Wed, 15 Oct 2014

Package NbClust updated to version 2.0.3 with previous version 2.0.2 dated 2014-09-06

Title: NbClust package for determining the best number of clusters
Description: NbClust package provides 30 indices for determining the optimal number of clusters in a dataset.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad

Diff between NbClust versions 2.0.2 dated 2014-09-06 and 2.0.3 dated 2014-10-15

 DESCRIPTION    |    8 +++---
 MD5            |    5 ++-
 inst           |only
 man/NbClust.Rd |   74 +++++++++++++++++++++++++++++----------------------------
 4 files changed, 45 insertions(+), 42 deletions(-)

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New package rfoaas with initial version 0.0.4
Package: rfoaas
Type: Package
Title: R Interface to FOAAS
Version: 0.0.4
Date: 2014-10-15
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
Description: R access to the FOAAS (F... Off As A Service) web service
License: GPL (>= 2)
Packaged: 2014-10-15 10:55:44.845568 UTC; edd
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 01:17:17

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New package metaMix with initial version 0.1
Package: metaMix
Title: Bayesian Mixture Analysis for Metagenomic Community Profiling
Version: 0.1
Author: Sofia Morfopoulou
Maintainer: Sofia Morfopoulou
Depends: R (>= 3.0.1)
Imports: data.table (>= 1.9.2), Matrix, gtools, Rmpi, ggplot2
Suggests: knitr
VignetteBuilder: knitr
Description: metaMix resolves complex metagenomic mixtures by analysing deep sequencing data, using a Mixture Model based approach. The use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species more likely to contribute to the mixture.
License: GPL-3
LazyData: true
SystemRequirements: Open MPI (>=1.4.3)
Packaged: 2014-10-15 11:36:19 UTC; psofaki
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-16 01:26:14

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New package windex with initial version 1.0
Package: windex
Type: Package
Title: windex: Analysing convergent evolution using the Wheatsheaf index
Version: 1.0
Date: 2014-09-05
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle
Description: Analysing convergent evolution using the Wheatsheaf index.
License: GPL-2
Depends: geiger (>= 2.0), ape, scatterplot3d, utils, R (>= 3.0.0)
Packaged: 2014-10-14 13:49:37 UTC; aminter
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 00:01:11

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Package SpecsVerification updated to version 0.3-0 with previous version 0.2-0 dated 2014-09-12

Title: Forecast verification routines for the SPECS FP7 project
Description: A collection of new forecast verification routines for the SPECS FP7 project. The emphasis is on comparative verification of ensemble forecasts.
Author: Stefan Siegert [aut, cre]
Maintainer: Stefan Siegert

Diff between SpecsVerification versions 0.2-0 dated 2014-09-12 and 0.3-0 dated 2014-10-15

 DESCRIPTION                    |    8 ++++----
 MD5                            |   32 ++++++++++++++++++++++++++------
 NAMESPACE                      |   11 +++++++++++
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 R/Rankhist.R                   |   39 ++++++++-------------------------------
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 27 files changed, 55 insertions(+), 45 deletions(-)

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Package PubMedWordcloud updated to version 0.3.2 with previous version 0.3.1 dated 2014-06-23

Title: PubMed Word Clouds
Description: create a word cloud using the abstract of publications from PubMed
Author: Felix Yanhui Fan
Maintainer: Felix Yanhui Fan

Diff between PubMedWordcloud versions 0.3.1 dated 2014-06-23 and 0.3.2 dated 2014-10-15

