New package StochKit2R with initial version 0.2
Package: StochKit2R
Type: Package
Title: Efficient Discrete Stochastic Simulation
Version: 0.2
Date: 2015-01-29
Author: Kevin R. Sanft
Maintainer: Kevin R. Sanft
Copyright: Kevin R. Sanft, Linda R. Petzold
Description: Efficient discrete stochastic simulation using the Gillespie algorithm (aka the Stochastic Simulation Algorithm or SSA) and adaptive tau-leaping. It provides an R interface to simulation algorithms and it provides functions for visualizing (plotting) simulation output.
License: GPL-3
Imports: Rcpp (>= 0.11.2), reshape, ggplot2, XML
LinkingTo: Rcpp, BH
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-01-29 17:24:12 UTC; kevinsanft
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-29 21:39:56

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Package portfolio updated to version 0.4-7 with previous version 0.4-6 dated 2013-07-09

Title: Analysing equity portfolios
Description: Classes for analysing and implementing equity portfolios.
Author: Jeff Enos and David Kane , with contributions from Daniel Gerlanc and Kyle Campbell
Maintainer: Daniel Gerlanc

Diff between portfolio versions 0.4-6 dated 2013-07-09 and 0.4-7 dated 2015-01-29

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 portfolio-0.4-7/portfolio/DESCRIPTION                    |    9 +++--
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 14 files changed, 48 insertions(+), 30 deletions(-)

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New package devEMF with initial version 2.0
Package: devEMF
Type: Package
Title: EMF Graphics Output Device
Version: 2.0
Date: 2015-1-29
Author: Philip Johnson
Maintainer: Philip Johnson
Depends: R (>= 2.10.1)
SystemRequirements: Xft (only needed for platforms other than OSX and Windows)
Description: Output graphics to EMF (enhanced metafile).
License: GPL-3
Packaged: 2015-01-29 18:45:58 UTC; pjohnson
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-29 20:37:36

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Package AGSDest updated to version 2.2 with previous version 2.1 dated 2013-11-06

Title: Estimation in Adaptive Group Sequential Trials
Description: Calculation of repeated confidence intervals as well as confidence intervals based on the stage-wise ordering in group sequential designs and adaptive group sequential designs. For adaptive group sequential designs the confidence intervals are based on the conditional rejection probability principle. Currently the procedures do not support the use of futility boundaries or more than one adaptive interim analysis.
Author: Niklas Hack, Werner Brannath, Matthias Brueckner
Maintainer: Matthias Brueckner

Diff between AGSDest versions 2.1 dated 2013-11-06 and 2.2 dated 2015-01-29

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 72 files changed, 2492 insertions(+), 1306 deletions(-)

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Package StatMatch updated to version 1.2.3 with previous version 1.2.2 dated 2014-06-19

Title: Statistical Matching
Description: Integration of two data sources referred to the same target population which share a number of common variables (aka data fusion). Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio

Diff between StatMatch versions 1.2.2 dated 2014-06-19 and 1.2.3 dated 2015-01-29

 DESCRIPTION                                       |   16 +++---
 MD5                                               |   38 +++++++-------
 NAMESPACE                                         |    5 +
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 R/Fbwidths.by.x.R                                 |   14 +++--
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 R/NND.hotdeck.R                                   |    2 
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 man/Fbwidths.by.x.Rd                              |   21 +++-----
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 20 files changed, 114 insertions(+), 119 deletions(-)

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New package elastic with initial version 0.3.0
Package: elastic
Title: General Purpose Interface to Elasticsearch
Description: Connect to Elasticsearch, a NoSQL database built on the Java Virtual Machine. Interacts with the Elasticsearch HTTP API (http://elasticsearch.org), including functions for setting connection details to Elasticsearch instances, loading bulk data, searching for documents with both HTTP query variables and JSON based body requests. In addition, elastic provides functions for interacting with APIs for indices, documents, nodes, clusters, an interface to the cat API, and more.
Version: 0.3.0
Date: 2015-01-29
License: MIT + file LICENSE
Authors@R: person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com")
URL: https://github.com/sckott/elastic
BugReports: https://github.com/sckott/elastic/issues
VignetteBuilder: knitr
Imports: httr, jsonlite
Suggests: testthat, roxygen2, knitr
Packaged: 2015-01-29 15:54:32 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 18:08:01

