Wed, 24 Dec 2014

New package uniftest with initial version 1.0
Package: uniftest
Version: 1.0
Date: 2014-12-24
Title: Tests for Uniformity
Author: Maxim Melnik, Ruslan Pusev
Maintainer: Ruslan Pusev
Description: Tests for the hypothesis of uniformity
License: GPL (>= 3)
Packaged: 2014-12-24 21:27:38 UTC; Ruslan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-25 01:28:18

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Package rfoaas updated to version 0.0.4.20141224 with previous version 0.0.4.20141212 dated 2014-12-13

Title: R Interface to FOAAS
Description: R access to the FOAAS (F... Off As A Service) web service
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

Diff between rfoaas versions 0.0.4.20141212 dated 2014-12-13 and 0.0.4.20141224 dated 2014-12-24

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 DESCRIPTION           |    8 +++---
 MD5                   |   10 ++++----
 R/foaas.R             |   62 +++++++++++++++++++++++++++-----------------------
 README.md             |   20 ++++++++++++++--
 man/rfoaas-package.Rd |   15 ++++++++++++
 6 files changed, 84 insertions(+), 39 deletions(-)

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Package verification updated to version 1.41 with previous version 1.40 dated 2014-07-09

Title: Weather Forecast Verification Utilities.
Description: This package contains utilities for verification of discrete,continuous, probabilistic forecasts and forecast expressed as parametric distributions.
Author: NCAR - Research Applications Laboratory
Maintainer: Eric Gilleland

Diff between verification versions 1.40 dated 2014-07-09 and 1.41 dated 2014-12-24

 DESCRIPTION     |    6 +++---
 MD5             |    6 +++---
 R/table.stats.R |   12 ++++++------
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 4 files changed, 13 insertions(+), 13 deletions(-)

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Package ismev updated to version 1.40 with previous version 1.39 dated 2012-11-13

Title: An Introduction to Statistical Modeling of Extreme Values
Description: Functions to support the computations carried out in `An Introduction to Statistical Modeling of Extreme Values' by Stuart Coles. The functions may be divided into the following groups; maxima/minima, order statistics, peaks over thresholds and point processes.
Author: Original S functions written by Janet E. Heffernan with R port and R documentation provided by Alec G. Stephenson.
Maintainer: Eric Gilleland

Diff between ismev versions 1.39 dated 2012-11-13 and 1.40 dated 2014-12-24

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Package dpcR updated to version 0.1.3.2 with previous version 0.1.3.1 dated 2014-10-07

Title: Digital PCR Analysis
Description: Analysis, visualisation and simulation of digital PCR experiments.
Author: Michal Burdukiewicz [cre, aut], Stefan Roediger [aut]
Maintainer: Michal Burdukiewicz

Diff between dpcR versions 0.1.3.1 dated 2014-10-07 and 0.1.3.2 dated 2014-12-24

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 man/qpcrpp-class.Rd            |   78 ++---
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Package selectr updated to version 0.2-3 with previous version 0.2-2 dated 2014-02-21

Title: Translate CSS Selectors to XPath Expressions
Description: Translates a CSS3 selector into an equivalent XPath expression. This allows us to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package "cssselect" (http://packages.python.org/cssselect/).
Author: Simon Potter [aut, trl, cre], Simon Sapin [aut], Ian Bicking [aut]
Maintainer: Simon Potter

Diff between selectr versions 0.2-2 dated 2014-02-21 and 0.2-3 dated 2014-12-24

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 12 files changed, 134 insertions(+), 66 deletions(-)

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

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

2014-12-21 1.0.0

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Package raters updated to version 2.0 with previous version 1.1 dated 2014-03-20

Title: A Modification of Fleiss' Kappa in case of Nominal and Ordinal Variables
Description: The kappa statistic implemented by Fleiss is a very popular index for assessing the reliability of agreement between two raters or among multiple observers. It is used both in the psychological and in the psychiatric field. Other fields of application are typically medicine, biology and engineering. Unfortunately,the kappa statistic may behave inconsistently in case of strong agreement between raters, since this index assumes lower values than it would have been expected. We propose a modification kappa implemented by Fleiss in case of nominal and ordinal variables. Monte Carlo simulations are used both to testing statistical hypotheses and to calculating percentile bootstrap confidence intervals based on proposed statistic in case of nominal and ordinal data.
Author: Daniele Giardiello [cre], Piero Quatto [aut], Enrico Ripamonti [aut], Stefano Vigliani [ctb]
Maintainer: Daniele Giardiello

