (>= 1.0), ggplot2 (>= 2.1.0), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-10 23:30:28 UTC; brookeanderson
Author: Brooke Anderson [aut, cre]
Maintainer: Brooke Anderson <brooke.anderson@colostate.edu>
Repository: CRAN
Date/Publication: 2016-06-11 09:32:52

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Package corHMM updated to version 1.19 with previous version 1.18 dated 2016-01-07

Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>

Diff between corHMM versions 1.18 dated 2016-01-07 and 1.19 dated 2016-06-13

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New package config with initial version 0.1.0
Package: config
Type: Package
Title: Manage Environment Specific Configuration Values
Version: 0.1.0
Authors@R: c( person("JJ", "Allaire", role = c("aut", "cre"), email = "jj@rstudio.com"), person(family = "RStudio, Inc.", role = "cph"))
Imports: tools, yaml (>= 2.1.13)
Suggests: testthat, knitr
Description: Manage configuration values across multiple environments (e.g. development, test, production). Read values using a function that determines the current environment and returns the appropriate value.
License: GPL-3
URL: https://github.com/rstudio/config
BugReports: https://github.com/rstudio/config/issues
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-08 12:44:46 UTC; jjallaire
Author: JJ Allaire [aut, cre], RStudio, Inc. [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Repository: CRAN
Date/Publication: 2016-06-08 15:40:19

More information about config at CRAN
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New package CombinePortfolio with initial version 0.3
Package: CombinePortfolio
Type: Package
Title: Estimation of Optimal Portfolio Weights by Combining Simple Portfolio Strategies
Version: 0.3
Date: 2016-06-09
Author: Author: Florian Ziel
Maintainer: Florian Ziel <ziel@europa-uni.de>
Description: Estimation of optimal portfolio weights as combination of simple portfolio strategies, like the tangency, global minimum variance (GMV) or naive (1/N) portfolio. It is based on a utility maximizing 8-fund rule. Popular special cases like the Kan-Zhou(2007) 2-fund and 3-fund rule or the Tu-Zhou(2011) estimator are nested.
Depends: R (>= 3.0.2)
License: GPL (>= 2)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-06-10 07:49:01
Packaged: 2016-06-09 16:42:03 UTC; florian

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Package clusrank updated to version 0.2-0 with previous version 0.1-4 dated 2016-06-03

Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre], Mei-Ling Ting Lee [ctb], Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>

Diff between clusrank versions 0.1-4 dated 2016-06-03 and 0.2-0 dated 2016-06-13

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Package cloudUtil updated to version 0.1.12 with previous version 0.1.10 dated 2013-12-10

Title: Cloud Utilization Plots
Description: Provides means of plots for comparing utilization data of compute systems.
Author: Christian Panse <cp@fgcz.ethz.ch>, Ermir Qeli <ermir.qeli@gmail.com>
Maintainer: Christian Panse <cp@fgcz.ethz.ch>

Diff between cloudUtil versions 0.1.10 dated 2013-12-10 and 0.1.12 dated 2016-06-13

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Package catR updated to version 3.8 with previous version 3.7 dated 2016-05-09

Title: Procedures to Generate Patterns under Computerized Adaptive Testing
Description: Generation of response patterns under dichotomous and polytomous computerized adaptive testing (CAT) framework.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@ulg.ac.be>

Diff between catR versions 3.7 dated 2016-05-09 and 3.8 dated 2016-06-13

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Package catnet updated to version 1.15.0 with previous version 1.14.8 dated 2015-02-04

Title: Categorical Bayesian Network Inference
Description: Structure learning and parameter estimation of discrete Bayesian networks using likelihood-based criteria. Exhaustive search for fixed node orders and stochastic search of optimal orders via simulated annealing algorithm are implemented.
Author: Nikolay Balov, Peter Salzman
Maintainer: Nikolay Balov <nhbalov@gmail.com>

Diff between catnet versions 1.14.8 dated 2015-02-04 and 1.15.0 dated 2016-06-13

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Package cartography updated to version 1.3.0 with previous version 1.2 dated 2016-02-12

Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package allows various cartographic representations such as proportional symbols, chroropleth, typology, flows or discontinuities. In addition, it also proposes some useful features like cartographic palettes, layout (scale, north arrow, title...), labels, legends or access to cartographic API to ease the graphic presentation of maps.
Author: Timothée Giraud [cre, aut], Nicolas Lambert [aut]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>

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Package caret updated to version 6.0-70 with previous version 6.0-68 dated 2016-04-11

Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer, Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau, Andrew Ziem, Luca Scrucca, Yuan Tang, and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>

