Tue, 30 Jun 2015

Package TSP updated to version 1.1-2 with previous version 1.1-1 dated 2015-05-15

Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling salesperson problem (also traveling salesman problem; TSP). The package provides some simple algorithms and an interface to the Concorde TSP solver and its implementation of the Chained-Lin-Kernighan heuristic. Concorde itself is not included in the package and has to be obtained separately from http://www.math.uwaterloo.ca/tsp/concorde.html.
Author: Michael Hahsler [aut, cre, cph], Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between TSP versions 1.1-1 dated 2015-05-15 and 1.1-2 dated 2015-06-30

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More information about TSP at CRAN
Permanent link

New package scatterD3 with initial version 0.1.1
Package: scatterD3
Type: Package
Title: D3 Javascript Scatterplot from R
Version: 0.1.1
Date: 2015-06-30
Authors@R: c(person("Julien", "Barnier", email = "julien.barnier@ens-lyon.fr", role = c("aut", "cre")))
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive features : panning, zooming, tooltips, etc.
License: GPL (>= 3)
VignetteBuilder: knitr
URL: https://github.com/juba/scatterD3
BugReports: https://github.com/juba/scatterD3/issues
LazyData: TRUE
Enhances: shiny
Imports: htmlwidgets
Suggests: knitr
NeedsCompilation: no
Packaged: 2015-06-30 08:09:40 UTC; julien
Author: Julien Barnier [aut, cre]
Repository: CRAN
Date/Publication: 2015-07-01 01:07:34

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Package seriation updated to version 1.1-1 with previous version 1.1-0 dated 2015-06-09

Title: Infrastructure for Seriation
Description: Infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).
Author: Michael Hahsler [aut, cre, cph], Christian Buchta [aut, cph], Kurt Hornik [aut, cph], Fionn Murtagh [ctb, cph], Michael Brusco [ctb, cph], Stephanie Stahl [ctb, cph], Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between seriation versions 1.1-0 dated 2015-06-09 and 1.1-1 dated 2015-06-30

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More information about seriation at CRAN
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Package sampling updated to version 2.7 with previous version 2.6 dated 2013-11-08

Title: Survey Sampling
Description: Functions for drawing and calibrating samples.
Author: Yves Tillé , Alina Matei
Maintainer: Alina Matei <alina.matei@unine.ch>

Diff between sampling versions 2.6 dated 2013-11-08 and 2.7 dated 2015-06-30

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Package random updated to version 0.2.5 with previous version 0.2.4 dated 2015-05-17

Title: True Random Numbers using RANDOM.ORG
Description: The true random number service provided by the RANDOM.ORG website created by Mads Haahr samples atmospheric noise via radio tuned to an unused broadcasting frequency together with a skew correction algorithm due to John von Neumann. More background is available in the included vignette based on an essay by Mads Haahr. In its current form, the package offers functions to retrieve random integers, randomized sequences and random strings.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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More information about random at CRAN
Permanent link

Package koRpus updated to version 0.05-6 with previous version 0.05-5 dated 2014-03-19

Title: An R Package for Text Analysis
Description: A set of tools to analyze texts. Includes, amongst others, functions for automatic language detection, hyphenation, several indices of lexical diversity (e.g., type token ratio, HD-D/vocd-D, MTLD) and readability (e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for language corpora are also provided, to enable frequency analyses (supports Celex and Leipzig Corpora Collection file formats) and measures like tf-idf. Note: For full functionality a local installation of TreeTagger is recommended. 'koRpus' also includes a plugin for the R GUI and IDE RKWard, providing graphical dialogs for its basic features. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard. To make full use of this feature, please install RKWard from https://rkward.kde.org (plugins are detected automatically). Due to some restrictions on CRAN, the full package sources are only available from the project homepage.
Author: m.eik michalke [aut, cre], Earl Brown [ctb], Alberto Mirisola [ctb], Alexandre Brulet [ctb], Laura Hauser [ctb]
Maintainer: m.eik michalke <meik.michalke@hhu.de>

