Planet R

July 03, 2009

R Wiki

packages:r-forge:jeditr - error handling

This page discusses development of the jeditr package. The package intends to support embedding of R within jedit. Error Handling For now, until we get some useful error manager, there is the ExceptionManager class, to which we can send exceptio...

by Romain Francois (francoisromain@free.fr) at July 03, 2009 10:23 PM

CRANberries

Package BiodiversityR updated to version 1.3 with previous version 1.2 dated 2008-05-13

Author: Roeland Kindt
Title: GUI for biodiversity and community ecology analysis
Description: This package provides a GUI (Graphical User Interface, via the R-Commander) and some utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website.

Diff between BiodiversityR versions 1.2 dated 2008-05-13 and 1.3 dated 2009-07-03

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More information about BiodiversityR at CRAN

July 03, 2009 04:16 PM

Package tcltk2 updated to version 1.1-0 with previous version 1.0-9 dated 2009-06-28

Author: Philippe Grosjean
Title: Tcl/Tk Additions
Description: A series of additional Tcl commands and Tk widgets with style and various functions (under Windows: DDE exchange, access to the registry and icon manipulation) to supplement the tcltk package.

Diff between tcltk2 versions 1.0-9 dated 2009-06-28 and 1.1-0 dated 2009-07-03

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More information about tcltk2 at CRAN

July 03, 2009 10:16 AM

Package sgeostat updated to version 1.0-22 with previous version 1.0-21 dated 2007-04-11

Author: S original by James J. Majure Iowa State University, R port + extensions by Albrecht Gebhardt
Title: An Object-oriented Framework for Geostatistical Modeling in S+
Description: An Object-oriented Framework for Geostatistical Modeling in S+

Diff between sgeostat versions 1.0-21 dated 2007-04-11 and 1.0-22 dated 2009-07-03

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More information about sgeostat at CRAN

July 03, 2009 10:16 AM

Package picante updated to version 0.7-1 with previous version 0.7-0 dated 2009-05-24

Author: Steven Kembel , David Ackerly , Simon Blomberg , Peter Cowan , Matthew Helmus , Helene Morlon , Campbell Webb
Title: R tools for integrating phylogenies and ecology
Description: Phylocom integration, community analyses, null-models, traits and evolution in R

Diff between picante versions 0.7-0 dated 2009-05-24 and 0.7-1 dated 2009-07-03

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More information about picante at CRAN

July 03, 2009 10:16 AM

Package distrDoc updated to version 2.1.1 with previous version 2.1 dated 2009-04-15

Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla
Title: Documentation for packages distr, distrEx, distrSim, distrTEst
Description: provides documentation in form of a common vignette to packages distr, distrEx, distrMod, distrSim, distrTEst

Diff between distrDoc versions 2.1 dated 2009-04-15 and 2.1.1 dated 2009-07-03

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More information about distrDoc at CRAN

July 03, 2009 10:16 AM

Package distr updated to version 2.1.3 with previous version 2.1.1 dated 2009-06-17

Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla
Title: Object orientated implementation of distributions
Description: Object orientated implementation of distributions

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More information about distr at CRAN

July 03, 2009 10:16 AM

Package Rlabkey updated to version 0.0.8 with previous version 0.0.7 dated 2009-04-01

Author: Valerie Obenchain
Title: Data retrieval from a Labkey database
Description: This package imports data from a labkey database into an R data frame

Diff between Rlabkey versions 0.0.7 dated 2009-04-01 and 0.0.8 dated 2009-07-03

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More information about Rlabkey at CRAN

July 03, 2009 10:16 AM

R Wiki

packages:r-forge:jeditr:eclipse

This page contains a few notes on developping the java part of the jeditr package within eclipse. The java part is all contained in the pkg/jeditr/src directory, with a build.xml file. Although the plugin is build by the default ant target (build)...

by Romain Francois (francoisromain@free.fr) at July 03, 2009 09:40 AM

Romain Francois

RGG#153: stars network

Graham Williams sent me this graph, now item 153 in the graph gallery.

graph_153.png

This plot draws a network but at the nodes we have simple segment plots (and in general we might have any other kind of plot at the nodes). This code constructs a network (from the network package), plots it with the nodes being invisibly plotted (using plot.network from the sna package) and then overlays the segment plots using the star function (with the key being located at a position determined by largest.empty from the Hmisc package.

by romain francois at July 03, 2009 07:26 AM

CRANberries

Package pedigreemm updated to version 0.2-3 with previous version 0.2-2 dated 2009-06-02

Author: Douglas Bates and Ana Ines Vazquez
Title: Pedigree-based mixed-effects models
Description: Fit pedigree-based mixed-effects models.