 PubMedWordcloud-0.3.1/PubMedWordcloud/R/pmWordCloud.R           |only
 PubMedWordcloud-0.3.1/PubMedWordcloud/man/pmWordCloud.Rd        |only
 PubMedWordcloud-0.3.2/PubMedWordcloud/DESCRIPTION               |   10 ++--
 PubMedWordcloud-0.3.2/PubMedWordcloud/MD5                       |   22 ++++------
 PubMedWordcloud-0.3.2/PubMedWordcloud/NAMESPACE                 |    2 
 PubMedWordcloud-0.3.2/PubMedWordcloud/R/plotWordCloud.R         |    3 -
 PubMedWordcloud-0.3.2/PubMedWordcloud/man/cleanAbstracts.Rd     |    2 
 PubMedWordcloud-0.3.2/PubMedWordcloud/man/colSets.Rd            |    2 
 PubMedWordcloud-0.3.2/PubMedWordcloud/man/editPMIDs.Rd          |    2 
 PubMedWordcloud-0.3.2/PubMedWordcloud/man/getAbstracts.Rd       |    2 
 PubMedWordcloud-0.3.2/PubMedWordcloud/man/getPMIDs.Rd           |    2 
 PubMedWordcloud-0.3.2/PubMedWordcloud/man/getPMIDsByKeyWords.Rd |    2 
 PubMedWordcloud-0.3.2/PubMedWordcloud/man/plotWordCloud.Rd      |    7 ---
 13 files changed, 24 insertions(+), 32 deletions(-)

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Package matrixStats updated to version 0.10.3 with previous version 0.10.0 dated 2014-06-08

Title: Methods that apply to rows and columns of a matrix
Description: This packages provides methods operating on rows and columns of matrices, e.g. col/rowMedians() and col/rowRanks(). There are also some vector-based methods, e.g. anyMissing(), weightedMedians(), and binMeans(). The objective is to have all methods being optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson

Diff between matrixStats versions 0.10.0 dated 2014-06-08 and 0.10.3 dated 2014-10-15

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 matrixStats-0.10.3/matrixStats/DESCRIPTION                                    |   10 -
 matrixStats-0.10.3/matrixStats/MD5                                            |   80 ++++------
 matrixStats-0.10.3/matrixStats/NEWS                                           |   16 ++
 matrixStats-0.10.3/matrixStats/R/binMeans.R                                   |    6 
 matrixStats-0.10.3/matrixStats/inst/benchmarking/binCounts.md.rsp             |    2 
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 matrixStats-0.10.3/matrixStats/inst/benchmarking/includes/setup.md.rsp        |   37 ++--
 matrixStats-0.10.3/matrixStats/inst/benchmarking/index.md.rsp                 |   54 +-----
 matrixStats-0.10.3/matrixStats/inst/benchmarking/product.md.rsp               |    2 
 matrixStats-0.10.3/matrixStats/inst/benchmarking/weightedMedian.md.rsp        |    1 
 matrixStats-0.10.3/matrixStats/man/binMeans.Rd                                |    6 
 matrixStats-0.10.3/matrixStats/man/matrixStats-package.Rd                     |    2 
 matrixStats-0.10.3/matrixStats/src/binMeans-BINBY-template.h                  |   28 +--
 matrixStats-0.10.3/matrixStats/src/templates-types.h                          |    7 
 matrixStats-0.10.3/matrixStats/tests/binMeans,binCounts.R                     |   20 ++
 65 files changed, 149 insertions(+), 141 deletions(-)

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New package ggRandomForests with initial version 1.0.0
Package: ggRandomForests
Type: Package
Title: Creating and Plotting Data Objects for Understanding Random Forests
Version: 1.0.0
Date: 2014-10-15
Author: John Ehrlinger
Maintainer: John Ehrlinger
License: GPL (>= 3)
URL: https://github.com/ehrlinger/ggRandomForests
Description: The ggRandomForests package contains tools for creating and plotting data structures to visually understand random forest models. The functions are designed for use with the randomForestSRC package. This package is structured to extract intermediate data objects from the random forest. S3 Plot functions, which use the ggplot2 package, are included for each data object.
Depends: R (>= 3.1.0), ggplot2, randomForestSRC, reshape2, survival, dplyr
Suggests: testthat
Packaged: 2014-10-15 18:13:42 UTC; ehrlinj
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 23:53:25

