Planet R

January 27, 2012

CRANberries

New package bit64 with initial version 0.8-2

Package: bit64
Type: Package
Title: A S3 class for vectors of 64bit integers
Version: 0.8-2
Date: 2011-12-12
Author: Jens Oehlschl\xE4gel
Maintainer: Jens Oehlschl\xE4gel
Depends: R (>= 2.14.0), bit (>= 1.1-8), 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 as well as many elementwise and summary functions. With 'integer64' vectors you can store very large integers at the expense of 64 bits, which is by factor 7 better than 'int64' from package 'int64'. Due to the smaller memory footprint, the atomic vector architecture and using only S3 instead of S4 classes, most operations are one to three orders of magnitude faster: Example speedups are 4x for serialization, 250x for adding, 900x for coercion and 2000x for object creation. Also 'integer64' avoids an ongoing (potentially infinite) penalty for garbage collection observed during existence of 'int64' objects (see code in example section). Last but not least, this package has no commercial copyright attached, it is not sponsored by any commercial company or otherwise influenced by commercial interests. Its mix of high-level R code with low-level C-code protects against misuse outside the GPLed R context.
License: GPL-2
LazyLoad: yes
ByteCompile: yes
URL: http://ff.r-forge.r-project.org/
Encoding: latin1
Packaged: 2012-01-26 21:52:56 UTC; rforge
Repository: CRAN
Repository/R-Forge/Project: ff
Repository/R-Forge/Revision: 94
Date/Publication: 2012-01-27 21:44:43

More information about bit64 at CRAN

January 27, 2012 11:16 PM

Revolutions

Because it's Friday: Movie Poster Cliches

The principle of "small multiples" — displaying multiple charts of the same type to compare differences — was introduced by Bill Cleveland and popularized by Edward Tufte and the "lattice" package in R. Now, the same principle is applied to movie posters in this display of "Over-Used Movie Poster Clichés":

 Back-to-back

Apparently, a couple standing back-to-back on the poster is a good indicator of a tough-love relationship between the protagonists, and an all-yellow background indicates an adorable indie-flick. Follow the link below for more examples:

FlavorWire: Visual Representations of 15 Over-Used Movie Poster Clichés

 

by David Smith at January 27, 2012 09:58 PM

New R User Group in Cleveland

Another new local R user group has just started up, this time in Cleveland, OH. The Cleveland R User Group is the brainchild of R user Nicholas Hermez, and their first meeting on February 22 is a get-together to plan future topics, presenters and venues. If you're in the Cleveland area why not drop by and contribute your ideas?

By the way, don't forget that both existing R user groups and new R user groups like the Cleveland group are eligible for sponsor that sponsorships from Revolution Analytics.

MeetUp: Greater Cleveland useR Group

by David Smith at January 27, 2012 05:55 PM

CRANberries

New package PopGenome with initial version 1.0

Package: PopGenome
Type: Package
Title: Population genetic analysis
Version: 1.0
Date: 2011-03-17
Author: Bastian Pfeifer
Maintainer: Bastian Pfeifer
Depends: R (>= 1.8.0), methods
Description: PopGenome is an R-library for Population Genetic Analysis
License: GPL-2
LazyLoad: yes
Packaged: Fri Jan 27 11:21:33 2012; bapfe
Repository: CRAN
Date/Publication: 2012-01-27 12:51:08

More information about PopGenome at CRAN

January 27, 2012 02:16 PM

Removed CRANberries

Package glpk (with last version 4.8-0.5) was removed from CRAN

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

2006-10-13 4.8-0.5

January 27, 2012 02:16 PM

Package SubpathwayMiner (with last version 3.1) was removed from CRAN

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

2010-09-01 3.1
2010-06-01 3.0
2009-09-03 2.0
2008-11-28 1.1
2008-11-27 1.0

January 27, 2012 02:16 PM

Package SpatioTemporal (with last version 0.9.0) was removed from CRAN

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

2011-07-29 0.9.0

January 27, 2012 02:16 PM

Package rimage (with last version 0.5-8.2) was removed from CRAN

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

2011-06-09 0.5-8.2
2010-02-24 0.5-8.1
2009-06-05 0.5-8
2005-01-12 0.5-7

January 27, 2012 02:16 PM

Package OSACC (with last version 1.0) was removed from CRAN

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

2010-09-16 1.0

January 27, 2012 02:16 PM

CRANberries

New package paleotree with initial version 1.0

Package: paleotree
Type: Package
Version: 1.0
Title: Analyses for Paleontological Phylogenies
Date: 2012-01-17
Author: David Bapst
Depends: ape, phangorn, geiger
Suggests: paleoTS
Maintainer: David Bapst
Description: Analyzes, time-scales and simulates phylogenies of extinct/fossil lineages. Also plots diversity curves for stratigraphic range data and phylogenies, including combinations of the those two data types.
License: GPL (>= 2)
URL: http://home.uchicago.edu/~dwbapst/
Packaged: 2012-01-26 16:37:56 UTC; dwbapst_2
Repository: CRAN
Date/Publication: 2012-01-27 11:09:16