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Package CARBayesdata updated to version 2.0 with previous version 1.0 dated 2015-03-31

Title: Data Used in the Vignettes Accompanying the CARBayes and CARBayesST Packages
Description: Spatio-temporal data from Scotland used in the vignettes accompanying the CARBayes (spatial modelling) and CARBayesST (spatio-temporal modelling) packages. For the CARBayes vignette the data include the Scottish lip cancer data and property price and respiratory hospitalisation data from the Greater Glasgow and Clyde health board. For the CARBayesST vignette the data include spatio-temporal data on property sales and respiratory hospitalisation and air pollution from the Greater Glasgow and Clyde health board.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>

Diff between CARBayesdata versions 1.0 dated 2015-03-31 and 2.0 dated 2016-06-13

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Package CARBayes updated to version 4.6 with previous version 4.5 dated 2016-05-06

Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. Spatial autocorrelation is modelled by a set of random effects, which are assigned a conditional autoregressive (CAR) prior distribution. A number of different CAR priors are available for the random effects, including a multivariate CAR (MCAR) model for multivariate spatial data. Full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development was supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>

Diff between CARBayes versions 4.5 dated 2016-05-06 and 4.6 dated 2016-06-13

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Package cape updated to version 2.0.2 with previous version 2.0.1 dated 2016-04-06

Title: Combined Analysis of Pleiotropy and Epistasis
Description: Combines complementary information across multiple related phenotypes to infer directed epistatic interactions between genetic markers. This analysis can be applied to a variety of engineered and natural populations.
Author: Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and Greg W. Carter
Maintainer: Anna L. Tyler <Anna.Tyler@jax.org>

Diff between cape versions 2.0.1 dated 2016-04-06 and 2.0.2 dated 2016-06-13

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New package bigQueryR with initial version 0.1.0
Package: bigQueryR
Title: Interface with Google BigQuery with Shiny Compatibility
Version: 0.1.0
Authors@R: c(person("Mark", "Edmondson",email = "r@sunholo.com", role = c("aut", "cre")), person("Hadley", "Wickham", , "hadley@rstudio.com", role = "ctb") )
Description: Interface with Google BigQuery, see <https://cloud.google.com/bigquery/> for more information. This package uses 'googleAuthR' so is compatible with similar packages, including Google Cloud Storage (<https://cloud.google.com/storage/>) for result extracts.
URL: http://code.markedmondson.me/bigQueryR/
BugReports: https://github.com/MarkEdmondson1234/bigQueryR/issues
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 3.2.0)
Imports: googleAuthR (>= 0.2.0)
Suggests: shiny (>= 0.12.1), jsonlite (>= 0.9.21), httr (>= 1.1.0), knitr, rmarkdown
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-13 15:27:06 UTC; mark
Author: Mark Edmondson [aut, cre], Hadley Wickham [ctb]
Maintainer: Mark Edmondson <r@sunholo.com>
Repository: CRAN
Date/Publication: 2016-06-13 17:34:46

More information about bigQueryR at CRAN
Permanent link

Package Bclim updated to version 3.1.0 with previous version 2.3.1 dated 2014-04-18

Title: Bayesian Palaeoclimate Reconstruction from Pollen Data
Description: Takes pollen and chronology data from lake cores and produces a Bayesian posterior distribution of palaeoclimate from that location after fitting a non-linear non-Gaussian state-space model. For more details see the paper Parnell, A. C., et al. (2015), Bayesian inference for palaeoclimate with time uncertainty and stochastic volatility. Journal of the Royal Statistical Society: Series C (Applied Statistics), 64: 115–138.
Author: Andrew Parnell
Maintainer: Andrew Parnell <Andrew.Parnell@ucd.ie>

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Package bayesTFR updated to version 5.0-2 with previous version 5.0-1 dated 2016-03-04

Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu) with code contribution from Bailey Fosdick (bfosdick@uw.edu) and Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>

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New package BaPreStoPro with initial version 0.1
Package: BaPreStoPro
Type: Package
Title: Bayesian Prediction of Stochastic Processes
Version: 0.1
Date: 2016-06-07
Author: Simone Hermann
Maintainer: Simone Hermann <hermann@statistik.tu-dortmund.de>
Description: Bayesian estimation and prediction for stochastic processes based on the Euler approximation. Considered processes are: jump diffusion, (mixed) diffusion models, hidden (mixed) diffusion models, non-homogeneous Poisson processes (NHPP), (mixed) regression models for comparison and a regression model including a NHPP.
License: GPL (>= 2)
Depends: stats, methods, graphics
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-06-07 09:09:22 UTC; Simone
Repository: CRAN
Date/Publication: 2016-06-07 14:28:11

