Tue, 24 Feb 2015

Package tRakt updated to version 0.9.0 with previous version 0.7.4 dated 2015-02-23

Title: Pull Data from 'trakt.tv'
Description: A wrapper for the trakt.tv APIv2 which uses httr and jsonlite to send non-OAuth2 requests and receive tidied data.
Author: Lukas Burk [aut, cre]
Maintainer: Lukas Burk

Diff between tRakt versions 0.7.4 dated 2015-02-23 and 0.9.0 dated 2015-02-24

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New package sprex with initial version 1.0
Package: sprex
Type: Package
Title: Calculate Species Richness and Extrapolation Metrics
Description: Calculate species richness functions for rarefaction and extrapolation.
Version: 1.0
Date: 2015-02-23
Author: Eric Archer
Maintainer: Eric Archer
License: GNU General Public License
Packaged: 2015-02-24 18:47:46 UTC; eric.archer
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-25 00:51:16

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Package aroma.apd updated to version 0.6.0 with previous version 0.5.0 dated 2014-02-27

Title: A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
Description: DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.)
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

Diff between aroma.apd versions 0.5.0 dated 2014-02-27 and 0.6.0 dated 2015-02-24

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New package babar with initial version 1.0
Package: babar
Type: Package
Title: Bayesian Bacterial Growth Curve Analysis in R
Version: 1.0
Date: 2014-11-13
Author: Lydia Rickett, Matthew Hartley, Richard Morris and Nick Pullen
Maintainer: Matthew Hartley
Description: Babar is designed to use nested sampling (a Bayesian analysis technique) to compare possible models for bacterial growth curves, as well as extracting parameters. It allows model evidence and parameter likelihood values to be extracted, and also contains helper functions for comparing distributions as well as direct access to the underlying nested sampling code.
License: GPL-2
Suggests: knitr, R.rsp
VignetteBuilder: knitr, R.rsp
Packaged: 2015-02-24 12:09:25 UTC; hartleym
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-24 23:27:07

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Package speaq updated to version 1.2.1 with previous version 1.2.0 dated 2015-01-14

Title: Tools for Nuclear Magnetic Resonance Spectrum Alignment and Quantitative Analysis
Description: We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. Related publication is available at http://www.biomedcentral.com/1471-2105/12/405/.
Author: Trung Nghia Vu, Kris Laukens and Dirk Valkenborg
Maintainer: Trung Nghia Vu

Diff between speaq versions 1.2.0 dated 2015-01-14 and 1.2.1 dated 2015-02-24

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Package rfUtilities updated to version 1.0-1 with previous version 1.0 dated 2014-11-21

Title: Random Forests Model Selection and Performance Evaluation
Description: Utilities for Random Forest model selection, class balance correction, significance test, cross validation and partial dependency plots.
Author: Jeffrey S. Evans [cre, aut], Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans

Diff between rfUtilities versions 1.0 dated 2014-11-21 and 1.0-1 dated 2015-02-24

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Package rglobi updated to version 0.2.5 with previous version 0.2.4 dated 2015-01-28

Title: R interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods provided by Global Biotic Interactions (GloBI). GloBI provides access to spatial-temporal species interaction records from source all over the world. rglobi provides methods to search species interactions by location, interaction type, and taxonomic name. In addition, it supports Cypher, a graph query language, to allow for executing custom queries on the GloBI aggregate species interaction dataset.
Author: Jorrit Poelen [aut, cre], Stephen Gosnell [aut], Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen

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Package rasterVis updated to version 0.35 with previous version 0.32 dated 2014-10-25

Title: Visualization Methods for Raster Data
Description: Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
Author: Oscar Perpinan Lamigueiro [cre, aut], Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro

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Package phenability updated to version 2.0 with previous version 1.0 dated 2014-04-23

Title: Nonparametric Stability Analysis
Description: An alternative to carrying out phenotypic adaptability and stability analyses, taking into account nonparametric statistics. Can be used as a robust approach, less sensitive to departures from common genotypic, environmental, and GxE effects data assumptions (e.g., normal distribution of errors).
Author: Leonardo Castelo Branco
Maintainer: Leonardo C. Branco

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Package likelihood updated to version 1.7 with previous version 1.6 dated 2014-06-27

Title: Methods for Maximum Likelihood Estimation
Description: Tools for maximum likelihood estimation of parameters of scientific models.
Author: Lora Murphy
Maintainer: Lora Murphy