More information about paleotree at CRAN

January 27, 2012 11:16 AM

New package GWAtoolbox with initial version 2.0.1

Package: GWAtoolbox
Version: 2.0.1
Date: 2012-01-25
Title: GWAS Quality Control
Author: Daniel Taliun , Christian Fuchsberger , Cristian Pattaro
Maintainer: Daniel Taliun , Christian Fuchsberger
Description: Controls for duplicated IDs, distribution of betas, SEs, etc.
Depends: R (>= 2.13.1)
Suggests: snow
SystemRequirements: GNU GSL
License: GPL (>= 3)
Repository: CRAN
Repository/R-Forge/Project: gwatoolbox
Repository/R-Forge/Revision: 64
Date/Publication: 2012-01-27 11:45:23
Packaged: 2012-01-26 10:55:45 UTC; rforge

More information about GWAtoolbox at CRAN

January 27, 2012 11:16 AM

New package Ace with initial version 0.0.8

Package: Ace
Version: 0.0.8
Date: 2012-01-26
Title: Assay-based Cross-sectional Estimation of incidence rates
Author: Brian Claggett , Weiliang Qiu , Rui Wang
Maintainer: Brian Claggett
Depends: R (>= 2.9.0), stats
Description: The package contains functions for estimating incidence rate from assay-based cross-sectional studies
License: GPL (>= 2)
Packaged: 2012-01-26 22:53:16 UTC; stwxq
Repository: CRAN
Date/Publication: 2012-01-27 11:30:10

More information about Ace at CRAN

January 27, 2012 11:16 AM

January 26, 2012

Revolutions

Statistics: one of the cool kids

As I've mentioned before, I've always found it a little awkward to introduce myself as a Statistician -- it's not exactly the greatest conversation-generator at cocktail parties (or it just turns conversation to baseball, especially post-Moneyball). So it's nice to see that this is changing, as one of my heroes in Statistics relates:

“Most of my life I went to parties and heard a little groan when people heard what I did,” says Robert Tibshirani, a statistics professor at Stanford University. “Now they’re all excited to meet me.”

I've wholeheartedly embraced "data scientist" as a term because, frankly, it's had more sex appeal than "statistician". Good to see this is changing, and now maybe I can  be an out-and-proud Statistician.

NYT Bits Blog: What Are the Odds That Stats Would Be This Popular?

 

by David Smith at January 26, 2012 09:44 PM

Announcing the winners of the Applications of R in Business contest

It's with great pleasure that the team at Revolution Analytics announces the winners of the inaugural "Applications of R in Business" contest:

Grand Prize ($10,000): Shannon Terry and Ben Ogorek, Nationwide Insurance for 'A Direct Marketing In-flight Forecasting System'

Runner Up Prize ($5,000): Jeffrey Breen, Atmosphere Research Group for 'Mining Twitter for Airline Consumer Sentiment'

Congratulations to both winners, who were selected by a judging panel of industry experts, analysts, and R users. (The competition was also very close: there was only a coupe of points in the judges' aggregate scores separating the top two entries.) 

In addition, the following applications were selected for $1,000 Honorable Mention prizes by Revolution Analytics:

You can learn more about all of the winning applications in the slideshow on the Applications of R in Business Contest Winners page, in the press release and in the reports in Read Write Web, Enterprise Apps Today and Information Management.

Thanks to everyone who participated in the contest. A special mention is due to Shannon Terry and Ben Ogorek, both from Customer Analytics within Nationwide Insurance. They have been gracious enough to donate both their grand prize and honorable mention prizes to charity Mid-Ohio Foodbank, a 501(c)(3) organization based in Columbus, OH and a close community partner with Nationwide Insurance, will receive $11,000 to support their efforts in hunger relief. What a wonderful contribution!