Diff between pedigreemm versions 0.2-2 dated 2009-06-02 and 0.2-3 dated 2009-07-02

 DESCRIPTION  |    8 ++++----
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More information about pedigreemm at CRAN

July 03, 2009 02:16 AM

Package HTMLUtils updated to version 0.1.3 with previous version 0.1.2 dated 2009-06-08

Author: Markus Loecher, Sense Networks
Title: Facilitates automated HTML report creation
Description: Facilitates automated HTML report creation, in particular framed HTML pages and dynamically sortable tables.

Diff between HTMLUtils versions 0.1.2 dated 2009-06-08 and 0.1.3 dated 2009-07-02

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More information about HTMLUtils at CRAN

July 03, 2009 02:16 AM

July 02, 2009

CRANberries

Package lokern updated to version 1.0-8 with previous version 1.0-7 dated 2009-04-03

Author: Eva Herrmann (F77 & S original); Packaged for R and enhanced by Martin Maechler
Title: Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
Description: Kernel regression smoothing with adaptive local or global plug-in bandwidth selection.

Diff between lokern versions 1.0-7 dated 2009-04-03 and 1.0-8 dated 2009-07-02

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More information about lokern at CRAN

July 02, 2009 10:16 PM

Revolutions

More R at Google

Reader HW noticed this graphic (created by Gmail developers at Google) today on the Google Code blog, with the comment: "Post doesn't mention anything about R, but that's clearly an R boxplot!"

Google R boxplot
Thanks for the tip, HW!


by David Smith at July 02, 2009 09:09 PM

R Wiki

tips:data-frames:merge

— Paul Johnson 2004/04/23, adapted to R Wiki with permission by Nick Drew 2006/02/11 Purpose – Examples showing how to merge data frames. Demonstrate how to use the merge function: Merge two data frames by common columns or row names, ...

by Paul Johnson (pauljohn@ku.edu) at July 02, 2009 08:06 PM

Revolutions

Package Update Roundup: Jun 2009

This is a list of new or updated packages that were released for R in June, as announced on the r-packages mailing list. To include other updates on this list, please email David Smith. For a complete list of all updates on CRAN, see the CRANberries archive for June 2009

deSolve, a package to solve initial value problems of differential equations, has been updated with improved functionality, performance, and documentation.

metafor, a new package for meta-analysis, for has been released.

JM, a package for joint modelling of longitudinal and time-to-event data, has been updated with support for additional models and diagnostics.

plyr, a fast, memory-efficient, and consistent set of tools for processing subsegments of massive data structures, has been updated with bug fixes and improved functionality.

rimage, an image processing module for R, has been updated to work with the latest versions of R. Until a maintainer can be found, this packages is orphaned.

RHIPE, an integration between R and Hadoop for implementing map-reduce algorithms, has been updated. Red Hat 8 AMIs are available to test this functionality on Amazon's EC2 service.

RImageJ, a new package that provides the image processing and analysis tools of ImageJ to R, has been released.

RODBC, a package linking R to databases on Windows and other platforms supporting ODBC, has been updated with bug fixes and improved documentation.

WriteXLS, a package that creates Excel spreadsheets from data frames, has been updated to fix the order in which data frames appear in the spreadsheet and to support encoding schemes.

by David Smith at July 02, 2009 06:26 PM

CRANberries

Package pcse updated to version 1.7 with previous version 1.6 dated 2008-11-16

Author: Delia Bailey and Jonathan N. Katz
Title: Panel-Corrected Standard Error Estimation in R
Description: This package contains a function to estimate panel-corrected standard errors. Data may contain balanced or unbalanced panels.

Diff between pcse versions 1.6 dated 2008-11-16 and 1.7 dated 2009-07-02

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More information about pcse at CRAN

July 02, 2009 06:16 PM

Package Amelia updated to version 1.2-9 with previous version 1.2-2 dated 2009-04-27

Author: James Honaker , Gary King , Matthew Blackwell
Title: Amelia II: A Program for Missing Data
Description: Amelia II "multiply imputes" missing data in a single cross-section (such as a survey), from a time series (like variables collected for each year in a country), or from a time-series-cross-sectional data set (such as collected by years for each of several countries). Amelia II implements our bootstrapping-based algorithm that gives essentially the same answers as the standard IP or EMis approaches, is usually considerably faster than existing approaches and can handle many more variables. Unlike Amelia I and other statistically rigorous imputation software, it virtually never crashes (but please let us know if you find to the contrary!). The program also generalizes existing approaches by allowing for trends in time series across observations within a cross-sectional unit, as well as priors that allow experts to incorporate beliefs they have about the values of missing cells in their data. Amelia II also includes useful diagnostics of the fit of multiple imputation models. The program works from the R command line or via a graphical user interface that does not require users to know R.