Diff between likelihood versions 1.6 dated 2014-06-27 and 1.7 dated 2015-02-24

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Package FFD updated to version 1.0-6 with previous version 1.0-2 dated 2013-04-22

Title: Freedom from Disease
Description: Functions, S4 classes/methods and a graphical user interface (GUI) to design surveys to substantiate freedom from disease using a modified hypergeometric function (see Cameron and Baldock, 1997). Herd sensitivities are computed according to sampling strategies "individual sampling" or "limited sampling" (see M. Ziller, T. Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002). Methods to compute the a-posteriori alpha-error are implemented. Risk-based targeted sampling is supported.
Author: Ian Kopacka
Maintainer: Ian Kopacka

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Package clinfun updated to version 1.0.9 with previous version 1.0.6 dated 2014-07-22

Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan

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Package AER updated to version 1.2-3 with previous version 1.2-2 dated 2014-01-28

Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. (See the vignette for a package overview.)
Author: Christian Kleiber [aut], Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis

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New package assist with initial version 3.1.3
Package: assist
Version: 3.1.3
Title: A Suite of R Functions Implementing Spline Smoothing Techniques
Author: Yuedong Wang , and Chunlei Ke .
Maintainer: Chunlei Ke
Depends: R (>= 3.0.2), nlme, lattice
Description: A comprehensive package for fitting various non-parametric/semi-parametric linear/nonlinear fixed/mixed smoothing spline models.
License: GPL (>= 2)
URL: http://www.pstat.ucsb.edu/faculty/yuedong/software.html
Packaged: 2015-02-20 00:07:50 UTC; Yuedong
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-02-24 20:17:43

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Package SvyNom updated to version 1.1 with previous version 1.0 dated 2012-12-07

Title: Nomograms for Right-Censored Outcomes from Survey Designs
Description: Builds, evaluates and validates a nomogram with survey data and right-censored outcomes.
Author: Mithat Gonen, Marinela Capanu
Maintainer: Mithat Gonen

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New package LLSR with initial version 0.0.1.9000
Package: LLSR
Type: Package
Title: Data Analysis of Liquid-Liquid Systems
Version: 0.0.1.9000
Date: 2015-02-24
Author: Diego F Coelho
Maintainer: Diego F Coelho
Description: The methods implemented here were based in the protocol proposed by Merchuk et al. (1998) and Murugesan & Perumalsamy (2005) to analyse Aqueous Two-Phases Systems. Each function brings in its description the reference for the original article which described it. These methods defines nonlinear equations that can be used to fit experimental data through regression methods and also allow us calculate other important system parameters (such as its critical composition, equivolume concentration and phase's composition). The package will include (every other update) new functions in order to comprise useful functions in liquid-liquid analysis.
License: GPL-3
LazyData: TRUE
Depends: R (>= 2.10)
Imports: rootSolve
URL: http://diegofcoelho.github.io/code/
BugReports: https://github.com/eqipehub/LLSR/issues
Suggests: testthat
Packaged: 2015-02-24 13:07:42 UTC; dfcoelho
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-24 15:29:59

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Package HistDAWass updated to version 0.1.1 with previous version 0.1 dated 2015-02-18

Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new approach to the statistical analysis of multi-valued data, we consider histogram-valued data, i.e., data described by univariate histograms. The methods and the basic statistics for histogram-valued data are mainly based on the L2 Wasserstein metric between distributions, i.e., a Euclidean metric between quantile functions. The package contains unsupervised classification techniques, least square regression and tools for histogram-valued data and for histogram time series.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino

Diff between HistDAWass versions 0.1 dated 2015-02-18 and 0.1.1 dated 2015-02-24

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Package CombinS updated to version 1.1 with previous version 1.0 dated 2013-12-12

Title: Construction Methods of some Series of PBIB Designs
Description: The Combinatory Method (s) to Construct a series of PBIB designs and we give their associated U-type design.
Author: Mohamed Laib, Imane Rezgui, Zebida Gheribi-Aoulmi and Herve Monod
Maintainer: Mohamed Laib

Diff between CombinS versions 1.0 dated 2013-12-12 and 1.1 dated 2015-02-24

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Package autopls updated to version 1.3 with previous version 1.2-7 dated 2013-08-13

Title: Partial Least Squares Regression with Backward Selection of Predictors
Description: Some convenience functions for pls regression, including backward variable selection and validation procedures, image based predictions and plotting.
Author: Sebastian Schmidtlein, with contributions from C. Oldenburg and H. Feilhauer and with a code snipped borrowed from Bjorn-Helge Mevik
Maintainer: Sebastian Schmidtlein