Revolution Analytics: Applications of R in Business Contest: 2012 Winners 

by David Smith at January 26, 2012 12:22 AM

January 25, 2012

CRANberries

New package Rquake with initial version 1.2-2

Package: Rquake
Type: Package
Title: Seismic Hypocenter Determination
Version: 1.2-2
Date: 2012-01-02
Depends: R (>= 2.12), RPMG, RSEIS,GEOmap, RFOC, minpack.lm, cluster
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
Description: Rquake is a package for analaysis of seismic data collected continuously, or in trigger mode. The functions organize other functions from RSEIS and GEOmap to help researchers pick, locate, and store hypocenters for detailed seismic investigation.
License: GPL
Packaged: 2012-01-25 14:45:16 UTC; lees
Repository: CRAN
Date/Publication: 2012-01-25 19:56:41

More information about Rquake at CRAN

January 25, 2012 08:16 PM

Removed CRANberries

Package parDEoptim (with last version 0.1) was removed from CRAN

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

2012-01-23 0.1

January 25, 2012 02:16 PM

Journal of Statistical Software

A Multi-Language Computing Environment for Literate Programming and Reproducible Research

Vol. 46, Issue 3, Jan 2012

Abstract:

We present a new computing environment for authoring mixed natural and computer language documents. In this environment a single hierarchically-organized plain text source file may contain a variety of elements such as code in arbitrary programming languages, raw data, links to external resources, project management data, working notes, and text for publication. Code fragments may be executed in situ with graphical, numerical and textual output captured or linked in the file. Export to LATEX, HTML, LATEX beamer, DocBook and other formats permits working reports, presentations and manuscripts for publication to be generated from the file. In addition, functioning pure code files can be automatically extracted from the file. This environment is implemented as an extension to the Emacs text editor and provides a rich set of features for authoring both prose and code, as well as sophisticated project management capabilities.

by Thomas Dye, Dan Davison, Eric Schulte, Carsten Dominik at January 25, 2012 08:00 AM

BIEMS: A Fortran 90 Program for Calculating Bayes Factors for Inequality and Equality Constrained Models

Vol. 46, Issue 2, Jan 2012

Abstract:

This paper discusses a Fortran 90 program referred to as BIEMS (Bayesian inequality and equality constrained model selection) that can be used for calculating Bayes factors of multivariate normal linear models with equality and/or inequality constraints between the model parameters versus a model containing no constraints, which is referred to as the unconstrained model. The prior that is used under the unconstrained model is the conjugate expected-constrained posterior prior and the prior under the constrained model is proportional to the unconstrained prior truncated in the constrained space. This results in Bayes factors that appropriately balance between model fit and complexity for a broad class of constrained models. When the set of equality and/or inequality constraints in the model represents a hypothesis that applied researchers have in, for instance, (M)AN(C)OVA, (multivariate) regression, or repeated measurements, the obtained Bayes factor can be used to determine how much evidence is provided by the data in favor of the hypothesis in comparison to the unconstrained model. If several hypotheses are under investigation, the Bayes factors between the constrained models can be calculated using the obtained Bayes factors from BIEMS. Furthermore, posterior model probabilities of constrained models are provided which allows the user to compare the models directly with each other.

by Herbert Hoijtink, Joris Mulder, Christiaan de Leeuw at January 25, 2012 08:00 AM

Interactive and Animated Scalable Vector Graphics and R Data Displays

Vol. 46, Issue 1, Jan 2012

Abstract:

We describe an approach to creating interactive and animated graphical displays using R’s graphics engine and Scalable Vector Graphics, an XML vocabulary for describing two-dimensional graphical displays. We use the svg() graphics device inR and then post-process the resulting XML documents. The post-processing identifies the elements in the SVG that correspond to the different components of the graphical display, e.g., points, axes, labels, lines. One can then annotate these elements to add interactivity and animation effects. One can also use JavaScript to provide dynamic interactive effects to the plot, enabling rich user interactions and compelling visualizations. The resulting SVG documents can be embedded within HTML documents and can involve JavaScript code that integrates the SVG and HTML objects. The functionality is provided via the SVGAnnotation package and makes static plots generated viaR graphics functions available as stand-alone, interactive and animated plots for the Web and other venues.

by Duncan Temple Lang, Deborah Nolan at January 25, 2012 08:00 AM

Analysis of Questionnaire Data with R

Vol. 46, Book Review 1, Jan 2012

Analysis of Questionnaire Data with R
Bruno Falissard
Chapman & Hall/CRC, 2012
ISBN: 978-1-4398-1766-7

by Ronald D. Fricker at January 25, 2012 08:00 AM

Modern Toolmaking

My first R package: parallel differential evolution

UPDATE: a better parallel algorythm will be included in a future version of DEoptim, so I've removed my package from CRAN.  You can still use the code from this post, but keep Josh's comments in mind.