Diff between Amelia versions 1.2-2 dated 2009-04-27 and 1.2-9 dated 2009-07-02

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More information about Amelia at CRAN

July 02, 2009 04:16 PM

Package spatstat updated to version 1.16-0 with previous version 1.15-4 dated 2009-06-16

Author: Adrian Baddeley and Rolf Turner , with substantial contributions of code by Marie-Colette van Lieshout, Rasmus Waagepetersen, Kasper Klitgaard Berthelsen and Dominic Schuhmacher. Additional contributions by Ang Qi Wei, C. Beale, B. Biggerstaff, R. Bivand, F. Bonneu, J. Burgos, J.B. Chen, Y.C. Chin, M. de la Cruz, P.J. Diggle, S. Eglen, A. Gault, M. Genton, P. Grabarnik, C. Graf, J. Franklin, U. Hahn, M. Hering, M.B. Hansen, M. Hazelton, J. Heikkinen, K. Hornik, R. Ihaka, R. John-Chandran, D. Johnson, J. Laake, J. Mateu, P. McCullagh, X.C. Mi, J. Moller, L.S. Nielsen, E. Parilov, J. Picka, M. Reiter, B.D. Ripley, B. Rowlingson, J. Rudge, A. Sarkka, K. Schladitz, B.T. Scott, I.-M. Sintorn, M. Spiess, M. Stevenson, P. Surovy, B. Turlach, A. van Burgel, H. Wang and S. Wong.
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Contains functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, and pixel images. Point process models can be fitted to point pattern data. Cluster type models are fitted by the method of minimum contrast. Very general Gibbs point process models can be fitted to point pattern data using a function ppm similar to lm or glm. Models may include dependence on covariates, interpoint interaction and dependence on marks. Fitted models can be simulated automatically. Also provides facilities for formal inference (such as chi-squared tests) and model diagnostics (including simulation envelopes, residuals, residual plots and Q-Q plots).

Diff between spatstat versions 1.15-4 dated 2009-06-16 and 1.16-0 dated 2009-07-02

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More information about spatstat at CRAN

July 02, 2009 02:16 PM

Package Metabonomic updated to version 3.2.1 with previous version 3.2 dated 2009-07-01

Author: Jose L. Izquierdo Instituto de Estudios Biofuncionales(U.C.M.).
Title: GUI for Metabonomic Analysis
Description: Graphical User Interface for the Metabonomic Analysis (Baseline, Normalization, Peak Detection, PCA, PLS, Nearest Neigbourgt, Neural Network) developed to make easy this data analysis.

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More information about Metabonomic at CRAN

July 02, 2009 02:16 PM

Package tlemix updated to version 0.0.6 with previous version 0.0.5 dated 2009-05-06

Author: P. Neytchev, P. Filzmoser, R. Patnaik, A. Eisl and R. Boubela
Title: Trimmed Maximum Likelihood Estimation
Description: TLE implements a general framework for robust fitting of finite mixture models. Parameter estimation is performed using the EM algorithm.

Diff between tlemix versions 0.0.5 dated 2009-05-06 and 0.0.6 dated 2009-07-02

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More information about tlemix at CRAN

July 02, 2009 10:16 AM

Package SweaveListingUtils updated to version 0.3 with previous version 0.2 dated 2009-04-15

Author: Peter Ruckdeschel
Title: Utilities for Sweave together with TeX listings package
Description: provides utilities for defining R / Rd as Tex-package-listings "language" and including R / Rd source file (sniplets) copied from R-forge in its most recent version (or another url) thereby avoiding inconsistencies between vignette and documented source code

Diff between SweaveListingUtils versions 0.2 dated 2009-04-15 and 0.3 dated 2009-07-02

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More information about SweaveListingUtils at CRAN

July 02, 2009 10:16 AM

Package mixtools updated to version 0.4.1 with previous version 0.4.0 dated 2009-04-28

Author: Derek Young Tatiana Benaglia Didier Chauveau Ryan Elmore Tom Hettmansperger David Hunter Hoben Thomas Fengjuan Xuan
Title: Tools for analyzing finite mixture models
Description: A collection of R functions for analyzing finite mixture models. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.