More information about BaPreStoPro at CRAN
Permanent link

Package BAMMtools updated to version 2.1.4 with previous version 2.1.3 dated 2016-05-24

Title: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>

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Package AUtests updated to version 0.98 with previous version 0.97 dated 2016-03-31

Title: Approximate Unconditional and Permutation Tests
Description: Performs approximate unconditional and permutation testing for 2x2 contingency tables. Motivated by testing for disease association with rare genetic variants in case-control studies. When variants are extremely rare, these tests give better control of Type I error than standard tests.
Author: Arjun Sondhi, Ken Rice
Maintainer: Arjun Sondhi <asondhi@uw.edu>

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Package archivist.github updated to version 0.2.0 with previous version 0.1.1 dated 2016-03-25

Title: Tools for Archiving, Managing and Sharing R Objects via GitHub
Description: The extension of the 'archivist' package integrating the archivist with GitHub via GitHub API, 'git2r' packages and 'httr' package.
Author: Marcin Kosinski [aut, cre], Przemyslaw Biecek [aut]
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>

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Package agricolae updated to version 1.2-4 with previous version 1.2-3 dated 2015-10-06

Title: Statistical Procedures for Agricultural Research
Description: Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Author: Felipe de Mendiburu
Maintainer: Felipe de Mendiburu <f.mendiburu@cgiar.org>

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 agricolae-1.2-4/agricolae/man/VanderWarden.Rd       |   10 
 agricolae-1.2-4/agricolae/man/agricolae-package.Rd  |    4 
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 agricolae-1.2-4/agricolae/man/duncan.test.Rd        |    4 
 agricolae-1.2-4/agricolae/man/friedman.Rd           |    7 
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 agricolae-1.2-4/agricolae/man/index.smith.Rd        |    3 
 agricolae-1.2-4/agricolae/man/indexAMMI.Rd          |    4 
 agricolae-1.2-4/agricolae/man/kruskal.Rd            |   10 
 agricolae-1.2-4/agricolae/man/lineXtester.Rd        |   10 
 agricolae-1.2-4/agricolae/man/median.rd             |    4 
 agricolae-1.2-4/agricolae/man/nonadditivity.Rd      |    4 
 agricolae-1.2-4/agricolae/man/normal.freq.Rd        |    8 
 agricolae-1.2-4/agricolae/man/orderPvalue.Rd        |only
 agricolae-1.2-4/agricolae/man/plotAMMI.Rd           |    4 
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 agricolae-1.2-4/agricolae/man/polygon.freq.Rd       |    6 
 agricolae-1.2-4/agricolae/man/reg.homog.Rd          |    4 
 agricolae-1.2-4/agricolae/man/scheffe.test.Rd       |    6 
 agricolae-1.2-4/agricolae/man/sp.plot.Rd            |    4 
 agricolae-1.2-4/agricolae/man/stat.freq.Rd          |    4 
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 agricolae-1.2-4/agricolae/man/waller.test.Rd        |    4 
 agricolae-1.2-4/agricolae/vignettes/tutorial.Rnw    |   27 
 171 files changed, 1207 insertions(+), 1287 deletions(-)

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New package admixturegraph with initial version 1.0.0
Package: admixturegraph
Type: Package
Title: Admixture Graph Manipulation and Fitting
Version: 1.0.0
Date: 2015-09-24
Authors@R: c(person("Thomas", "Mailund", email = "mailund@birc.au.dk", role = c("cre", "aut")), person("Kalle", "Leppala", email = "kalle.m.leppala@gmail.com", role = c("aut")))
Description: Implements tools for building and visualising admixture graphs and for extracting equations from them. These equations can be compared to f- statistics obtained from data to test the consistency of a graph against data -- for example by comparing the sign of f_4-statistics with the signs predicted by the graph -- and graph parameters (edge lengths and admixture proportions) can be fitted to observed statistics.
License: GPL-2
Depends: R (>= 3.2.2)
Imports: doParallel, dplyr, foreach, ggplot2, graphics, MASS, neldermead, parallel, pracma, stats, utils
Suggests: knitr, testthat
URL: https://github.com/mailund/admixture_graph
BugReports: https://github.com/mailund/admixture_graph/issues
VignetteBuilder: knitr
LazyData: true
RoxygenNote: 5.0.0
NeedsCompilation: no
Packaged: 2016-06-10 09:27:43 UTC; Luku
Author: Thomas Mailund [cre, aut], Kalle Leppala [aut]
Maintainer: Thomas Mailund <mailund@birc.au.dk>
Repository: CRAN
Date/Publication: 2016-06-10 13:48:40

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