Last night I was working on a difficult optimization problems, using the wonderful DEoptim package for R. Unfortunately, the optimization was taking a long time, so I thought I'd speed it up using a foreach loop, which resulted in the following function:


Here's what's going on: I divide the bounds for each parameter into n segments, and use a foreach loop to run DEoptim on each segment, collect the results of the loop, and then return the optimization results for the segment with the lowest value of the objective function.  Additionally, I defined a "parDEoptim" class to make it easier to combine the results during the foreach loop.  All of the work is still being done by the DEoptim algorithm.  All I've done is split up the problem into several chunks.

Here is an example, straight out of the DEoptim documentation:


In theory, on a 20-core machine, this should run a bit faster than the serial example.  Note that you may need to set itermax for the parallel run at a higher value than (itermax for the serial run)/(number of segments), as you want to make sure the algorithm can find the minimum of each segment.  Also note that, in this example, there are 20 segments on the interval c(-10,-10) to c(10,10), which means that 2 of the segments have boundaries at c(1,1), which is the global minimum of the function.  The DEoptim algorithm has no trouble finding a solution at the boundary of the parameter space, which is why it's so easy to parallelize.

Rumor has it that the next version of DEoptim will include foreach parallelization, but if you can't wait until then, I rolled up the above function into an R package and posted it to CRAN.  Let me know what you think!


by Zach Mayer (noreply@blogger.com) at January 25, 2012 06:27 AM

January 24, 2012

Revolutions

BBBT Podcast with David Smith

Last Friday I was fortunate enough to have the opportunity to travel to Boulder, CO and present R and Revolution Analytics to about 20 analysts as part of the Boulder BI Brain Trust (BBBT). It was a great pleasure to describe the vision for Revolution R Enterprise and got some great feedback from the particpants.

During the event, I had a great 10-minute conversation with BBBT president and founder Claudia Imhoff about the R project, how Revolution R Enterprise is used, and the future of Revolution Analytics. The podcast is now live on the web, and you can listen to it at the link below.

BBBT Podcasts: Revolution Analytics 

by David Smith at January 24, 2012 07:36 PM

CRANberries

New package OneHandClapping with initial version 1.0

Package: OneHandClapping
Type: Package
Title: Prediction of condition-specific transcription factor interactions
Version: 1.0
Date: 2012-01-17
Author: Sebastian DĂźmcke
Maintainer: Sebastian DĂźmcke
Encoding: UTF-8
Description: Predictions of condition-specific TF interactions using gene activity data, such as mRNA expression measurements and a TF-target graph.
License: GPL (>= 2)
Imports: methods, graphics
Packaged: 2012-01-24 17:30:28 UTC; duemcke
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2012-01-24 18:13:06

More information about OneHandClapping at CRAN

January 24, 2012 05:16 PM

New package occ with initial version 1.0

Package: occ
Type: Package
Title: Estimates PET neuroreceptor occupancies
Version: 1.0
Date: 2012-01-24
Author: Joaquim Radua
Maintainer: Joaquim Radua
Description: This package provides a generic function for estimating positron emission tomography (PET) neuroreceptor occupancies from the total volumes of distribution of a set of regions of interest. Fittings methods include the simple 'reference region' and 'ordinary least squares' (sometimes known as occupancy plot) methods, as well as the more efficient 'restricted maximum likelihood estimation'.
License: GPL
LazyLoad: yes
Packaged: 2012-01-24 15:58:16 UTC; quim
Repository: CRAN
Date/Publication: 2012-01-24 16:52:50

More information about occ at CRAN

January 24, 2012 05:16 PM

New package oc with initial version 0.93

Package: oc
Version: 0.93
Date: 2012-01-24
Title: OC Roll Call Analysis Software.
Author: Keith Poole , Jeffrey Lewis , James Lo and Royce Carroll
Maintainer: James Lo
Depends: R (>= 2.3.1), pscl (>= 0.59)
Description: Estimates Optimal Classification scores from roll call votes supplied though a 'rollcall' object from package 'pscl'.
License: GPL-2
Repository: CRAN
Date/Publication: 2012-01-24 16:52:48
Packaged: 2012-01-24 14:37:08 UTC; jalo

More information about oc at CRAN

January 24, 2012 05:16 PM

New package psgp with initial version 0.3-0

Package: psgp
Version: 0.3-0
Date: 2012-01-23
Title: Projected Spatial Gaussian Process (psgp) methods
Author: Ben Ingram , Remi Barillec
Maintainer: Remi Barillec
Depends: intamap, Rcpp (>= 0.8.0), RcppArmadillo (>= 0.2.0), doSNOW
LinkingTo: Rcpp, RcppArmadillo
Description: Implements projected sparse Gaussian process kriging for the intamap package
License: GPL (>= 2)
Repository: CRAN
Date/Publication: 2012-01-24 06:50:19
Packaged: 2012-01-23 22:28:13 UTC; barillrl