Diff between mixtools versions 0.4.0 dated 2009-04-28 and 0.4.1 dated 2009-07-02

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More information about mixtools at CRAN

July 02, 2009 10:16 AM

New package speff2trial with initial version 1.0.0

Package: speff2trial
Version: 1.0.0
Date: 2009-07-01
Title: Semiparametric efficient estimation for a two-sample treatment effect
Author: Michal Juraska , with contributions from Peter B. Gilbert , Min Zhang , Marie Davidian , Anastasios A. Tsiatis and Xiaomin Lu
Maintainer: Michal Juraska
Depends: R (>= 2.7.2), leaps
Description: The package performs estimation and testing of the treatment effect in a 2-group randomized clinical trial with a quantitative or dichotomous endpoint. The method is a special case of Robins, Rotnitzky, and Zhao (1994, JASA). It improves efficiency by leveraging baseline predictors of the endpoint. The method uses inverse probability weighting to provide unbiased estimation when the endpoint is missing at random.
License: GPL-2
LazyLoad: yes
LazyData: yes
Packaged: Wed Jul 1 13:37:21 2009; mjuraska
Repository: CRAN
Date/Publication: 2009-07-02 06:52:09

More information about speff2trial at CRAN

July 02, 2009 10:16 AM

Package gsubfn updated to version 0.5-0 with previous version 0.3-8 dated 2008-12-15

Author: G. Grothendieck
Title: Utilities for strings and function arguments.
Description: gsubfn is like gsub but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. gsubfn can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions. This can be used with R functions such as apply, sapply, lapply, optim, integrate, xyplot, Filter and any other function that expects another function as an input argument or functions like cat or sql calls that may involve strings where substitution is desirable.

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More information about gsubfn at CRAN

July 02, 2009 10:16 AM

Package gstat updated to version 0.9-61 with previous version 0.9-60 dated 2009-05-15

Author: Edzer J. Pebesma and others
Title: geostatistical modelling, prediction and simulation
Description: variogram modelling; simple, ordinary and universal point or block (co)kriging, sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.

Diff between gstat versions 0.9-60 dated 2009-05-15 and 0.9-61 dated 2009-07-02

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More information about gstat at CRAN

July 02, 2009 10:16 AM

Package gmm updated to version 1.0-7 with previous version 1.0-6 dated 2009-05-12

Author: Pierre Chausse
Title: Generalized Method of Moments and Generalized Empirical Likelihood
Description: It is a complete suite to estimate models based on moment conditions. It includes the two step Generalized method of moments (GMM) of Hansen(1982), the iterated GMM and continuous updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several methods that belong to the Generalized Empirical Likelihood (GEL) family of estimators, as presented by Smith(1997), Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).

Diff between gmm versions 1.0-6 dated 2009-05-12 and 1.0-7 dated 2009-07-02

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July 02, 2009 10:16 AM

Package flexclust updated to version 1.2-1 with previous version 1.2-0 dated 2009-06-19

Author: Friedrich Leisch
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.

Diff between flexclust versions 1.2-0 dated 2009-06-19 and 1.2-1 dated 2009-07-02

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More information about flexclust at CRAN

July 02, 2009 10:16 AM

Chris Lawrence

Blogging beyond my comparative advantage

I really don’t have any particular insight to add to others’ discussion of the sorta-kinda-maybe coup d’état in Honduras, but Steven Taylor (both here and here) and Greg Weeks have had some fairly insightful posts on the matter.

While I’d probably say that many Hondurans’ fears that maybe-ex-President Zelaya was plotting in some way to perpetuate his own rule at the expense of democratic accountability—as both Hugo Chávez and Álvaro Uribe have recently done in the broader region—were possibly justified, employing the military to raid his house and toss him on an airplane in the middle of the night doesn’t exactly strike me as the most measured response by the other branches of government. On the other hand I’ll gladly concede that the Honduran constitution appears to be a giant mess of epic proportions (amendment by decree and the lack of an impeachment mechanism being among its defects) that didn’t exactly help in avoiding an escalation of the situation to the use of extralegal means.

Elsewhere: John Carey (via John Sides) presents some data on extraordinary Latin American presidential replacements since 1990. It almost, but not quite, tempts me to dust off my old paper on stability and presidential government and add some new data, but I think it’s best for all involved if it just stays in Ukrainian, at least until I can find a sucker graduate student interested in collecting the data to update the damn thing to the present.

by Chris Lawrence at July 02, 2009 12:51 AM

July 01, 2009

R Wiki

tips:programming:extend_parameter_matching

Very often I write functions which have a lot parameters for subfunctions I call, for example: createTagCloud <- function (g, fontsize.method="page.rank", fontsize.min=7.5, fontsize.max=20.5, fontsize.transform="log", buildHTML...

by Sigbert Klinke (sigbert@wiwi.hu-berlin.de) at July 01, 2009 07:39 PM

CRANberries

Package tm updated to version 0.4 with previous version 0.3-4.1 dated 2009-05-04

Author: Ingo Feinerer
Title: Text Mining Package
Description: A framework for text mining applications within R.

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More information about tm at CRAN

July 01, 2009 06:18 PM

Package spcosa updated to version 0.1-4 with previous version 0.1-3 dated 2009-05-17

Author: D.J.J. Walvoort, D.J. Brus, and J.J. de Gruijter
Title: Spatial Coverage Sampling
Description: Spatial coverage sampling and random sampling from compact geographical strata created by k-means.