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New package DVHmetrics with initial version 0.1
Package: DVHmetrics
Type: Package
Title: Analyze Dose-Volume Histograms and Check Constraints
Version: 0.1
Date: 2015-01-29
Authors@R: c(person("Daniel", "Wollschlaeger", role = c("aut", "cre"), email = "wollschlaeger@uni-mainz.de"), person("Heiko", "Karle", role="aut"), person("Heinz", "Schmidberger", role="ctb"))
Depends: R (>= 3.0.0)
Imports: ggplot2, reshape2, grid, shiny
Suggests: knitr
VignetteBuilder: knitr
LazyData: yes
Description: Functionality for analyzing dose-volume histograms (DVH) in radiation oncology: Read DVH text files, calculate DVH metrics, show DVH diagrams, check and visualize quality assurance constraints for the DVH. Includes web-based graphical user interface.
License: GPL (>= 2)
URL: https://github.com/dwoll/DVHmetrics/
NeedsCompilation: no
Packaged: 2015-01-29 15:17:47 UTC; dwollsch
Author: Daniel Wollschlaeger [aut, cre], Heiko Karle [aut], Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger
Repository: CRAN
Date/Publication: 2015-01-29 18:07:24

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Package biotools updated to version 2.0 with previous version 1.2 dated 2014-05-25

Title: Tools for Biometry and Applied Statistics in Agricultural Science
Description: Tools designed to perform and work with cluster analysis (including Tocher's algorithm), discriminant analysis and path analysis (standard and under collinearity), as well as some useful miscellaneous tools for dealing with sample size and optimum plot size calculations.
Author: Anderson Rodrigo da Silva
Maintainer: Anderson Rodrigo da Silva

Diff between biotools versions 1.2 dated 2014-05-25 and 2.0 dated 2015-01-29

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 14 files changed, 96 insertions(+), 35 deletions(-)

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New package cchs with initial version 0.1.0
Package: cchs
Type: Package
Title: Cox Model for Case-Cohort Data with Stratified Subcohort-Selection
Version: 0.1.0
Date: 2015-01-29
Author: E. Jones
Maintainer: E. Jones
Description: Contains a function, also called cchs, that calculates Estimator III of Borgan et al (2000), Exposure-stratified Case-cohort Designs. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
License: GPL-3
Depends: R (>= 2.15.0), survival (>= 2.36-12)
LazyData: yes
Packaged: 2015-01-29 15:12:28 UTC; anon
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 18:00:19

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Package GetoptLong updated to version 0.0.9 with previous version 0.0.8 dated 2014-11-05

Title: Parsing Command-line Arguments and Variable Interpolation
Description: Parsing command-line arguments by Perl module Getopt::Long. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu

Diff between GetoptLong versions 0.0.8 dated 2014-11-05 and 0.0.9 dated 2015-01-29

 DESCRIPTION                          |   10 ++++----
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 13 files changed, 85 insertions(+), 38 deletions(-)

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Package cluster updated to version 2.0.0 with previous version 1.15.3 dated 2014-09-04

Title: Cluster Analysis Extended Rousseeuw et al.
Description: Cluster Analysis Methods. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990)
Author: Martin Maechler [aut, cre], Peter Rousseeuw [aut] (Fortran original), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)), Matthias Studer [ctb], Pierre Roudier [ctb]
Maintainer: Martin Maechler

Diff between cluster versions 1.15.3 dated 2014-09-04 and 2.0.0 dated 2015-01-29

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 44 files changed, 790 insertions(+), 451 deletions(-)

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New package ppiPre with initial version 1.6
Package: ppiPre
Type: Package
Title: Predict protein-protein interactions based on functional and topological similarities.
Version: 1.6
Date: 2015-01-25
Author: Yue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun, with contributions from Guangchuang Yu.
Maintainer: Yue Deng
Description: This package provides functions for computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions are derived from R package GOSemSim authored by Guangchuang Yu.
License: GPL-2
LazyLoad: yes
Depends: R (>= 3.0.0)
Imports: AnnotationDbi, igraph, e1071, GOSemSim, GO.db
Enhances: KEGG.db, org.Hs.eg.db, org.Sc.sgd.db, org.Ag.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db, org.Xl.eg.db
NeedsCompilation: no
Packaged: 2015-01-29 10:13:00 UTC; Administrator
X-CRAN-Comment: Earlier versions were removed as source code had been copied uncredited.
Repository: CRAN
Date/Publication: 2015-01-29 11:45:23

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New package mousetrack with initial version 1.0.0
Package: mousetrack
Type: Package
Title: Mouse-Tracking Measures from Trajectory Data
Version: 1.0.0
Date: 2015-01-29
Author: Moreno I. Coco and Nicholas D. Duran with contributions of Rick Dale, Denis O'Hora and Michael J. Spivey.
Maintainer: Moreno I. Coco
Description: Extract from two-dimensional x-y coordinates of an arm-reaching trajectory, several dependent measures such as area under the curve, latency to start the movement, x-flips, etc.; which characterize the action-dynamics of the response. Mainly developed to analyze data coming from mouse-tracking experiments.
License: GPL (>= 2)
Depends: R (>= 3.0.0), pracma
Collate: 'angdiffvec.R' 'areaunder.R' 'getmouseDV.R' 'interpltraj.R' 'makerun.R' 'maxdev.R' 'pathoffset.R' 'sampen.R' 'sampenc.R' 'sampense.R' 'trim0.R' 'trim1.R' 'velaj.R' 'xflip.R'
Packaged: 2015-01-29 10:21:39 UTC; root
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 11:43:37