More information about psgp at CRAN

January 24, 2012 08:16 AM

New package CALINE3 with initial version 1.0

Package: CALINE3
Type: Package
Title: R interface to Fortran 77 implementation of CALINE3
Version: 1.0
Date: 2012-01-22
Author: David Holstius
Maintainer: David Holstius
Description: Used by Rcaline
License: file LICENSE
Collate: 'CALINE3-package.R' 'libcaline3.R'
Packaged: 2012-01-24 02:34:41 UTC; holstius
Repository: CRAN
Date/Publication: 2012-01-24 06:50:14

More information about CALINE3 at CRAN

January 24, 2012 08:16 AM

Removed CRANberries

Package CoCoGraph (with last version 0.1.7.6) was removed from CRAN

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

2010-03-19 0.1.7.6

January 24, 2012 08:16 AM

Package CoCoCg (with last version 0.1.7.6) was removed from CRAN

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

2010-03-19 0.1.7.6

January 24, 2012 08:16 AM

Package gmvalid (with last version 1.22) was removed from CRAN

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

2010-04-13 1.22
2009-11-03 1.21
2008-12-21 1.2
2008-07-28 1.1
2007-11-08 1.0

January 24, 2012 08:16 AM

Package CoCo (with last version 0.1.7.6) was removed from CRAN

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

2010-03-19 0.1.7.6
2009-04-04 0.1.7.5
2007-11-03 0.1.7.4
2007-10-15 0.1.7.3
2007-10-10 0.1.7.2
2006-04-20 0.1.6.8

January 24, 2012 08:16 AM

January 23, 2012

CRANberries

New package SPIn with initial version 1.0

Package: SPIn
Type: Package
Title: Optimal Shortest Probability Intervals
Version: 1.0
Date: 2011-12-30
Author: Ying Liu
Maintainer: Ying Liu
Depends: R (>= 1.8.0), quadprog
Description: Adopt an optimal weighting strategy to compute better shortest probability intervals (SPIns).
License: GPL (>= 2)
Packaged: 2012-01-23 19:42:38 UTC; Ying
Repository: CRAN
Date/Publication: 2012-01-23 20:13:43

More information about SPIn at CRAN

January 23, 2012 08:16 PM

Revolutions

New R User Group in Belgium

RBelgium is the latest local R user group to join the R community. Led by R user Jean-Baptiste Poullet, the group will host meetings on the first Friday of each month at the Alfot Hotel in Brussels, as well as weekly coffee get-togethers. The group also provides an on-line discussion forum on statistics and applications with R. 

You can find more information and join the group at MeetUp site linked below.

MeetUp: RBelgium

by David Smith at January 23, 2012 07:33 PM

CRANberries

New package sitools with initial version 1.2

Package: sitools
Type: Package
Title: Format a number to a string with SI prefix
Version: 1.2
Date: 2012-01-23
Author: Jonas Stein, Ben Tupper
Maintainer: Jonas Stein
Description: Format a number (or a list of numbers) to a string (or a list of strings) with SI prefix. Use SI prefixes as constants like (4 * milli)^2
License: GPL-3
LazyLoad: yes
LazyData: yes
Packaged: 2012-01-23 01:24:49 UTC; stein
Repository: CRAN
Date/Publication: 2012-01-23 07:38:52

More information about sitools at CRAN

January 23, 2012 08:16 AM

New package parDEoptim with initial version 0.1

Package: parDEoptim
Type: Package
Title: Parallel Differential Evolution
Version: 0.1
Date: 2012-01-22
Author: Zach Mayer
Maintainer:
Depends: R (>= 1.14.0), methods, DEoptim, foreach, iterators (>= 1.0.0), codetools, utils
Description: Parallel Differential Evolution
License: GPL (>= 2)
Packaged: 2012-01-23 04:56:15 UTC; zachmayer
Repository: CRAN
Date/Publication: 2012-01-23 07:38:46

More information about parDEoptim at CRAN

January 23, 2012 08:16 AM

January 22, 2012

Removed CRANberries

Package bild (with last version 1.0) was removed from CRAN

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

2010-06-06 1.0

January 22, 2012 05:16 PM

CRANberries

New package SEER2R with initial version 1.0

Package: SEER2R
Type: Package
Title: reading and writing SEER*STAT data files
Version: 1.0
Date: 2011-09-28
Author: Jun Luo
Maintainer: Jun Luo
Description: read and write SEER*STAT data files
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2012-01-22 01:38:21 UTC; junluo
Repository: CRAN
Date/Publication: 2012-01-22 07:58:41