Diff between raters versions 1.1 dated 2014-03-20 and 2.0 dated 2014-12-24

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Package latentnet updated to version 2.6.0 with previous version 2.5.1 dated 2014-03-19

Title: Latent Position and Cluster Models for Statistical Networks
Description: A package to fit and simulate latent position and cluster models for statistical networks.
Author: Pavel N. Krivitsky [aut, cre], Mark S. Handcock [aut], Susan M. Shortreed [ctb], Jeremy Tantrum [ctb], Peter D. Hoff [ctb], Li Wang [ctb], Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky

Diff between latentnet versions 2.5.1 dated 2014-03-19 and 2.6.0 dated 2014-12-24

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 latentnet-2.6.0/latentnet/src/ergmm_probs.c             |   29 ++
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Package USAboundaries updated to version 0.1.1 with previous version 0.1 dated 2014-11-25

Title: Historical Boundaries of the United States of America, 1629-2000
Description: This package provides spatial objects with the boundaries of states or counties in the United States of America from 1629 to 2000. It provides data from the Atlas of Historical County Boundaries.
Author: Lincoln Mullen [aut, cre], Dr. William M. Scholl Center for American History and Culture, The Newberry Library [cph]
Maintainer: Lincoln Mullen

Diff between USAboundaries versions 0.1 dated 2014-11-25 and 0.1.1 dated 2014-12-24

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 MD5                     |   14 +++++++-------
 NAMESPACE               |    2 +-
 README.md               |    2 +-
 man/USAboundaries.Rd    |    3 ++-
 man/hist_us_counties.Rd |    3 ++-
 man/hist_us_states.Rd   |    3 ++-
 man/us_boundaries.Rd    |    3 ++-
 8 files changed, 21 insertions(+), 17 deletions(-)

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Package pbdSLAP updated to version 0.2-0 with previous version 0.1-9 dated 2014-05-31

Title: Programming with Big Data -- Scalable Linear Algebra Packages
Description: pbdSLAP utilizes scalable linear algebra packages mainly including BLACS, PBLAS, and ScaLAPACK in double precision via pbdMPI based on ScaLAPACK version 2.0.2.
Author: Wei-Chen Chen [aut, cre], Drew Schmidt [aut], George Ostrouchov [aut], Pragneshkumar Patel [aut], Brian Ripley [ctb] (Solaris & Mac)
Maintainer: Wei-Chen Chen

Diff between pbdSLAP versions 0.1-9 dated 2014-05-31 and 0.2-0 dated 2014-12-24

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 16 files changed, 75 insertions(+), 36 deletions(-)

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New package historydata with initial version 0.1
Package: historydata
Title: Data Sets for Historians
Version: 0.1
Authors@R: c(person("Lincoln", "Mullen", role = c("aut", "cre"), email = "lincoln@lincolnmullen.com"))
Description: These sample data sets are intended for historians learning R. They include population, institutional, religious, military, and prosopographical data suitable for mapping, quantitative analysis, and network analysis.
Depends: R (>= 3.0.2)
Suggests: ggplot2 (>= 1.0.0)
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/ropensci/historydata
BugReports: https://github.com/ropensci/historydata/issues
Packaged: 2014-12-24 00:51:11 UTC; lmullen
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-24 06:08:09

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Package GlobalOptions updated to version 0.0.5 with previous version 0.0.4 dated 2014-12-01

Title: Generate Functions to Get or Set Global Options
Description: It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.
Author: Zuguang Gu
Maintainer: Zuguang Gu

Diff between GlobalOptions versions 0.0.4 dated 2014-12-01 and 0.0.5 dated 2014-12-24

 DESCRIPTION                |   11 ++++++-----
 MD5                        |   10 +++++-----
 NEWS                       |    5 +++++
 R/setGlobalOptions.R       |    2 +-
 build/vignette.rds         |binary
 inst/doc/GlobalOptions.pdf |binary
 6 files changed, 17 insertions(+), 11 deletions(-)

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Package CORElearn updated to version 0.9.44 with previous version 0.9.43 dated 2014-05-12