Diff between spcosa versions 0.1-3 dated 2009-05-17 and 0.1-4 dated 2009-07-01

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More information about spcosa at CRAN

July 01, 2009 06:18 PM

Package slam updated to version 0.1-1 with previous version 0.1 dated 2009-06-26

Author: Kurt Hornik, David Meyer, Christian Buchta
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.

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July 01, 2009 06:18 PM

Package seqinr updated to version 2.0-4 with previous version 2.0-3 dated 2009-04-28

Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Include also utilities for sequence data management under the ACNUC system.

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More information about seqinr at CRAN

July 01, 2009 06:18 PM

Package rgrs updated to version 0.2-11 with previous version 0.2-10 dated 2009-06-09

Author: Julien Barnier
Title: Functions to make R usage in social sciences easier (in french)
Description: This package provides functions for beginners and social sciences students or researchers. Currently it includes functions for cross-tabulation, weighting, results export, and maps plotting. The documentation and help pages are written in french.

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July 01, 2009 06:17 PM

Package relations updated to version 0.5-2 with previous version 0.5-1 dated 2009-02-20

Author: Kurt Hornik and David Meyer
Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.

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More information about relations at CRAN

July 01, 2009 06:17 PM

Package qtlbook updated to version 0.17-2 with previous version 0.17-1 dated 2009-04-28

Author: Karl W Broman
Title: Datasets for the R/qtl book
Description: Datasets for the book, A Guide to QTL Mapping with R/qtl

Diff between qtlbook versions 0.17-1 dated 2009-04-28 and 0.17-2 dated 2009-07-01

 DESCRIPTION     |   10 +++++-----
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More information about qtlbook at CRAN

July 01, 2009 06:17 PM

Package qtl updated to version 1.12-26 with previous version 1.11-12 dated 2009-03-29

Author: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Brian Yandell
Title: Tools for analyzing QTL experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.

Diff between qtl versions 1.11-12 dated 2009-03-29 and 1.12-26 dated 2009-07-01

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 179 files changed, 2449 insertions(+), 1463 deletions(-)

More information about qtl at CRAN

July 01, 2009 06:17 PM

Revolutions

In case you missed it: June roundup

In case you missed them, here are some articles from last month of particular interest to R users.

This post announced the release of the "foreach" and "iterators" packages on CRAN, for simple scalable parallel programming in R.

This post linked to Thomas Levin's Joy-Division-esque band T-shirt made with R

This post discussed R's involvement in the Netflix Prize

This post revealed that the New York Times uses R to create graphics, including an interactive chart of Michael Jackson's musical career

This post described how to run batch jobs using R CMD BATCH

This post reviewed "Data Mashups in R", an extended example of corralling foreclosure data from various sources

This post announced a new "statistical learning web service" implemented with R

This post was one of a series of posts looking at fraud in the Iranian election (including a now-famous analysis done in R)

This post linked to a widely-reproduced R graph on gay marriage support

This post linked to free source code of many R graphs on Wikimedia Commons

This post demonstrated animation of R graphics using Flash

This post linked to a comparison of various statistical analyses done in R, SAS and SPSS

This post showed how Twitter users can "tweet" using R code

This post linked to an analysis of basketball plays done in R

This post linked to a video walkthrough and code for bagged decision trees in R

This post gave some tips, tricks and pitfalls on working with dates and time zones in R

This post brought the news that R was used in a winning entry of KDD 2009

Other non-R-specific stories in June covered Simpson's Paradox in polling data, Google Squared, real random numbers, the chances of a meteor bringing down an aircraft, amusing article titles from PubMed, and open-source user interfaces.

June was a record-breaking traffic month for the blog. The "Data Mashups" article and the discussion of the Iranian Election were highly visited. Thanks to everyone who provided comments and tips and
please keep them coming to david@revolution-computing.com.

by David Smith at July 01, 2009 06:16 PM

CRANberries

Package psych updated to version 1.0-75 with previous version 1.0-74 dated 2009-06-26

Author: William Revelle
Title: Procedures for Psychological, Psychometric, and Personality Research
Description: A number of routines for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. For more information, see the personality-project.org/r webpage.

Diff between psych versions 1.0-74 dated 2009-06-26 and 1.0-75 dated 2009-07-01

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More information about psych at CRAN

July 01, 2009 06:16 PM

Package negenes updated to version 0.98-8 with previous version 0.98-7 dated 2007-10-09

Author: Karl W Broman
Title: Estimating the number of essential genes in a genome
Description: Estimating the number of essential genes in a genome on the basis of data from a random transposon mutagenesis experiment, through the use of a Gibbs sampler.