Diff between koRpus versions 0.05-5 dated 2014-03-19 and 0.05-6 dated 2015-06-30

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More information about koRpus at CRAN
Permanent link

Package intergraph updated to version 2.0-2 with previous version 2.0-1 dated 2015-01-17

Title: Coercion Routines for Network Data Objects
Description: Functions implemented in this package allow to coerce (i.e. convert) network data between classes provided by other R packages. Currently supported classes are those defined in packages: network and igraph.
Author: Michal Bojanowski
Maintainer: Michal Bojanowski <m.bojanowski@icm.edu.pl>

Diff between intergraph versions 2.0-1 dated 2015-01-17 and 2.0-2 dated 2015-06-30

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More information about intergraph at CRAN
Permanent link

New package iNEXT with initial version 2.0.3
Package: iNEXT
Type: Package
Title: Interpolation and Extrapolation for Species Diversity
Version: 2.0.3
Date: 2015-06-30
Authors@R: c(person("T. C.", "Hsieh", role = c("aut", "cre", "cph"), email = "euler96@gmail.com"), person("K. H.", "Ma", role = "ctb", email = "smallmar123@gmail.com"), person("Anne", "Chao", role = "ths", email = "chao@stat.nthu.edu.tws"))
Description: Interpolation and extrapolation for species diversity: a unified approach for both individual-based (abundance) data and sample-based (incidence) data.
License: GPL (>= 3)
URL: http://chao.stat.nthu.edu.tw/blog/software-download/
Maintainer: T. C. Hsieh <euler96@gmail.com>
Depends: R (>= 2.14)
Imports: stats, graphics, ggplot2
BugReports: https://github.com/JohnsonHsieh/iNEXT/issues
Packaged: 2015-06-30 07:37:43 UTC; Johnson
Author: T. C. Hsieh [aut, cre, cph], K. H. Ma [ctb], Anne Chao [ths]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-30 18:06:41

More information about iNEXT at CRAN
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Package hoardeR updated to version 0.1 with previous version 0.0-2 dated 2014-06-06

Title: Information Retrieval for Genetic Datasets
Description: Information retrieval from National Center for Biotechnology Information (NCBI) databases, with main focus on identifying genes in unannotated organisms via Blast similarity search in annotated organisms.
Author: Daniel Fischer [aut, cre], Anu Sironen [aut]
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>

Diff between hoardeR versions 0.0-2 dated 2014-06-06 and 0.1 dated 2015-06-30

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Package CARBayes updated to version 4.2 with previous version 4.1 dated 2015-04-01

Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of 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. The 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, and 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 is 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 4.1 dated 2015-04-01 and 4.2 dated 2015-06-30

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More information about CARBayes at CRAN
Permanent link

Package XML updated to version 3.98-1.3 with previous version 3.98-1.2 dated 2015-05-31

Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: Duncan Temple Lang <duncan@r-project.org>

Diff between XML versions 3.98-1.2 dated 2015-05-31 and 3.98-1.3 dated 2015-06-30

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Package TAM updated to version 1.9-0 with previous version 1.8-0 dated 2015-06-26

Title: Test Analysis Modules
Description: Includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models). Latent regression models and plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

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Package RCurl updated to version 1.95-4.7 with previous version 1.95-4.6 dated 2015-04-24

Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.
Author: Duncan Temple Lang and the CRAN team
Maintainer: Duncan Temple Lang <duncan@r-project.org>

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Package randomizeBE updated to version 0.3-2 with previous version 0.3-1 dated 2012-12-27

Title: Function to Create a Random List for Crossover Studies
Description: Contains a function to randomize subjects, patients in groups of sequences (treatment sequences). If a blocksize is given, the randomization will be done within blocks. The randomization may be controlled by a Wald-Wolfowitz runs test. Functions to obtain the p-value of that test are included. The package is mainly intended for randomization of bioequivalence studies but may be used also for other clinical crossover studies. Contains two helper functions sequences() and williams() to get the sequences of commonly used designs in BE studies.
Author: D. Labes
Maintainer: D. Labes <detlewlabes@gmx.de>