More information about SEER2R at CRAN

January 22, 2012 08:16 AM

New package pmc with initial version 0.0-4

Package: pmc
Type: Package
Title: Phylogenetic Monte Carlo
Version: 0.0-4
Author: Carl Boettiger
Maintainer: Carl Boettiger
Description: Monte Carlo based model choice for applied phylogenetics of continuous traits
URL: http://www.carlboettiger.info
License: BSD
Imports: ape, geiger, reshape, snowfall, TreeSim, methods, ouch
Depends: ggplot2, ouch
Collate: 'format_data.R' 'pmc.R' 'powercurve.R' 'wrappers_geiger.R' 'wrappers_laser.R' 'wrappers_ouch.R' 'wrappers_treepar.R' 'convert.R' 'treepalette.R' 'generics.R' 'data_documentation.R' 'maticce.R'
Packaged: 2012-01-21 18:30:46 UTC; cboettig
Repository: CRAN
Date/Publication: 2012-01-22 08:02:42

More information about pmc at CRAN

January 22, 2012 08:16 AM

January 20, 2012

CRANberries

New package scam with initial version 1.0

Package: scam
Type: Package
Title: Shape constrained additive models
Version: 1.0
Date: 2012-17-01
Author: Natalya Pya
Maintainer: Natalya Pya
Description: Routines for generalized additive modelling under shape constraints on the component functions of the linear predictor. Models can contain multiple shape constrained (univariate and/or bivariate) and unconstrained terms. The routines of mgcv(gam) package are used for setting up the model matrix, printing and plotting the results. Penalized likelihood maximization based on Newton-Raphson method to fit a model with multiple smoothing parameter selection by GCV or UBRE/AIC.
Depends: R (>= 2.3.0)
Imports: mgcv, graphics, stats
Suggests: mgcv, splines, Matrix
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2012-01-20 11:01:08 UTC; natalya
Repository: CRAN
Date/Publication: 2012-01-20 15:18:49

More information about scam at CRAN

January 20, 2012 05:16 PM

Revolutions

Because it's Friday: Movie stars sing 'Hello'

This is just wonderful:

From the description, I'd assumed that the movie clips would be autotuned to the song, but that appears not to be the case. Matthijs Vlot spent a lot of time finding lines of (approximately) the right pitch here. I predict many other songs will follow in this vein.

Have a great weekend!

Vimeo: Hello from ant1mat3rie  

 

by David Smith at January 20, 2012 02:32 PM

Hadley Wickham goes behind the scenes on ggplot2

Hadley Wickham, creator of the ggplot2 packages for R (as well as several others) will present a webinar on February 8 going behind the scenes of the popular graphics package. If you've never used ggplot2 before, this will be a great way to learn about the kinds of charts you can create with it; and if you're a regular ggplot2 user Hadley will give a preview of some of the new big-data visualizations coming soon to the package. Here's the webinar overview:

Date: Wednesday, February 8, 2012
Time: 11:00AM - 12:00PM Pacific Time (Click here for time in your local time zone)
Presenter: Hadley Wickham, Professor of Statistics, Rice University
 

Register Now

GGplot2 is one of R’s most popular, widely used packages, developed by Rice University’s Hadley Wickham. Ggplot2’s exploratory graphics capabilities are driving the use of R as a complement to legacy analytics tools such as SAS. SAS is well-regarded for its strength in data management and "production" statistics, where you know what you want to do and need to do it repeatedly. On the other hand, R is strong in data analysis and exploration in situations where figuring out what is needed is the biggest challenge. In this important way, SAS and R are strong companions.

This webinar will provide an all-access pass to Hadley’s latest work. He’ll discuss:

  • A brief overview of ggplot2, and how it's different to other plotting systems
  • A sneak peek at some of the new features coming to the next version of ggplot2
  • What’s been learned about good development practices in the 5 years since first starting to develop ggplot
  • Some of the internals of ggplot2, and talk about how he is gradually making it easier for others to contribute

Join this webinar to understand how ggplot2 adds valuable, unmatched capabilities to your analytics toolbox. 

To register for this webinar, follow the link below.