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New package cwhmisc with initial version 5.0
Package: cwhmisc
Version: 5.0
Date: 2014-10-15
Title: Miscellaneous Functions for math, plotting, printing, statistics, strings, and tools
Author: Christian W. Hoffmann
Maintainer: Christian W. Hoffmann
Depends: R (>= 2.0), lattice, grid
Description: Miscellaneous useful or interesting functions. Some parameters of functions may have changed, so beware!
License: GPL (>= 2)
Packaged: 2014-10-15 14:05:48 UTC; hoffmann
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 23:37:39

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New package bio3d with initial version 2.1-1
Package: bio3d
Title: Biological Structure Analysis
Version: 2.1-1
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
VignetteBuilder: knitr
Imports: parallel, grid
Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat
Depends: R (>= 3.0.0)
LazyData: yes
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Maintainer: Barry Grant
License: GPL (>= 2)
URL: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d
Packaged: 2014-10-15 20:07:48 UTC; xinqyao
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 23:56:55

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Package strvalidator updated to version 1.3.1 with previous version 1.3.0 dated 2014-08-11

Title: Process Control And Internal Validation Of Forensic STR Kits
Description: strvalidator is an open source platform for validation and process control. It provide tools to analyse data from internal validation of forensic short tandem repeat (STR) kits. The tools are developed to provide the necessary data to conform with the ENFSI guidelines for internal validation. More information about each function can be found in the respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson

Diff between strvalidator versions 1.3.0 dated 2014-08-11 and 1.3.1 dated 2014-10-15

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 strvalidator-1.3.1/strvalidator/NAMESPACE                              |   95 ++-
 strvalidator-1.3.1/strvalidator/NEWS                                   |   36 +
 strvalidator-1.3.1/strvalidator/R/addColor.r                           |    2 
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 strvalidator-1.3.1/strvalidator/R/trim.r                               |    4 
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 strvalidator-1.3.1/strvalidator/README.md                              |   16 
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Package MVN updated to version 3.5 with previous version 3.4 dated 2014-04-26

Title: Multivariate Normality Tests
Description: Assessing the assumption of multivariate normality is required by many parametric multivariate statistical methods, such as discriminant analysis, principal component analysis, MANOVA, etc. Here, we present an R package to asses multivariate normality. The MVN package contains three widely used multivariate normality tests, including Mardia's, Henze-Zirkler's, Royston's, graphical approaches, including chi-square Q-Q plot, perspective plot and contour plot and two outlier detection methods based on Mahalanobis distance. We have also developed web-tool version of the package which is available at http://www.biosoft.hacettepe.edu.tr/MVN/.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz

Diff between MVN versions 3.4 dated 2014-04-26 and 3.5 dated 2014-10-15

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More information about MVN at CRAN
Permanent link

Package crayon updated to version 1.1.0 with previous version 1.0.0 dated 2014-09-23

Title: Colored Terminal Output
Description: Crayon adds support for colored terminal output on terminals that support ANSI color and highlight codes. ANSI color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the chalk JavaScript project.
Author: "Gabor Csardi" [aut, cre]
Maintainer: "Gabor Csardi"

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New package gets with initial version 0.1
Package: gets
Type: Package
Title: General-to-Specific (GETS) Model Selection
Version: 0.1
Depends: R (>= 2.4.1), zoo, lgarch
Date: 2014-10-14
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat
Description: Automated multi-path General-to-Specific (GETS) model selection of either an AR-X model with log-ARCH-X errors, or a log-ARCH-X model of the log-variance. The three main functions of the package are arx, getsm and getsv. The first function estimates an AR-X model with log-ARCH-X errors. The second function undertakes GETS model selection of the mean specification of an arx object, whereas the third function undertakes GETS model selection of the log-variance specification of an arx object.
License: GPL-2
Packaged: 2014-10-15 09:28:20 UTC; admin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 13:16:36

More information about gets at CRAN
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Package GA updated to version 2.2 with previous version 2.1 dated 2014-05-06

Title: Genetic Algorithms
Description: An R package for optimization 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. GAs can be run sequentially or in parallel.
Author: Luca Scrucca
Maintainer: Luca Scrucca