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Package daff updated to version 0.1.2 with previous version 0.1.1 dated 2015-02-23

Title: Diff, Patch and Merge for Data.frames
Description: Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches. Changes to data can be made visible by using render_diff. Daff uses the V8 package to wrap the 'daff.js' javascript library which is included in the package. Daff exposes a subset of 'daff.js' functionality, tailored for usage within R.
Author: Paul Fitzpatrick [aut] (javascript original, http://paulfitz.github.io/daff/), Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge

Diff between daff versions 0.1.1 dated 2015-02-23 and 0.1.2 dated 2015-02-24

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Package cds updated to version 1.0.1 with previous version 1.0 dated 2015-02-16

Title: Constrained Dual Scaling for Detecting Response Styles
Description: This is an implementation of constrained dual scaling for detecting response styles in categorical data, including utility functions. The procedure involves adding additional columns to the data matrix representing the boundaries between the rating categories. The resulting matrix is then doubled and analyzed by dual scaling. One-dimensional solutions are sought which provide optimal scores for the rating categories. These optimal scores are constrained to follow monotone quadratic splines. Clusters are introduced within which the response styles can vary. The type of response style present in a cluster can be diagnosed from the optimal scores for said cluster, and this can be used to construct an imputed version of the data set which adjusts for response styles.
Author: Pieter Schoonees [aut, cre]
Maintainer: Pieter Schoonees

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Package TAM updated to version 1.5-2 with previous version 1.4-1 dated 2015-01-16

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, Cognitive Diagnostic 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

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Package survival updated to version 2.38-1 with previous version 2.37-7 dated 2014-01-22

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau

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More information about survival at CRAN
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Package mwa updated to version 0.4.1 with previous version 0.4 dated 2014-12-17

Title: Causal Inference in Spatiotemporal Event Data
Description: Matched Wake Analysis (mwa) grants insights into causal relationships in spatiotemporal event data.
Author: Sebastian Schutte and Karsten Donnay
Maintainer: Sebastian Schutte

Diff between mwa versions 0.4 dated 2014-12-17 and 0.4.1 dated 2015-02-24

 DESCRIPTION                |   12 ++---
 MD5                        |   20 ++++----
 R/mwa.R                    |  107 +++++++++++++++++++++++++++++++++++++--------
 man/matchedwake.Rd         |    8 +--
 man/mwa-package.Rd         |    6 +-
 man/mwa_data.Rd            |    6 +-
 man/plot.matchedwake.Rd    |    2 
 man/print.matchedwake.Rd   |    2 
 man/slideWakeMatch.Rd      |    2 
 man/slidingWake.Rd         |    2 
 man/summary.matchedwake.Rd |    4 -
 11 files changed, 122 insertions(+), 49 deletions(-)

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Package dpcR updated to version 0.1.3.3 with previous version 0.1.3.2 dated 2014-12-24

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 0.1.3.2 dated 2014-12-24 and 0.1.3.3 dated 2015-02-24

 CHANGELOG                |    3 +
 DESCRIPTION              |    8 ++--
 MD5                      |   80 +++++++++++++++++++++++------------------------
 NAMESPACE                |    2 -
 R/count_test-class.R     |    1 
 R/qpcrpp.R               |    2 -
 man/adpcr-class.Rd       |    3 +
 man/adpcr2ppp.Rd         |    3 +
 man/binarize.Rd          |    3 +
 man/bind_dpcr-methods.Rd |    3 +
 man/bioamp.Rd            |    3 +
 man/compare_dens.Rd      |    3 +
 man/count_test-class.Rd  |    7 ++--
 man/create_dpcr.Rd       |    3 +
 man/ddpcr-class.Rd       |    3 +
 man/dpcR-package.Rd      |    3 +
 man/dpcr_density.Rd      |    3 +
 man/dpcr_density_gui.Rd  |    3 +
 man/extract_dpcr.Rd      |    3 +
 man/limit_cq.Rd          |    3 +
 man/many_peaks.Rd        |    3 +
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 man/pds.Rd               |    3 +
 man/pds_raw.Rd           |    3 +
 man/plot.qpcrpp.Rd       |    4 +-
 man/plot_panel.Rd        |    3 +
 man/plot_vic_fam.Rd      |    3 +
 man/qpcr2pp.Rd           |    3 +
 man/qpcr_analyser.Rd     |    3 +
 man/qpcrpp-class.Rd      |    3 +
 man/rtadpcr-class.Rd     |    3 +
 man/show-methods.Rd      |    3 +
 man/sim_adpcr.Rd         |    3 +
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 man/summary-methods.Rd   |    3 +
 man/test_counts.Rd       |    3 +
 man/test_counts_gui.Rd   |    3 +
 man/test_panel.Rd        |    3 +
 man/test_peaks.Rd        |    3 +
 man/test_ratio.Rd        |    3 +
 41 files changed, 124 insertions(+), 82 deletions(-)

