Wed, 24 Oct 2012

Package texreg updated to version 1.14 with previous version 1.06 dated 2012-10-03

Title: Conversion of R regression output to LaTeX tables.
Description: texreg converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables. Either a single model or a list of models can be combined in a single table. The output is customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld

Diff between texreg versions 1.06 dated 2012-10-03 and 1.14 dated 2012-10-24

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 15 files changed, 485 insertions(+), 450 deletions(-)

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Package proftools updated to version 0.0-5 with previous version 0.0-4 dated 2011-07-29

Title: Profile Output Processing Tools for R
Description: Tools for examining Rprof profile output.
Author: Luke Tierney
Maintainer: Luke Tierney

Diff between proftools versions 0.0-4 dated 2011-07-29 and 0.0-5 dated 2012-10-24

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Package BDgraph updated to version 1.2 with previous version 1.1 dated 2012-10-08

Title: Gaussian Graphical Model determination based on birth-death MCMC methodology
Description: The R package BDgraph is a statistical tool for Bayesian model determination in undirected Gaussian graphical models. The Bayesian methodology is based on birth-death MCMC algorithm. The main function is 'bdmcmc' which is a birth-death MCMC algorithm for Bayesian model determination in undirected Gaussian graphical models.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi

Diff between BDgraph versions 1.1 dated 2012-10-08 and 1.2 dated 2012-10-24

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Package bcrm updated to version 0.4.1 with previous version 0.4 dated 2012-09-18

Title: Bayesian continuous reassessment method (CRM) designs for Phase I dose-finding trials.
Description: This package implements a wide variety of one and two-parameter Bayesian CRM designs. The program can run interactively, allowing the user to enter outcomes after each cohort has been recruited, or via simulation to assess operating characteristics.
Author: Michael Sweeting
Maintainer: Michael Sweeting

Diff between bcrm versions 0.4 dated 2012-09-18 and 0.4.1 dated 2012-10-24

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Package Synth updated to version 1.1-3 with previous version 1.1-2 dated 2011-12-27

Title: Synthetic Control Group Method for Comparative Case Studies
Description: Implements the synthetic control group method for comparative case studies developed in Abadie and Gardeazabal (2003) and Abadie, Diamond, and Hainmueller (2010). The synthetic control method allows for effect estimation in settings where a single unit (a state, country, firm, etc.) is exposed to an event or intervention. It provides a data-driven procedure to construct synthetic control units based on a weighted combination of comparison units that approximates the characteristics of the unit that is exposed to the intervention. A combination of comparison units often provides a better comparison for the unit exposed to the intervention than any comparison unit alone.
Author: Jens Hainmueller and Alexis Diamond
Maintainer: Jens Hainmueller

Diff between Synth versions 1.1-2 dated 2011-12-27 and 1.1-3 dated 2012-10-24

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New package sprint with initial version 1.0.3
Package: sprint
Title: Simple Parallel R INTerface
Version: 1.0.3
Date: 2012-10-23
Author: University of Edinburgh SPRINT Team
Maintainer: Eilidh Troup
Contact: University of Edinburgh SPRINT Team
Depends: R (>= 2.9.2), rlecuyer
Suggests: ff (>= 2.1-1), randomForest, RankProd, cluster, multtest, IRanges, RUnit
Imports: boot
SystemRequirements: MPI2, Unix
Description: SPRINT (Simple Parallel R INTerface) is a parallel framework for R. It provides a High Performance Computing (HPC) harness which allow R scripts to run on HPC clusters. SPRINT contains a library of selected R functions that have been parallelized. Functions are named after the original R function with the added prefix 'p', i.e. the parallel version of cor() in SPRINT is called pcor(). Call to the parallel R functions are included directly in standard R scripts.
License: GPL (>= 3)
URL: http://www.r-sprint.org
Repository: CRAN
Packaged: 2012-10-24 11:00:06 UTC; egrant1
Date/Publication: 2012-10-24 12:31:19

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Package RHRV updated to version 3.0.3 with previous version 3.0.0 dated 2012-10-15

Title: Heart rate variability analysis of ECG data
Description: This is a package for developing heart rate variability studies of ECG records
Author: A. Mendez, L. Rodriguez-Linares, A. Otero, C.A. Garcia, X. Vila, M. Lado
Maintainer: L. Rodriguez-Linares

Diff between RHRV versions 3.0.0 dated 2012-10-15 and 3.0.3 dated 2012-10-24

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Package ff updated to version 2.2-9 with previous version 2.2-7 dated 2012-05-08