Diff between negenes versions 0.98-7 dated 2007-10-09 and 0.98-8 dated 2009-07-01

 DESCRIPTION     |   14 +++++++++-----
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More information about negenes at CRAN

July 01, 2009 06:16 PM

Package mclust updated to version 3.3.1 with previous version 3.2.1 dated 2009-06-19

Author: Chris Fraley and Adrian Raftery
Title: Model-Based Clustering / Normal Mixture Modeling
Description: Model-based clustering and normal mixture modeling including Bayesian regularization

Diff between mclust versions 3.2.1 dated 2009-06-19 and 3.3.1 dated 2009-07-01

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More information about mclust at CRAN

July 01, 2009 06:16 PM

New package gsDesign with initial version 2.0-5

Package: gsDesign
Version: 2.0-5
Title: Group Sequential Design
Author: Keaven Anderson
Maintainer: Keaven Anderson
Description: gsDesign is a package that derives group sequential designs and describes their properties.
License: GPL (>= 2)
Repository: CRAN
Repository/R-Forge/Project: gsdesign
Repository/R-Forge/Revision: 173
Date/Publication: 2009-07-01 12:03:13
Packaged: 2009-06-29 20:38:34 UTC; rforge

More information about gsDesign at CRAN

July 01, 2009 06:16 PM

Package dtw updated to version 1.13-1 with previous version 1.12-5 dated 2009-01-07

Author: Toni Giorgino ,
Title: Dynamic Time Warping algorithms
Description: Comprehensive implementation of Dynamic Time Warping algorithms in R. DTW finds the optimal (least cumulative distance) mapping between two time series. All common DTW variants are covered, including local and global constraints, arbitrary timeseries lenghts, distance definitions, MVM, etc. Package computes cumulative distance, warping functions, plots, normalizations, etc.

Diff between dtw versions 1.12-5 dated 2009-01-07 and 1.13-1 dated 2009-07-01

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 tests/dtw_test.Rout.save |   25 ++++++++++++++++++-----
 16 files changed, 159 insertions(+), 88 deletions(-)

More information about dtw at CRAN

July 01, 2009 06:16 PM

New package dlnm with initial version 0.1.0

Package: dlnm
Type: Package
Title: Distributed Lag Non-linear Models
Version: 0.1.0
Date: 2009-07-01
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini
Imports: stats, graphics, grDevices, splines, tsModel
Depends: splines, NMMAPSlite
Description: The package dlnm contains functions to specify basis and cross-basis matrices in order to run distributed lag models and their non-linear extension, then to predict and graph the results for a fitted model.
License: GPL (>= 2)
LazyLoad: yes
Packaged: Wed Jul 1 11:40:23 2009; ppehagas
Repository: CRAN
Date/Publication: 2009-07-01 17:19:48

More information about dlnm at CRAN

July 01, 2009 06:16 PM

Package caret updated to version 4.19 with previous version 4.18 dated 2009-06-18

Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer and Allan Engelhardt
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models

Diff between caret versions 4.18 dated 2009-06-18 and 4.19 dated 2009-07-01

 DESCRIPTION                 |    8 
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More information about caret at CRAN

July 01, 2009 06:16 PM

New package bvpSolve with initial version 1.0

Package: bvpSolve
Version: 1.0
Title: Solvers for boundary value problems of ordinary differential equations
Author: Karline Soetaert
Maintainer: Karline Soetaert
Depends: R (>= 2.01), rootSolve, deSolve
Description: Functions that solve boundary value problems (BVP) of systems of ordinary differential equations (ODE). The functions provide an interface to the FORTRAN function twpbvp and an R-implementation of the shooting method.
License: GPL
LazyData: yes
Repository: CRAN
Repository/R-Forge/Project: bvpsolve
Repository/R-Forge/Revision: 27
Date/Publication: 2009-07-01 14:47:11
Packaged: 2009-06-30 20:34:36 UTC; rforge

More information about bvpSolve at CRAN

July 01, 2009 06:16 PM

Package aCGH.Spline updated to version 2.1 with previous version 1.0 dated 2009-06-24

Author: Tomas William Fitzgerald
Title: Robust spline interpolation for dual color array comparative genomic hybridisation data
Description: Spline fitting and interpolation

Diff between aCGH.Spline versions 1.0 dated 2009-06-24 and 2.1 dated 2009-07-01

 DESCRIPTION    |   10 +++++-----
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More information about aCGH.Spline at CRAN

July 01, 2009 06:16 PM

Package QCA updated to version 0.5-4 with previous version 0.5-3 dated 2009-03-28

Author: Adrian Dusa
Title: Qualitative Comparative Analysis
Description: Performs the Quine-McCluskey algorithm for Qualitative Comparative Analysis, as described in Ragin, Charles C. 1987 "The Comparative Method. Moving beyond qualitative and quantitative strategies", Berkeley: University of California Press. In the classical approach it currently handles about 15 conditions and one outcome, but since version 0.4-5 the package has an enhanced, faster function that obtains the same exact solutions with a substantially lower memory consumption, and it handles even more causal conditions. The next versions of this algorithm will be oriented towards multi-value and fuzzy-set functions. Also, in the near future the current functions will deal with missing values in the data