Title: Classification, Regression and Feature Evaluation
Description: CORElearn is machine learning suite ported to R from standalone C++ package. It contains several model learning techniques in classification and regression, for example classification and regression trees with optional constructive induction and models in the leafs, random forests, kNN, naive Bayes, and locally weighted regression. It is especially strong in feature evaluation where it contains several variants of Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, DKM... Its additional strength is OrdEval algorithm and its visualization used for evaluation of data sets with ordinal features and class. Several algorithms support parallel multithreaded execution via OpenMP. The top level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja"

Diff between CORElearn versions 0.9.43 dated 2014-05-12 and 0.9.44 dated 2014-12-24

 ChangeLog                |    1 
 DESCRIPTION              |   18 +++++--------
 MD5                      |   64 +++++++++++++++++++++++------------------------
 NAMESPACE                |   46 +++++----------------------------
 R/init.R                 |    4 +-
 R/testCore.R             |    6 ++--
 man/CORElearn-package.Rd |    5 ++-
 man/CoreModel.Rd         |    6 ++--
 man/calibrate.Rd         |    2 -
 man/classDataGen.Rd      |    3 +-
 man/classPrototypes.Rd   |    2 -
 man/destroyModels.Rd     |    3 +-
 man/getCoreModel.Rd      |    3 +-
 man/getRFsizes.Rd        |    3 +-
 man/modelEval.Rd         |    3 +-
 man/paramCoreIO.Rd       |    3 +-
 man/plot.CoreModel.Rd    |    2 -
 man/rfAttrEval.Rd        |    3 +-
 man/rfClustering.Rd      |    2 -
 man/rfOOB.Rd             |    3 +-
 man/rfOutliers.Rd        |    2 -
 man/rfProximity.Rd       |    2 -
 man/saveRF.Rd            |    3 +-
 src/Rfront.cpp           |   10 +++----
 src/constrct.h           |    5 ++-
 src/dataStore.cpp        |    3 +-
 src/expr.h               |    4 +-
 src/frontend.cpp         |    2 -
 src/general.h            |    2 -
 src/menu.cpp             |    3 +-
 src/options.cpp          |    9 +++---
 src/rndforest.cpp        |    4 +-
 src/rndforest.h          |    1 
 33 files changed, 109 insertions(+), 123 deletions(-)

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Package BayClone2 updated to version 1.1 with previous version 1.0 dated 2014-12-22

Title: Bayesian Feature Allocation Model for Tumor Heterogeneity
Description: A Bayesian feature allocation model is implemented for inference on tumor heterogeneity using next-generation sequencing data. The model identifies the subclonal copy number and single nucleotide mutations at a selected set of loci and provides inference on genetic tumor variation.
Author: Juhee Lee, Peter Mueller, Subhajit Sengupta, Kamalakar Gulukota, Yuan Ji
Maintainer: Subhajit Sengupta

Diff between BayClone2 versions 1.0 dated 2014-12-22 and 1.1 dated 2014-12-24

 DESCRIPTION       |    8 ++++----
 MD5               |    6 +++---
 R/fn_BayClone2.R  |    1 -
 src/BayClone2.cpp |   12 +++++++-----
 4 files changed, 14 insertions(+), 13 deletions(-)

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Package AFLPsim updated to version 0.3-4 with previous version 0.3-3 dated 2014-04-16

Title: Hybrid simulation and genome scan for dominant markers
Description: This package is developed in the Plant Reproductive Biology Lab (RNM-214) - University of Seville. It contains hybrid simulation functions for dominant genetic data. It also provides several genome scan methods.
Author: Francisco Balao [aut, cre], Juan Luis García-Castaño [aut]
Maintainer: Francisco Balao

Diff between AFLPsim versions 0.3-3 dated 2014-04-16 and 0.3-4 dated 2014-12-24

 DESCRIPTION            |    8 ++++----
 MD5                    |   18 +++++++++---------
 README.md              |    4 ++--
 inst/CITATION          |   26 ++++++++++----------------
 inst/NEWS.Rd           |    7 ++++++-
 man/AFLPsim-package.Rd |    6 +++---
 man/gscan.Rd           |    4 +++-
 man/hybridize.Rd       |    4 ++++
 man/hybridsim.Rd       |    4 ++++
 man/sim2newhybrids.Rd  |    2 +-
 10 files changed, 46 insertions(+), 37 deletions(-)

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