Diff between GA versions 2.1 dated 2014-05-06 and 2.2 dated 2014-10-15

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Package evtree updated to version 1.0-0 with previous version 0.1-5 dated 2014-07-01

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

Diff between evtree versions 0.1-5 dated 2014-07-01 and 1.0-0 dated 2014-10-15

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Package rbison updated to version 0.4.3 with previous version 0.3.2 dated 2014-02-18

Title: R interface to the USGS BISON API
Description: This package is an R interface to the USGS BISON API, a database for species occurrence data on the web. Data comes from species in the United States, from participating data providers. This package focuses on getting the data from BISON - but does provide a function to help visualize data quickly.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain

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Package clustvarsel updated to version 2.1 with previous version 2.0 dated 2013-10-25

Title: Variable Selection for Model-Based Clustering
Description: A function which implements variable selection methodology for model-based clustering which allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting MCLUST models. By default the algorithm uses a sequential search, but parallelization is also available.
Author: Nema Dean, Adrian E. Raftery, and Luca Scrucca
Maintainer: Luca Scrucca

Diff between clustvarsel versions 2.0 dated 2013-10-25 and 2.1 dated 2014-10-15

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More information about clustvarsel at CRAN
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New package vetools with initial version 1.3-28
Encoding: UTF-8
Package: vetools
Depends: R (>= 2.10), sp
Imports: stringr, tis, lubridate, maptools, plyr, xts, scales
Maintainer: Andrew Sajo-Castelli
License: GPL
Title: Tools for Venezuelan Environmental Data
LazyData: false
Type: Package
Authors@R: c(person("Andrew", "Sajo-Castelli", email="asajo@usb.ve", role = c("aut", "cre")), person("Desiree", "Villalta", role = "ctb"),person("Lelys", "Bravo", role = "ctb"))
Description: Integrated data management library that offers a variety of tools concerning the loading and manipulation of environmental data available from different Venezuelan governmental sources. Facilities are provided to plot temporal and spatial data as well as understand the health of a collection of meteorological data.
Version: 1.3-28
Revision: $Rev: 4 $
BugReports: https://github.com/talassio/vetools/issues
Packaged: 2014-10-15 05:41:42 UTC; cesma
Author: Andrew Sajo-Castelli [aut, cre], Desiree Villalta [ctb], Lelys Bravo [ctb]
NeedsCompilation: no
Repository: CRAN
Date: 2013-08-01 14:10:01
Date/Publication: 2014-10-15 08:47:53

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Package alm updated to version 0.3.0 with previous version 0.1.9 dated 2014-06-18

Title: R Wrapper to the Almetrics API Platform Developed by PLOS
Description: An R interface to the open source article level metrics API created by the Public Library of Science (PLOS). A number of publishers are using the open source app created by PLOS, so you can drop in a different base URL to the functions in this package to get to not only PLOS data, but data for Crossref, and more as the open source PLOS software is used. rCharts is in Enhances; and can be used for creating interactive charts (e.g., in the function plot_signposts in this package); obtain rCharts at https://github.com/ramnathv/rCharts.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut], Fenner Martin [aut]
Maintainer: Scott Chamberlain

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 alm-0.3.0/alm/R/plot_signposts.R                    |   65 -
 alm-0.3.0/alm/R/zzz.R                               |   64 +
 alm-0.3.0/alm/README.md                             |  743 ++++++++++++--------
 alm-0.3.0/alm/build/vignette.rds                    |binary
 alm-0.3.0/alm/man/addmissing.Rd                     |    2 
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 alm-0.3.0/alm/man/almcompact.Rd                     |    3 
 alm-0.3.0/alm/man/concat_todf.Rd                    |    2 
 alm-0.3.0/alm/man/getkey.Rd                         |    2 
 alm-0.3.0/alm/man/plot_density.Rd                   |   46 -
 alm-0.3.0/alm/man/plot_signposts.Rd                 |   21 
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 alm-0.3.0/alm/tests/testthat/test-plot_signposts.R  |    6 
 alm-0.3.0/alm/vignettes/alm_vignette.html           |  100 +-
 81 files changed, 777 insertions(+), 591 deletions(-)