Diff between QCA versions 0.5-3 dated 2009-03-28 and 0.5-4 dated 2009-07-01

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More information about QCA at CRAN

July 01, 2009 06:16 PM

Revolutions

Simple, scalable parallel computing in R

REvolution Computing has just released three new packages for R to CRAN (under the open-source Apache 2.0 license): foreach, iterators, and doMC. Together, they provide a simple, scalable parallel computing framework for R that lets you take advantage of your multicore or multiprocessor workstation to program loops that run faster than traditional loops in R.

The three packages build on each other to implement a new loop construct for R -- foreach -- where iterations may run in parallel on separate cores or processors.

iterators implements the iterator object familiar to users of languages like Java, C# and Python to make it easy to program useful sequences - from all the prime numbers to the columns of a matrix or the rows of an external database. Iterators objects are used as the index variable for the parallel loops.
 
foreach builds on the "iterators" package to introduce a new way of programming loops in R. Unlike the traditional for loop, a foreach loop can run multiple iterations simultaneously, in parallel. If you only have a single-processor machine, foreach runs iterations sequentially. But with a multiprocessor workstation and a connection to a parallel programming backend, multiple iterations of the loop will run in parallel. This means that without any changes to your code, the loop will run faster (and with a speedup scaled by the number of available cores or processors, potentially much faster).
 
doMC provides such a link between "foreach" and a parallel programming backend -- in this case, the multicore package (from Simon Urbanek). With this connection, foreach loops on MacOS and Unix/Linux systems will make use of all the available cores/processors on the local workstation to run iterations in parallel.

The "iterators" and "foreach" packages were previously available only in REvolution R Enterprise as part of the ParallelR suite: now, we've made versions available on CRAN for all R users. 

In REvolution R Enterprise, "iterators" and "foreach" connect with our NetworkSpaces parallel backend (which comes pre-installed and pre-configured in our distribution). Not only does this additionally enable parallel programming on Windows 32-bit and Windows 64-bit systems, it also allows iterations of foreach loops to run on separate machines on a cluster, or in a cloud environment like Amazon EC2. The cluster can even be a mixed collection of Windows, MacOS and/or Unix/Linux machines. REvolution R Enterprise with NetworkSpaces also provides some other benefits, including fault tolerance (so a parallel computation will complete correctly even if some nodes in the cluster fail), and high-performance mathematics libraries to make the computations run even faster.

You can see an example of foreach in action in this financial backtesting example. That example will run as written in REvolution R Enterprise, and in the latest version of R by installing the "multicore" package and replacing the call to registerDoNWS() with registerDoMC(). You'll need the relevant packages installed, which you can do easily in R as follows:

install.packages("foreach")
install.packages("doMC")

I'll be posting more examples using the "foreach" and "iterators" packages in the coming weeks. I'll also be talking about them at UseR! later this month. You can also read more in today's press release. In the meantime, feedback and comments are always welcome to packages@revolution-computing.com.


by David Smith at July 01, 2009 04:39 PM

R makes a T-shirt

Here's a new use for R: designing T-shirts for a band:

The_Probable_Error_of_a_Mean-09b0vt-s

Despite having a cool name, "The Probable Error of a Mean" isn't a real band. Taking inspiration from the title of the 1908 paper where Fisher Student introduced the concept of the t distribution, Thomas Levine used R to design this T-shirt for the Shirt.Woot competition. The typeface is even the same as that used in the original paper!

by David Smith at July 01, 2009 03:52 PM

CRANberries

Package RandomFields updated to version 1.3.40 with previous version 1.3.39 dated 2009-06-29

Author: Martin Schlather
Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields; conditional simulation; kriging

Diff between RandomFields versions 1.3.39 dated 2009-06-29 and 1.3.40 dated 2009-07-01

 DESCRIPTION      |    6 +++---
 src/auxiliary.cc |    6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

More information about RandomFields at CRAN

July 01, 2009 02:19 PM

Package RWeka updated to version 0.3-20 with previous version 0.3-19 dated 2009-06-09

Author: Kurt Hornik, with contributions from Christian Buchta, Torsten Hothorn, Alexandros Karatzoglou, David Meyer, and Achim Zeileis
Title: R/Weka interface
Description: An R interface to Weka (Version 3.6.1). Weka is a collection of machine learning algorithms for data mining tasks written in Java, containing tools for data pre-processing, classification, regression, clustering, association rules, and visualization. Both the R interface and Weka itself are contained in the RWeka package. For more information on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.