Revolution Analytics webinars: A backstage tour of ggplot2 with Hadley Wickham

by David Smith at January 20, 2012 02:27 PM

Removed CRANberries

Package marelacTeaching (with last version 1.1) was removed from CRAN

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

2009-11-19 1.1
2009-09-07 1.0

January 20, 2012 08:16 AM

Package Animal (with last version 1.02) was removed from CRAN

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

2009-04-03 1.02
2009-03-28 1.01
2009-03-18 1.0

January 20, 2012 08:16 AM

Package nonrandom (with last version 1.1) was removed from CRAN

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

2011-01-10 1.1
2009-12-01 1.0

January 20, 2012 08:16 AM

Package psgp (with last version 0.2-11) was removed from CRAN

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

2010-06-17 0.2-11
2010-01-21 0.2-10
2009-10-26 0.2-8
2009-09-29 0.2-7

January 20, 2012 08:16 AM

Package varcompci (with last version 1.0) was removed from CRAN

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

2011-02-14 1.0

January 20, 2012 08:16 AM

Package svcR (with last version 1.6.5.1) was removed from CRAN

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

2011-02-11 1.6.5.1
2010-08-04 1.6.5
2010-05-03 1.6.4
2009-12-21 1.6.3
2009-09-12 1.6.2
2009-09-10 1.6.1
2009-05-06 1.4.2
2008-07-14 1.4.1
2008-05-27 1.4
2007-06-20 1.3

January 20, 2012 08:16 AM

Package mirf (with last version 1.0) was removed from CRAN

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

2008-09-10 1.0

January 20, 2012 08:16 AM

Package FactoClass (with last version 1.0.7) was removed from CRAN

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

2011-05-17 1.0.7
2011-05-16 1.0.6
2010-11-06 1.0.5
2010-07-30 1.0.4
2009-11-26 1.0.3
2009-07-21 1.0.1
2009-05-06 0.7.7
2008-11-19 0.7.6
2008-11-06 0.7.5

January 20, 2012 08:16 AM

Package GWAtoolbox (with last version 2.0.0) was removed from CRAN

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

2011-11-22 2.0.0
2011-06-19 1.1.0

January 20, 2012 08:16 AM

Package marelac (with last version 2.1) was removed from CRAN

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

2010-04-06 2.1
2009-09-07 2.0
2009-02-23 1.2-1
2008-11-04 1.2
2008-10-16 1.1

January 20, 2012 08:16 AM

January 19, 2012

Revolutions

Visualize your Facebook friends network with R

A few days ago, Romain François explained how to interface with the Facebook Graph API explorer with R. This was a low-level interface, giving the R programmer the ability to the raw data that Facebook can provide about your connections. Now, just four days later, the first application in R (that I know of) based on the Facebook Graph API has been published.

 describes how to use R to visualize your Facebook friends as an interconnected graph. Petr uses Romain's facebook function to download the friends list via the API, and then constructs the friendship graph using the Rgraphviz package. To enhance the presentation, Petr goes one step further and downloads his friend's profile pictures (again, using the Facebook API and the download.file function), and uses the addlogo function (from the pixmap package) to decorate the nodes of the graph with faces. Here's the final result:

Facebook

To find the R code to create a chart like this for your own Facebook friend network, follow the link to Petr's blog below.

Apply R: Mining Facebook Data: Most "Liked" Status and Friendship Network (via)

by David Smith at January 19, 2012 04:52 PM

January 18, 2012

Revolutions

RInside updated

The RInside package provides C++ classes that make it easier to embed R in C++ code on many platforms. According to a post from package co-maintainer Dirk Eddelbuettel, the package has just been updated to version 0.2.6 with improved support on Windows, and compatibility with R's standard random number generator. You can download the latest version from CRAN or from the RInside homepage.

Thinking inside the box: RInside 0.2.6

by David Smith at January 18, 2012 10:23 PM

CRANberries

New package XMLSchema with initial version 0.6-1

Package: XMLSchema
Version: 0.6-1
Title: R facilities to read XML schema
Author: Duncan Temple Lang
Depends: R (>= 1.5.0), methods, XML
Suggests: RCurl
Maintainer: Duncan Temple Lang
Description: A package that reads XML schema into an R representation and can perform some operations on the resulting information to generate class definitions and code to read documents using this schema. This is code that was originally in the SSOAP package for reading WSDL files that describe Web Services and use XML schema.
LazyLoad: yes
Imports: RCurl, codetools
License: GPL-2
Collate: ClassDefs.S processSchemaTypes.R SOAPTypes.S resolve.R genCode.R parseSchema.R createConverters.R schema.R array.S basicTypes.R utils.R selfRefs.R enums.R restriction.R makeSchemaCollection.R gatherNamespaceDefs.R targetNamespace.R fixTypeNames.R serialize.R toXML.R dependencies.R validity.R
URL: http://www.omegahat.org/XMLSchema, http://www.omegahat.org http://www.omegahat.org/bugs
Packaged: 2012-01-04 21:02:55 UTC; duncan
Repository: CRAN
Date/Publication: 2012-01-18 20:24:10