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New package roughrf with initial version 1.0
Package: roughrf
Type: Package
Title: Roughened Random Forests for Binary Classification
Version: 1.0
Date: 2015-01-28
Author: Kuangnan Xiong
Maintainer: Kuangnan Xiong
Depends: R (>= 2.5.0), randomForest, mice, nnet
Suggests: MASS, caTools
Description: A set of functions to support Xiong K, 'Roughened Random Forests for Binary Classification' (2014). The functions include RRFA, RRFB, RRFC1-RRFC7, RRFD and RRFE. RRFB and RRFC6 are usually recommended. RRFB is much faster than RRFC6.
License: GPL (>= 2)
URL: http://pqdtopen.proquest.com/pqdtopen/doc/1554346548.html?FMT=ABS
Packaged: 2015-01-29 06:58:24 UTC; LAPTOP15
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 11:08:31

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Package Luminescence updated to version 0.4.1 with previous version 0.4.0 dated 2014-12-18

Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre], Michael Dietze [aut], Christoph Burow [aut], Margret C. Fuchs [aut], Christoph Schmidt [aut], Manfred Fischer [aut, trl], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer

Diff between Luminescence versions 0.4.0 dated 2014-12-18 and 0.4.1 dated 2015-01-29

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 NAMESPACE                        |    1 
 NEWS                             |  124 ++++++
 R/RLum.Analysis-class.R          |   64 ++-
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 R/RisoeBINfileData-class.R       |   24 -
 R/analyse_IRSAR.RF.R             |   50 ++
 R/analyse_SAR.CWOSL.R            |  136 ++++---
 R/analyse_pIRIRSequence.R        |   33 -
 R/calc_OSLLxTxRatio.R            |   10 
 R/fit_CWCurve.R                  |    2 
 R/fit_LMCurve.R                  |   10 
 R/merge_RLum.Data.Curve.R        |only
 R/merge_RLum.R                   |    8 
 R/plot_AbanicoPlot.R             |  627 +++++++++++++++++++++++++++------
 R/plot_GrowthCurve.R             |   90 +++-
 R/readBIN2R.R                    |  728 +++++++++++++++++++++------------------
 R/readSPE2R.R                    |    6 
 R/writeR2BIN.R                   |   16 
 inst/NEWS.Rd                     |  157 ++++++++
 man/ExampleData.RLum.Analysis.Rd |    4 
 man/Luminescence-package.Rd      |   21 -
 man/analyse_IRSAR.RF.Rd          |    9 
 man/analyse_SAR.CWOSL.Rd         |   14 
 man/analyse_pIRIRSequence.Rd     |   16 
 man/calc_OSLLxTxRatio.Rd         |   12 
 man/fit_CWCurve.Rd               |    2 
 man/fit_LMCurve.Rd               |    4 
 man/merge_RLum.Data.Curve.Rd     |only
 man/merge_RLum.Rd                |    2 
 man/plot_AbanicoPlot.Rd          |   38 +-
 man/plot_GrowthCurve.Rd          |   16 
 man/readBIN2R.Rd                 |    2 
 man/readSPE2R.Rd                 |    2 
 man/writeR2BIN.Rd                |    2 
 36 files changed, 1601 insertions(+), 718 deletions(-)

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Package teigen updated to version 2.0.8 with previous version 2.0.7 dated 2014-08-19

Title: Model-Based Clustering and Classification with the Multivariate t Distribution
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the multi-cycle ECM algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews

Diff between teigen versions 2.0.7 dated 2014-08-19 and 2.0.8 dated 2015-01-29

 ChangeLog              |   10 +++++++---
 DESCRIPTION            |   12 ++++++------
 MD5                    |   20 ++++++++++----------
 R/teigen.R             |    3 +++
 inst/CITATION          |    2 +-
 man/plot.teigen.Rd     |    2 +-
 man/print.teigen.Rd    |    2 +-
 man/summary.teigen.Rd  |    2 +-
 man/teigen-package.Rd  |    6 +++---
 man/teigen.Rd          |    6 ++++--
 man/teigen.parallel.Rd |    2 +-
 11 files changed, 38 insertions(+), 29 deletions(-)

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New package divo with initial version 0.1
Package: divo
Version: 0.1
Type: Package
Date: 2015-01-28
Title: Tools for Analysis of Diversity and Similarity in Biological Systems
Author: Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak
Depends: R (>= 3.1.0), RcppCNPy, cluster
SystemRequirements: Python (>=2.76), NumPy
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
License: GPL (>= 2)
Packaged: 2015-01-29 03:22:30 UTC; Maciej
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 07:24:08

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