More information about alm at CRAN
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New package nsgp with initial version 1.0.5
Package: nsgp
Title: Non-Stationary Gaussian Process Regression
Version: 1.0.5
Date: 2014-10-14
Author: Markus Heinonen
Maintainer: Markus Heinonen
Depends: R (>= 3.0.0)
Imports: MASS
Description: A Gaussian process regression using a Gaussian kernel for both one-sample and two-sample cases. Includes non-stationary Gaussian kernel (exponential decay function) and several likelihood ratio tests for differential testing along target points.
License: GPL-2
URL: http://amis-group.fr/software/nsgp
Packaged: 2014-10-14 14:29:42 UTC; markusheinonen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 06:54:09

More information about nsgp at CRAN
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Package mirtCAT updated to version 0.2 with previous version 0.1 dated 2014-08-14

Title: Computerized Adaptive Testing with Multidimensional Item Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive and non-adaptive educational and psychological tests using the shiny package. Suitable for applying unidimensional and multidimensional computerized adaptive tests using item response theory methodology and for creating simple questionnaires forms to collect response data directly in R.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers

Diff between mirtCAT versions 0.1 dated 2014-08-14 and 0.2 dated 2014-10-15

 mirtCAT-0.1/mirtCAT/tests/tests/test-mirtCAT_one.R     |only
 mirtCAT-0.1/mirtCAT/tests/tests/test-mirtCAT_two.R     |only
 mirtCAT-0.2/mirtCAT/DESCRIPTION                        |   11 
 mirtCAT-0.2/mirtCAT/MD5                                |   54 ++-
 mirtCAT-0.2/mirtCAT/NAMESPACE                          |    6 
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 mirtCAT-0.2/mirtCAT/R/DesignClass.R                    |   45 ++-
 mirtCAT-0.2/mirtCAT/R/FI.R                             |only
 mirtCAT-0.2/mirtCAT/R/PersonClass.R                    |   29 +
 mirtCAT-0.2/mirtCAT/R/ShinyGUIClass.R                  |   16 -
 mirtCAT-0.2/mirtCAT/R/TestClass.R                      |   24 +
 mirtCAT-0.2/mirtCAT/R/findNextCATItem.R                |  138 +++++++--
 mirtCAT-0.2/mirtCAT/R/generate_pattern.R               |    6 
 mirtCAT-0.2/mirtCAT/R/mirtCAT-package.R                |    2 
 mirtCAT-0.2/mirtCAT/R/mirtCAT.R                        |  248 +++++++++++------
 mirtCAT-0.2/mirtCAT/R/run_pattern.R                    |   12 
 mirtCAT-0.2/mirtCAT/R/selection_criteria.R             |   92 ++++--
 mirtCAT-0.2/mirtCAT/R/server.R                         |   66 ++--
 mirtCAT-0.2/mirtCAT/R/ui.R                             |   12 
 mirtCAT-0.2/mirtCAT/R/updateDesign.R                   |only
 mirtCAT-0.2/mirtCAT/R/util.R                           |   15 -
 mirtCAT-0.2/mirtCAT/R/zzz-methods.R                    |    9 
 mirtCAT-0.2/mirtCAT/README.md                          |    9 
 mirtCAT-0.2/mirtCAT/build                              |only
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 mirtCAT-0.2/mirtCAT/man/findNextItem.Rd                |only
 mirtCAT-0.2/mirtCAT/man/generate_pattern.Rd            |    6 
 mirtCAT-0.2/mirtCAT/man/mirtCAT-package.Rd             |    2 
 mirtCAT-0.2/mirtCAT/man/mirtCAT.Rd                     |  212 +++++++++-----
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 mirtCAT-0.2/mirtCAT/tests/tests/test-mirtCAT_ordered.R |only
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 mirtCAT-0.2/mirtCAT/vignettes                          |only
 34 files changed, 737 insertions(+), 277 deletions(-)

More information about mirtCAT at CRAN
Permanent link


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