Title: memory-efficient storage of large data on disk and fast access functions
Description: The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section (pagesize) in main memory - the effective virtual memory consumption per ff object. ff supports R's standard atomic data types 'double', 'logical', 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float with NAs). For example 'quad' allows efficient storage of genomic data as an 'A','T','G','C' factor. The unsigned types support 'circular' arithmetic. There is also support for close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom close-to-atomic types. ff not only has native C-support for vectors, matrices and arrays with flexible dimorder (major column-order, major row-order and generalizations for arrays). There is also a ffdf class not unlike data.frames and import/export filters for csv files. ff objects store raw data in binary flat files in native encoding, and complement this with metadata stored in R as physical and virtual attributes. ff objects have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R objects (using different data en/de-coding schemes) in the same process or from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without notable delay thanks to using sparse file allocation. Several access optimization techniques such as Hybrid Index Preprocessing and Virtualization are implemented to achieve good performance even with large datasets, for example virtual matrix transpose without touching a single byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard data types get stored native and compact on binary flat files i.e. logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond basic access functions, the ff package also provides compatibility functions that facilitate writing code for ff and ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely with functionality from package 'bit': chunked looping, fast bit operations and coercions between different objects that can store subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows to work interactively with selections of large datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request.
Author: Daniel Adler , Christian Gläser , Oleg Nenadic , Jens Oehlschlägel , Walter Zucchini
Maintainer: Jens Oehlschlägel

Diff between ff versions 2.2-7 dated 2012-05-08 and 2.2-9 dated 2012-10-24

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Package CARE1 updated to version 1.1.0 with previous version 1.0.2 dated 2012-02-07

Title: Statistical package for population size estimation in capture-recapture models.
Description: The R package CARE1, the first part of the program CARE (Capture-Recapture) in http://chao.stat.nthu.edu.tw/softwareCE.html, can be used to analyze epidemiological data via sample coverage approach (Chao et al. 2001a). Based on the input of records from several incomplete lists (or samples) of individuals, the R package CARE1 provides output of population size estimate and related statistics.
Author: T.C. Hsieh
Maintainer: Anne Chao

Diff between CARE1 versions 1.0.2 dated 2012-02-07 and 1.1.0 dated 2012-10-24

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New package bit64 with initial version 0.9-1
Package: bit64
Type: Package
Title: A S3 class for vectors of 64bit integers
Version: 0.9-1
Date: 2012-10-07
Author: Jens Oehlschlägel
Maintainer: Jens Oehlschlägel
Depends: R (>= 2.14.0), bit (>= 1.1-9), methods
Description: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers that can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support interactive data exploration and manipulation and optionally leverage caching.
License: GPL-2
LazyLoad: yes
ByteCompile: yes
URL: http://ff.r-forge.r-project.org/
Encoding: latin1
Packaged: 2012-10-23 19:08:17 UTC; root
Repository: CRAN
Date/Publication: 2012-10-24 12:23:08

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Package bit updated to version 1.1-9 with previous version 1.1-8 dated 2012-01-15

Title: A class for vectors of 1-bit booleans
Description: bitmapped vectors of booleans (no NAs), coercion from and to logicals, integers and integer subscripts; fast boolean operators and fast summary statistics. With 'bit' vectors you can store true binary booleans {FALSE,TRUE} at the expense of 1 bit only, on a 32 bit architecture this means factor 32 less RAM and ~ factor 32 more speed on boolean operations. Due to overhead of R calls, actual speed gain depends on the size of the vector: expect gains for vectors of size > 10000 elements. Even for one-time boolean operations it can pay-off to convert to bit, the pay-off is obvious, when such components are used more than once. Reading from and writing to bit is approximately as fast as accessing standard logicals - mostly due to R's time for memory allocation. The package allows to work with pre-allocated memory for return values by calling .Call() directly: when evaluating the speed of C-access with pre-allocated vector memory, coping from bit to logical requires only 70% of the time for copying from logical to logical; and copying from logical to bit comes at a performance penalty of 150%. the package now contains further classes for representing logical selections: 'bitwhich' for very skewed selections and 'ri' for selecting ranges of values for chunked processing. All three index classes can be used for subsetting 'ff' objects (ff-2.1-0 and higher).
Author: Jens Oehlschlägel
Maintainer: Jens Oehlschlägel

Diff between bit versions 1.1-8 dated 2012-01-15 and 1.1-9 dated 2012-10-24

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Package ExomeDepth updated to version 0.9.4 with previous version 0.9.2 dated 2012-10-20

Title: Calls CNV from exome sequence data
Description: Calls copy number variants (CNVs) from targeted sequence data
Author: Vincent Plagnol
Maintainer: Vincent Plagnol

Diff between ExomeDepth versions 0.9.2 dated 2012-10-20 and 0.9.4 dated 2012-10-24

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Package rpart.plot updated to version 1.4-1 with previous version 1.4-0 dated 2012-10-10

Title: Plot rpart models. An enhanced version of plot.rpart.
Description: Plot rpart models. Extends plot.rpart and text.rpart in the rpart package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow

Diff between rpart.plot versions 1.4-0 dated 2012-10-10 and 1.4-1 dated 2012-10-24

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Package R.oo updated to version 1.10.1 with previous version 1.9.9 dated 2012-09-12

Title: R object-oriented programming with or without references
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson

Diff between R.oo versions 1.9.9 dated 2012-09-12 and 1.10.1 dated 2012-10-24

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Package RAMpath updated to version 0.2 with previous version 0.1.5 dated 2012-10-08

Title: RAMpath
Description: RAMpath is a rewrite of RAMpath software developed by John McArdle and Steven Boker. However, it does more than the original software by providing flexible fit of growth curve models, univariate and bivariate latent change score models. It can also generate the vector field plot for the bivariate latent change score models.
Author: Zhiyong Zhang, Jack McArdle, Aki Hamagami, & Kevin Grimm
Maintainer: Zhiyong Zhang

Diff between RAMpath versions 0.1.5 dated 2012-10-08 and 0.2 dated 2012-10-24

 DESCRIPTION            |   14 +++----
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New package pheno2geno with initial version 1.0.0
Package: pheno2geno
Version: 1.0.0
Date: Sep 2012
Title: Pheno2Geno - Generating genetic markers and maps from molecular phenotypes
Author: Konrad Zych and Danny Arends
Maintainer: Konrad Zych
Description: Pheno2Geno is an R package for the computational generation genetic markers and maps from molecular phenotypes
Depends: R (>= 2.10.1), graphics, stats, utils, qtl, mixtools
Suggests: RankProd
License: GPL-3
Packaged: 2012-10-23 17:40:36 UTC; Konrad
Repository: CRAN
Date/Publication: 2012-10-24 06:49:33

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Package pander updated to version 0.3 with previous version 0.2 dated 2012-08-17

Title: An R pandoc writer
Description: Contains some functions catching all messages, stdout and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in Pandoc's markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex Pandoc documents to e.g. HTML, pdf, docx or odt. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching backend.
Author: Gergely Daróczi
Maintainer: Gergely Daróczi

Diff between pander versions 0.2 dated 2012-08-17 and 0.3 dated 2012-10-24

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New package GLDEX with initial version 1.0.4.4
Package: GLDEX
Version: 1.0.4.4
Date: 2012-10-19
Title: Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su
Depends: cluster
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
License: GPL (>= 3)
URL: http://www.uwa.edu.au/people/steve.su
Packaged: 2012-10-23 10:06:00 UTC; Owner
Repository: CRAN
Date/Publication: 2012-10-24 06:59:22

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Package ftsa updated to version 3.6 with previous version 3.5 dated 2012-09-13

Title: Functional time series analysis
Description: Functions for functional time series
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang

Diff between ftsa versions 3.5 dated 2012-09-13 and 3.6 dated 2012-10-24

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 ftsa-3.6/ftsa/man/centre.Rd                 |    5 
 ftsa-3.6/ftsa/man/diff.fts.Rd               |    4 
 ftsa-3.6/ftsa/man/dynupdate.Rd              |   15 +-
 ftsa-3.6/ftsa/man/error.Rd                  |    1 
 ftsa-3.6/ftsa/man/extract.Rd                |    4 
 ftsa-3.6/ftsa/man/fbootstrap.Rd             |   15 +-
 ftsa-3.6/ftsa/man/forecast.ftsm.Rd          |  174 ++++++++++++++--------------
 ftsa-3.6/ftsa/man/forecastfplsr.Rd          |    4 
 ftsa-3.6/ftsa/man/fplsr.Rd                  |   24 ++-
 ftsa-3.6/ftsa/man/ftsa-package.Rd           |   22 ++-
 ftsa-3.6/ftsa/man/ftsm.Rd                   |    9 -
 ftsa-3.6/ftsa/man/ftsmiterativeforecasts.Rd |  131 ++++++++++-----------
 ftsa-3.6/ftsa/man/is.fts.Rd                 |    3 
 ftsa-3.6/ftsa/man/mean.fts.Rd               |  110 ++++++++++-------
 ftsa-3.6/ftsa/man/median.fts.Rd             |   28 +++-
 ftsa-3.6/ftsa/man/pcscorebootstrapdata.Rd   |    9 -
 ftsa-3.6/ftsa/man/plot.fmres.Rd             |    3 
 ftsa-3.6/ftsa/man/plot.ftsf.Rd              |    2 
 ftsa-3.6/ftsa/man/plot.ftsm.Rd              |    5 
 ftsa-3.6/ftsa/man/plotfplsr.Rd              |    3 
 ftsa-3.6/ftsa/man/residuals.fm.Rd           |    6 
 ftsa-3.6/ftsa/man/sd.fts.Rd                 |  119 +++++++++++--------
 ftsa-3.6/ftsa/man/var.fts.Rd                |   25 +++-
 35 files changed, 643 insertions(+), 434 deletions(-)