Diff between RWeka versions 0.3-19 dated 2009-06-09 and 0.3-20 dated 2009-07-01

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More information about RWeka at CRAN

July 01, 2009 02:17 PM

Package Metabonomic updated to version 3.2 with previous version 3.1.3.3 dated 2009-05-12

Author: Jose L. Izquierdo Instituto de Estudios Biofuncionales(U.C.M.).
Title: GUI for Metabonomic Analysis
Description: Graphical User Interface for the Metabonomic Analysis (Baseline, Normalization, Peak Detection, PCA, PLS, Nearest Neigbourgt, Neural Network) developed to make easy this data analysis.

Diff between Metabonomic versions 3.1.3.3 dated 2009-05-12 and 3.2 dated 2009-07-01

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More information about Metabonomic at CRAN

July 01, 2009 02:17 PM

Package MCMCpack updated to version 1.0-1 with previous version 0.9-6 dated 2009-02-17

Author: Andrew D. Martin , Kevin M. Quinn , Jong Hee Park
Title: Markov chain Monte Carlo (MCMC) Package
Description: This package contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.2. All models return coda mcmc objects that can then be summarized using the coda package. MCMCpack also contains some useful utility functions, including some additional density functions and pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization.

Diff between MCMCpack versions 0.9-6 dated 2009-02-17 and 1.0-1 dated 2009-07-01

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More information about MCMCpack at CRAN

July 01, 2009 02:17 PM

Package JADE updated to version 1.0-3 with previous version 1.0-2 dated 2009-04-22

Author: Klaus Nordhausen, Jean-Francois Cardoso, Hannu Oja, Esa Ollila
Title: JADE and ICA performance criteria
Description: The package ports JF Cardoso's JADE algorithm as well as his function for joint diagonalization. There are also several criteria for performance evaluation of ICA algorithms.

Diff between JADE versions 1.0-2 dated 2009-04-22 and 1.0-3 dated 2009-07-01

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More information about JADE at CRAN

July 01, 2009 02:16 PM

Package DescribeDisplay updated to version 0.2.1 with previous version 0.2.0 dated 2009-05-15

Author: Hadley Wickham , Di Cook , Andreas Buja , Barret Schloerke
Title: R interface to DescribeDisplay (GGobi plugin)
Description: Produce publication quality graphics from output of GGobi's describe display plugin

Diff between DescribeDisplay versions 0.2.0 dated 2009-05-15 and 0.2.1 dated 2009-07-01

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More information about DescribeDisplay at CRAN

July 01, 2009 02:16 PM

June 30, 2009

Chris Lawrence

Professors behaving badly

Via an email correspondent (who seemed to be fishing for some reaction) and Margaret Soltan at University Diaries comes word of a rather sordid bit of misbehavior by a presumably-to-be-soon-if-not-already-former faculty member and administrator (probably more the latter than the former) at Duke University:

A Duke University official has been arrested and charged with offering a 5-year-boy for sex.

Frank Lombard, the school’s associate director of the Center for Health Policy, was arrested after an Internet sting, according to the FBI’s Washington field office and the city’s police department.

If these allegations are true—and I have no reason to believe they are not—it seems to me that Lombard should at the very least rot in jail for a very, very long time.

by Chris Lawrence at June 30, 2009 08:00 PM

Revolutions

How good open-source user interfaces get made

How is it that a company like Apple can produce wonderful user interfaces, but open-source UIs are generally, well, substandard? Matthew Thomas suggested back in 2002 that too many cooks can spoil the broth:

Every contributor to the [open-source] project tries to take part in the interface design, regardless of how little they know about the subject. And once you have more than one designer, you get inconsistency, both in vision and in detail. The quality of an interface design is inversely proportional to the number of designers.

The solution? According to Matt Asay, the key is to get a commercial company involved. He's seen an upcoming release of Ubuntu from Canonical, Ltd. that may rival MacOS for usability. He says:

You need a little more than open source, it seems, to make products usable. You need control, and control doesn't always jibe well with open-source development. This is one reason that we're seeing the emergence of the Open Core licensing model for open source.

by David Smith at June 30, 2009 04:56 PM

CRANberries

Package tweedie updated to version 1.6.7 with previous version 1.6.6 dated 2009-06-19

Author: Peter K Dunn
Title: Tweedie exponential family models
Description: Maximum likelihood computations for Tweedie families.

Diff between tweedie versions 1.6.6 dated 2009-06-19 and 1.6.7 dated 2009-06-30

 CHANGE.log             |    4 ++++
 DESCRIPTION            |    8 ++++----
 R/tweedie.R            |    2 +-
 man/tweedie-package.Rd |    6 +++---
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 5 files changed, 19 insertions(+), 15 deletions(-)

More information about tweedie at CRAN

June 30, 2009 10:16 AM