Diff between randomizeBE versions 0.3-1 dated 2012-12-27 and 0.3-2 dated 2015-06-30

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Package phenology updated to version 4.2.4 with previous version 4.2 dated 2015-05-09

Title: Tools to Manage a Parametric Function that Describes Phenology
Description: Functions used to fit and test the phenology of species based on counts.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

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Package Maeswrap updated to version 1.7 with previous version 1.4.11 dated 2012-05-25

Title: Wrapper Functions for MAESTRA/MAESPA
Description: A bundle of functions for modifying MAESTRA/MAESPA input files,reading output files, and visualizing the stand in 3D. Handy for running sensitivity analyses, scenario analyses, etc.
Author: Remko Duursma
Maintainer: Remko Duursma <remkoduursma@gmail.com>

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New package gkmSVM with initial version 0.55
Package: gkmSVM
Type: Package
Title: Gapped-Kmer Support Vector Machine
Version: 0.55
Date: 2015-06-29
Author: Mahmoud Ghandi
Maintainer: Mahmoud Ghandi <mghandi@gmail.com>
Description: Imports the 'gkmSVM' v2.0 functionalities into R (www.beerlab.org/gkmsvm). It also uses the 'kernlab' library (separate R package by different authors) for various SVM algorithms.
License: GPL (>= 2)
Imports: Rcpp, kernlab, seqinr, utils
LinkingTo: Rcpp
SystemRequirements: C++11
Packaged: 2015-06-30 07:01:01 UTC; mghandi
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-06-30 09:22:07

More information about gkmSVM at CRAN
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Package causaleffect updated to version 1.1.3 with previous version 1.1.1 dated 2015-04-28

Title: Deriving Expressions of Joint Interventional Distributions in Causal Models
Description: An implementation of a conditional causal effect identification algorithm constructed by Ilya Shpitser and Judea Pearl (2006) for deriving expressions of joint interventional distributions in causal models, which contain unobserved variables and induce directed acyclic graphs.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>

Diff between causaleffect versions 1.1.1 dated 2015-04-28 and 1.1.3 dated 2015-06-30

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Package stochvol updated to version 1.1.3 with previous version 1.1.2 dated 2015-06-29

Title: Efficient Bayesian Inference for Stochastic Volatility (SV) Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>

Diff between stochvol versions 1.1.2 dated 2015-06-29 and 1.1.3 dated 2015-06-30

 stochvol-1.1.2/stochvol/vignettes/heavytails.R   |only
 stochvol-1.1.2/stochvol/vignettes/heavytails.pdf |only
 stochvol-1.1.2/stochvol/vignettes/heavytails.tex |only
 stochvol-1.1.3/stochvol/DESCRIPTION              |    6 +++---
 stochvol-1.1.3/stochvol/MD5                      |   17 +++++++++--------
 stochvol-1.1.3/stochvol/NEWS                     |    3 +++
 stochvol-1.1.3/stochvol/build/vignette.rds       |binary
 stochvol-1.1.3/stochvol/inst/doc/article.pdf     |binary
 stochvol-1.1.3/stochvol/inst/doc/heavytails.R    |only
 stochvol-1.1.3/stochvol/inst/doc/heavytails.Rnw  |only
 stochvol-1.1.3/stochvol/inst/doc/heavytails.pdf  |only
 stochvol-1.1.3/stochvol/vignettes/Makefile       |    2 +-
 stochvol-1.1.3/stochvol/vignettes/heavytails.Rnw |only
 13 files changed, 16 insertions(+), 12 deletions(-)

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Package forestFloor updated to version 1.5 with previous version 1.4 dated 2015-05-28

Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>

Diff between forestFloor versions 1.4 dated 2015-05-28 and 1.5 dated 2015-06-30

 DESCRIPTION                |   19 ++---
 MD5                        |   12 +--
 NAMESPACE                  |   20 ++++-
 R/forestFloor_source.R     |  166 +++++++++++++++++++++------------------------
 man/forestFloor-package.Rd |    5 -
 man/plot.forestFloor.Rd    |   39 ++--------
 tests/stdUsage.R           |   12 ++-
 7 files changed, 130 insertions(+), 143 deletions(-)

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Package climdex.pcic updated to version 1.1-6 with previous version 1.1-5.1 dated 2015-03-13

Title: PCIC Implementation of Climdex Routines
Description: PCIC's implementation of Climdex routines for computation of extreme climate indices.
Author: David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate Impacts Consortium
Maintainer: James Hiebert <hiebert@uvic.ca>

Diff between climdex.pcic versions 1.1-5.1 dated 2015-03-13 and 1.1-6 dated 2015-06-30

 CHANGELOG                                   |    6 +
 DESCRIPTION                                 |    8 +-
 MD5                                         |  102 ++++++++++++++--------------
 R/climdex.r                                 |   80 ++++++++++++++-------
 man/climdex.cdd.Rd                          |    2 
 man/climdex.csdi.Rd                         |    2 
 man/climdex.cwd.Rd                          |    2 
 man/climdex.dtr.Rd                          |    2 
 man/climdex.fd.Rd                           |    2 
 man/climdex.get.available.indices.Rd        |    2 
 man/climdex.gsl.Rd                          |    2 
 man/climdex.id.Rd                           |    2 
 man/climdex.pcic.Rd                         |    2 
 man/climdex.prcptot.Rd                      |    2 
 man/climdex.quantile.Rd                     |    2 
 man/climdex.r10mm.Rd                        |    2 
 man/climdex.r20mm.Rd                        |    2 
 man/climdex.r95ptot.Rd                      |    2 
 man/climdex.r99ptot.Rd                      |    2 
 man/climdex.rnnmm.Rd                        |    2 
 man/climdex.rx1day.Rd                       |    2 
 man/climdex.rx5day.Rd                       |    2 
 man/climdex.sdii.Rd                         |    2 
 man/climdex.su.Rd                           |    2 
 man/climdex.tn10p.Rd                        |    2 
 man/climdex.tn90p.Rd                        |    2 
 man/climdex.tnn.Rd                          |    2 
 man/climdex.tnx.Rd                          |    2 
 man/climdex.tr.Rd                           |    2 
 man/climdex.tx10p.Rd                        |    2 
 man/climdex.tx90p.Rd                        |    2 
 man/climdex.txn.Rd                          |    2 
 man/climdex.txx.Rd                          |    2 
 man/climdex.wsdi.Rd                         |    2 
 man/climdexInput.Rd                         |    7 +
 man/climdexInput.csv.Rd                     |    4 -
 man/climdexInput.raw.Rd                     |   78 +++++++++++++++++++--
 man/ec.1018935.Rd                           |    2 
 man/get.last.monthday.of.year.Rd            |    2 
 man/get.outofbase.quantiles.Rd              |    4 -
 man/get.series.lengths.at.ends.Rd           |    2 
 man/growing.season.length.Rd                |    2 
 man/nday.consec.prec.max.Rd                 |    2 
 man/number.days.op.threshold.Rd             |    2 
 man/percent.days.op.threshold.Rd            |    2 
 man/select.blocks.gt.length.Rd              |    2 
 man/simple.precipitation.intensity.index.Rd |    2 
 man/spell.length.max.Rd                     |    2 
 man/threshold.exceedance.duration.index.Rd  |    2 
 man/total.precip.op.threshold.Rd            |    2 
 src/zhang_running_quantile.cc               |    4 -
 tests/test_primitives.R                     |    2 
 52 files changed, 239 insertions(+), 140 deletions(-)

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