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New package dpglasso with initial version 1.0
Package: dpglasso
Type: Package
Title: Primal Graphical Lasso
Version: 1.0
Date: 2012-08-28
Author: Rahul Mazumder and Trevor Hastie
Maintainer: Rahul Mazumder
Description: fits the primal graphical lasso, via one-at-a-time block-coordinate descent.
License: GPL-2
LazyLoad: yes
Packaged: 2012-10-23 22:10:59 UTC; hastie
Repository: CRAN
Date/Publication: 2012-10-24 07:09:18

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Package colorspace updated to version 1.2-0 with previous version 1.1-1 dated 2012-01-13

Title: Color Space Manipulation
Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.
Author: Ross Ihaka [aut], Paul Murrell [aut], Kurt Hornik [aut], Jason C. Fisher [aut], Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis

Diff between colorspace versions 1.1-1 dated 2012-01-13 and 1.2-0 dated 2012-10-24

 colorspace-1.1-1/colorspace/COPYRIGHT               |only
 colorspace-1.1-1/colorspace/inst/doc/color.bib      |only
 colorspace-1.2-0/colorspace/DESCRIPTION             |   31 +++++-----
 colorspace-1.2-0/colorspace/MD5                     |   60 +++++++++++---------
 colorspace-1.2-0/colorspace/NAMESPACE               |   43 ++++++++++++--
 colorspace-1.2-0/colorspace/NEWS                    |   18 ++++++
 colorspace-1.2-0/colorspace/R/choose_palette.R      |only
 colorspace-1.2-0/colorspace/R/colorspace.R          |   57 +++++++++++++++----
 colorspace-1.2-0/colorspace/data                    |only
 colorspace-1.2-0/colorspace/inst/CITATION           |    3 -
 colorspace-1.2-0/colorspace/inst/doc/hcl-colors.Rnw |   55 ++++++++++--------
 colorspace-1.2-0/colorspace/inst/doc/hcl-colors.pdf |binary
 colorspace-1.2-0/colorspace/man/HLS.Rd              |    2 
 colorspace-1.2-0/colorspace/man/HSV.Rd              |    2 
 colorspace-1.2-0/colorspace/man/LAB.Rd              |    8 ++
 colorspace-1.2-0/colorspace/man/LUV.Rd              |    8 ++
 colorspace-1.2-0/colorspace/man/RGB.Rd              |    3 -
 colorspace-1.2-0/colorspace/man/USSouthPolygon.Rd   |only
 colorspace-1.2-0/colorspace/man/XYZ.Rd              |    2 
 colorspace-1.2-0/colorspace/man/choose_palette.Rd   |only
 colorspace-1.2-0/colorspace/man/coords.Rd           |    2 
 colorspace-1.2-0/colorspace/man/desaturate.Rd       |    4 +
 colorspace-1.2-0/colorspace/man/hex.Rd              |    6 +-
 colorspace-1.2-0/colorspace/man/hex2RGB.Rd          |    2 
 colorspace-1.2-0/colorspace/man/polarLAB.Rd         |    8 ++
 colorspace-1.2-0/colorspace/man/polarLUV.Rd         |    8 ++
 colorspace-1.2-0/colorspace/man/rainbow_hcl.Rd      |    2 
 colorspace-1.2-0/colorspace/man/readRGB.Rd          |    6 +-
 colorspace-1.2-0/colorspace/man/readhex.Rd          |    6 +-
 colorspace-1.2-0/colorspace/man/sRGB.Rd             |    3 -
 colorspace-1.2-0/colorspace/man/writehex.Rd         |    3 -
 colorspace-1.2-0/colorspace/src/colorspace.c        |   35 +++++++++++
 colorspace-1.2-0/colorspace/tests                   |only
 colorspace-1.2-0/colorspace/vignettes               |only
 34 files changed, 269 insertions(+), 108 deletions(-)

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New package bursts with initial version 1.0
Package: bursts
Type: Package
Title: Markov model for bursty behavior in streams
Version: 1.0
Date: 2012-09-08
Author: Jeff Binder
Authors@R: person("Jeff", "Binder", role = c("aut", "cre"), email = "extruded@gmail.com")
Maintainer: Jeff Binder
Description: An implementation of Jon Kleinberg's burst detection algorithm. Uses an infinite Markov model to detect periods of increased activity in a series of discrete events with known times, and provides a simple visualization of the results.
License: MIT
Copyright: (c) 2012 NYU School of Medicine; (c) 2012 Jeff Binder
Packaged: 2012-10-23 14:55:24 UTC; jmb783
Repository: CRAN
Date/Publication: 2012-10-24 06:41:06

More information about bursts at CRAN
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