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New package coloredICA with initial version 1.0.0
Package: coloredICA
Type: Package
Title: Implementation of Colored Independent Component Analysis and Spatial Colored Independent Component Analysis
Version: 1.0.0
Date: 2014-03-04
Author: Lee, S., Shen, H., Truong, Y. and Zanini, P.
Maintainer: Paolo Zanini
Depends: MASS
Suggests: fastICA
Description: It implements colored Independent Component Analysis (Lee et al., 2011) and spatial colored Independent Component Analysis (Shen et al., 2014). They are two algorithms to perform ICA when sources are assumed to be temporal or spatial stochastic processes, respectively.
License: GPL (>= 2)
Packaged: 2015-02-24 08:46:57 UTC; paolo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-24 11:01:51

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Package spatialEco updated to version 0.1-1 with previous version 0.1-0 dated 2015-02-02

Title: Spatial Analysis and Modeling
Description: Utilities to support spatial data manipulation, query, sampling and modeling. Functions include models for species population density, download utilities for climate and global deforestation spatial products, spatial smoothing, multivariate separability, point process model for creating pseudo-absences and subsampling, polygon and point-distance landscape metrics, auto-logistic model, sampling models, cluster optimization and statistical exploratory tools.
Author: Jeffrey S. Evans [aut, cre], Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans

Diff between spatialEco versions 0.1-0 dated 2015-02-02 and 0.1-1 dated 2015-02-24

 DESCRIPTION                |    8 +-
 MD5                        |   81 +++++++++++++----------
 NAMESPACE                  |    3 
 R/breeding.density.R       |    6 -
 R/correlogram.R            |    4 -
 R/csi.R                    |only
 R/download.daymet.R        |    6 -
 R/download.prism.R         |    4 -
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 R/parea.sample.R           |    2 
 R/point.in.poly.R          |   13 +--
 R/pp.subsample.R           |    2 
 R/pseudo.absence.R         |    6 -
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 R/stratified.random.R      |    4 -
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 man/separability.Rd        |  152 ++++++++++++++++++++++-----------------------
 man/stratified.random.Rd   |  150 ++++++++++++++++++++++----------------------
 man/trend.line.Rd          |   86 ++++++++++++-------------
 45 files changed, 717 insertions(+), 690 deletions(-)

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Package RMySQL updated to version 0.10.2 with previous version 0.10.1 dated 2015-01-15

Title: Database Interface and MySQL Driver for R
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre], David James [aut], Saikat DebRoy [aut], Hadley Wickham [aut], Jeffrey Horner [aut], RStudio [cph]
Maintainer: Jeroen Ooms

Diff between RMySQL versions 0.10.1 dated 2015-01-15 and 0.10.2 dated 2015-02-24

 DESCRIPTION      |    6 +++---
 MD5              |    8 ++++----
 configure        |   10 ++++++++++
 src/Makevars.win |    4 ++--
 tools/winlibs.R  |    4 ++--
 5 files changed, 21 insertions(+), 11 deletions(-)

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Package js updated to version 0.2 with previous version 0.1 dated 2015-02-15

Title: Tools for Working with JavaScript in R
Description: A set of utility functions for working with JavaScript in R. Currently includes functions to compile, validate, reformat, optimize and analyze JavaScript code.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

Diff between js versions 0.1 dated 2015-02-15 and 0.2 dated 2015-02-24

 DESCRIPTION           |   12 ++--
 MD5                   |   17 ++++--
 NAMESPACE             |    1 
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 R/coffee.R            |only
 inst/doc/intro.R      |   13 +++++
 inst/doc/intro.Rmd    |   35 +++++++++++--
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 12 files changed, 208 insertions(+), 31 deletions(-)

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Package iBATCGH updated to version 1.2 with previous version 1.1 dated 2014-09-13

Title: Integrative Bayesian Analysis of Transcriptomic and CGH Data
Description: Bayesian integrative models of gene expression and comparative genomic hybridization data. The package provides inference on copy number variations and their association with gene expression.
Author: Alberto Cassese
Maintainer: Alberto Cassese