More information about XMLSchema at CRAN

January 18, 2012 08:17 PM

New package SSOAP with initial version 0.9-0

Package: SSOAP
Version: 0.9-0
Date: 2012/01/12
Title: Client-side SOAP access for S
Author: Duncan Temple Lang
Depends: R (>= 1.5.0), methods
Imports: XML, RCurl, XMLSchema
Maintainer: Duncan Temple Lang
Description: A package that provides a client interface to SOAP (Simple Object Access Protocol) servers from within R.
LazyLoad: yes
License: GPL-2
Collate: ClassDefns.R fault.S http.S parseSOAP.S print.S RPC.R SOAP.S SOAPServer.S zSOAP.S duration.S nativeWrite.R functionAccessors.R writeGeneratedCode.R wsdlProcess.R utils.R toSOAP.R httpGet.R wsse.R
Note: There is an opportunity to do a lot of optimization in the machine generated code to reduce the processing time. This is a simple approach that "works" with little regard for optimization.
URL: http://www.omegahat.org/SSOAP, http://www.omegahat.org http://www.omegahat.org/bugs
Repository: CRAN
Date/Publication: 2012-01-18 20:24:08

More information about SSOAP at CRAN

January 18, 2012 08:16 PM

New package bams with initial version 1.0

Package: bams
Maintainer: Toby Dylan Hocking
Author: Toby Dylan Hocking
Version: 1.0
License: GPL-3
Title: Breakpoint annotation model smoothing
Description: Data and code to allow reproduction of "Learning smoothing models with breakpoint annotations."
Suggests: GLAD, DNAcopy, xtable, cghFLasso, flsa, cghseg, plyr, ggplot2, RColorBrewer, reshape2, lattice
Depends: R (>= 2.10)
Packaged: 2012-01-18 10:56:14 UTC; hocking
Repository: CRAN
Date/Publication: 2012-01-18 12:52:01

More information about bams at CRAN

January 18, 2012 02:16 PM

New package RMendeley with initial version 0.1-1

Package: RMendeley
Description: A programmatic interface to the Web Service methods provided by the Mendeley open science project.
Title: Interface to Mendeley API methods
Version: 0.1-1
License: BSD
Author: Carl Boettiger, Duncan Temple Lang
Maintainer: Carl Boettiger
Imports: RJSONIO, RCurl (>= 1.6)
Collate: 'authored.R' 'authors.R' 'categories.R' 'details.R' 'groups.R' 'papers.R' 'public_groups_details.R' 'public_groups_documents.R' 'public_groups_overview.R' 'public_groups_people.R' 'publications.R' 'related.R' 'search.R' 'subcategories.R' 'tagged.R' 'tags.R' 'utilities.R'
Packaged: 2012-01-17 21:00:39 UTC; cboettig
Repository: CRAN
Date/Publication: 2012-01-18 06:51:55

More information about RMendeley at CRAN

January 18, 2012 08:16 AM

January 17, 2012

Revolutions

NYT uses R to map the 1%

Last Saturday, the New York Times published a feature article on the wealthiest 1% of Americans. The on-line version of the article included interactive features like this interactive map showing where your household ranks in the country and in local regions. The print edition, however, included some different (and necessarily static) representations of US wealth data, such as this map of where the wealthiest 1% live:

NYT-1-percent-map

(Image credit: New York Times, January 14 2002.)

Kevin Quealy, graphics editor at the New York Times, used R to help create this chart. The process began with an initial proof of concept, which used R's maptools package and required five lines of R code. 

Nyt-one-percent-POC

The original plan was to use ArcMap to generate the chart, but ArcView lacks the flexibility of styling the output that R has. Later iterations added color and algorithmically moved the labels around for legibility, and some final tweaking outside of R led to the chart in the print edition.

Interestingly, the chart doesn't appear in the on-line edition of the NYT. I knew that some features like interactive charts, were online only, but I wasn't aware that the reverse was also true, and that special content was made only for the print edition. Quealy points out that this is a necessity:

This is a good example, I think, of using each medium to its best potential, meeting the design constraints of each. More and more, this means making totally separate versions of things – admittedly, it frequently takes twice the time and energy – but the mediums are just so different that works well in one just doesn’t work well in another. 

For the full story of how this lovely chart was created, check out Kevin Quealy's tubmlr linked below.

chartsnthings: Before, During and After: The Richest 1 Percent

by David Smith at January 17, 2012 05:24 PM