Diff between iBATCGH versions 1.1 dated 2014-09-13 and 1.2 dated 2015-02-24

 DESCRIPTION        |   18 +++++++++---------
 MD5                |    8 ++++----
 src/Makevars       |    2 +-
 src/Makevars.win   |    3 +--
 src/ProbitMain.cpp |    8 +++++---
 5 files changed, 20 insertions(+), 19 deletions(-)

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Package FunChisq updated to version 2.0.1 with previous version 2.0.0 dated 2015-02-16

Title: Chi-Square Tests for Non-Parametric Functional Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on chi-square statistics. These tests were designed to reveal causality based on evidence from non-parametric functional dependencies. They include an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song

Diff between FunChisq versions 2.0.0 dated 2015-02-16 and 2.0.1 dated 2015-02-24

 FunChisq-2.0.0/FunChisq/src/Makevars                   |only
 FunChisq-2.0.0/FunChisq/src/Makevars.win               |only
 FunChisq-2.0.0/FunChisq/src/TransitionTableIO.cpp      |only
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 FunChisq-2.0.1/FunChisq/DESCRIPTION                    |   10 -
 FunChisq-2.0.1/FunChisq/MD5                            |   39 +++----
 FunChisq-2.0.1/FunChisq/NAMESPACE                      |    3 
 FunChisq-2.0.1/FunChisq/NEWS                           |   58 +++++------
 FunChisq-2.0.1/FunChisq/man/FunChisq-package.Rd        |   10 -
 FunChisq-2.0.1/FunChisq/man/cp.fun.chisq.test.Rd       |   16 +--
 FunChisq-2.0.1/FunChisq/man/fun.chisq.test.Rd          |   48 ++++-----
 FunChisq-2.0.1/FunChisq/src/AdjustPvalue.cpp           |   88 ++++++++---------
 FunChisq-2.0.1/FunChisq/src/ChisqDirTest.cpp           |    2 
 FunChisq-2.0.1/FunChisq/src/ChisqTests.cpp             |   66 ++++++------
 FunChisq-2.0.1/FunChisq/src/ChisqTests.h               |    2 
 FunChisq-2.0.1/FunChisq/src/ExactFunctionalTest.cpp    |   29 +----
 FunChisq-2.0.1/FunChisq/src/ExactFunctionalTest.h      |    4 
 FunChisq-2.0.1/FunChisq/src/ExactMultiTableTest.cpp    |   20 +--
 FunChisq-2.0.1/FunChisq/src/ExactMultiTableTest.h      |   10 +
 FunChisq-2.0.1/FunChisq/src/StatDistributions.cpp      |    4 
 FunChisq-2.0.1/FunChisq/src/TransitionTable.cpp        |   26 ++---
 FunChisq-2.0.1/FunChisq/src/TransitionTable.h          |    6 -
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 23 files changed, 214 insertions(+), 227 deletions(-)

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New package coxsei with initial version 0.1
Package: coxsei
Type: Package
Title: Fitting a CoxSEI Model
Version: 0.1
Date: 2015-02-23
Author: Feng Chen
Maintainer: Feng Chen
Description: It fits a CoxSEI (Cox type Self-Exciting Intensity) model to right-censored counting process data.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2015-02-24 00:46:09 UTC; z3243864
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-02-24 08:03:34

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Package cairoDevice updated to version 2.22 with previous version 2.21 dated 2015-01-20

Title: Cairo-based Graphics Device Driver
Description: This device uses Cairo and GTK to draw to the screen, file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable or Cairo context). The screen device may be embedded into RGtk2 interfaces and supports all interactive features of other graphics devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence

Diff between cairoDevice versions 2.21 dated 2015-01-20 and 2.22 dated 2015-02-24

 DESCRIPTION       |   12 ++++++------
 MD5               |    4 ++--
 src/cairoDevice.c |    3 ---
 3 files changed, 8 insertions(+), 11 deletions(-)

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Package aroma.cn updated to version 1.6.0 with previous version 1.5.0 dated 2013-10-17

Title: Copy-Number Analysis of Large Microarray Data Sets
Description: Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson

Diff between aroma.cn versions 1.5.0 dated 2013-10-17 and 1.6.0 dated 2015-02-24

 aroma.cn-1.5.0/aroma.cn/R/PSCBS.flips.R                                                                |only
 aroma.cn-1.5.0/aroma.cn/R/PairedPSCBS.calibrateC1C2.R                                                  |only
 aroma.cn-1.5.0/aroma.cn/R/PairedPSCBS.deShearC1C2.R                                                    |only
 aroma.cn-1.5.0/aroma.cn/inst/NEWS                                                                      |only
 aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R |only
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 aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/ortho                                                  |only
 aroma.cn-1.5.0/aroma.cn/man/calibrateC1C2.PairedPSCBS.Rd                                               |only
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 aroma.cn-1.6.0/aroma.cn/DESCRIPTION                                                                    |   27 
 aroma.cn-1.6.0/aroma.cn/MD5                                                                            |   90 
 aroma.cn-1.6.0/aroma.cn/NAMESPACE                                                                      |   47 
 aroma.cn-1.6.0/aroma.cn/NEWS                                                                           |only
 aroma.cn-1.6.0/aroma.cn/R/009.setup.R                                                                  |    6 
 aroma.cn-1.6.0/aroma.cn/R/021.dynamic_imports.R                                                        |only
 aroma.cn-1.6.0/aroma.cn/R/AbstractCurveNormalization.R                                                 |   11 
 aroma.cn-1.6.0/aroma.cn/R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R                              |only
 aroma.cn-1.6.0/aroma.cn/R/C1C2.R                                                                       |   72 
 aroma.cn-1.6.0/aroma.cn/R/MultiSourceCopyNumberNormalization.R                                         |   14 
 aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.CALL2.R                                                          |    2 
 aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.NORM.R                                                           |    4 
 aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.PLOT3.R                                                          |    5 
 aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.backgroundCorrect.R                                              |only
 aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.fitC1C2Peaks.R                                                   |only
 aroma.cn-1.6.0/aroma.cn/R/PairedPscbsModel.R                                                           |   10 
 aroma.cn-1.6.0/aroma.cn/R/PrincipalCurve.XTRAS.R                                                       |    2 
 aroma.cn-1.6.0/aroma.cn/R/PrincipalCurveNormalization.R                                                |    6 
 aroma.cn-1.6.0/aroma.cn/R/TotalFracBSnpData.R                                                          |    2 
 aroma.cn-1.6.0/aroma.cn/R/TumorBoostNormalization.R                                                    |    3 
 aroma.cn-1.6.0/aroma.cn/R/XYCurveNormalization.R                                                       |    4 
 aroma.cn-1.6.0/aroma.cn/R/callXXorXY.numeric.R                                                         |    6 
 aroma.cn-1.6.0/aroma.cn/R/normalizeMirroredBAFsByRegions.R                                             |    7 
 aroma.cn-1.6.0/aroma.cn/R/normalizePrincipalCurve.matrix.R                                             |    5 
 aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex             | 1020 +++++-----
 aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex                       |  414 ++--
 aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/00.setup.R                                |   54 
 aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R                     |   34 
 aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R                         |  204 +-
 aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/zzz.R                                     |   62 
 aroma.cn-1.6.0/aroma.cn/man/AbstractCurveNormalization.Rd                                              |    2 
 aroma.cn-1.6.0/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd                                      |    2 
 aroma.cn-1.6.0/aroma.cn/man/Non-documented_objects.Rd                                                  |   36 
 aroma.cn-1.6.0/aroma.cn/man/PairedPscbsModel.Rd                                                        |    2 
 aroma.cn-1.6.0/aroma.cn/man/PrincipalCurveNormalization.Rd                                             |    2 
 aroma.cn-1.6.0/aroma.cn/man/TotalCnBinnedSmoothing.Rd                                                  |    2 
 aroma.cn-1.6.0/aroma.cn/man/TotalCnKernelSmoothing.Rd                                                  |    2 
 aroma.cn-1.6.0/aroma.cn/man/TotalCnSmoothing.Rd                                                        |    2 
 aroma.cn-1.6.0/aroma.cn/man/TumorBoostNormalization.Rd                                                 |    2 
 aroma.cn-1.6.0/aroma.cn/man/XYCurveNormalization.Rd                                                    |    2 
 aroma.cn-1.6.0/aroma.cn/man/findAtomicAberrations.CopyNumberRegions.Rd                                 |   75 
 aroma.cn-1.6.0/aroma.cn/man/normalizeBAFsByRegions.PairedPSCBS.Rd                                      |   61 
 aroma.cn-1.6.0/aroma.cn/tests                                                                          |only
 52 files changed, 1100 insertions(+), 1201 deletions(-)

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