John Chambers “Programming with R”

## GUIs I

9:00-9:35 Eun Kyung Lee “arrayMissPattern: Software for Missing Pattern Analysis of Microarray Data”

9:35-10:10 John Verzani “gWidgets: a toolkit independent API for building GUIs in R”

10:10-10:30 Discussion

## Models I

9:00-9:25 D.G. Butler, B.R. Cullis, A.R. Gilmour “Asreml-R: an R package for mixed models using residual maximum likelihood”

9:25-9:50 Kenneth Knoblauch, Laurence T. Maloney “MLDS: Maximum Likelihood Difference Scaling in R”

9:50-10:15 Terry M. Therneau “The survival package: Updates and future directions”

10:15-10:30 Discussion

## Social science and statistics

Chair: Olivia Lau

10:45-11:20 Ben Hansen “Flexible, Optimal Matching for Comparative Studies using the optmatch package”

11:20-11:55 Jasjeet Sekhon “R and the Future of Social Science Data and Methods: NP-hard Problems and Large Datasets”

11:55-12:15 Discussion

## Practical Tools

10:45-11:10 Dirk Eddelbuettel, David Vernazobres, Albrecht Gebhardt, Steffen Moller “apt-get install cran bioc: On automated builds of 1700 R packages for Debian”

11:10-11:35 Adam L. Lyon “Analysis of Experimental Particle Physics Data in R with the RootTreeToR Package”

11:35-12:00 Dirk Eddelbuettel and Robert Brown “RDieHarder: An R interface to the DieHarder suite of Random Number Generator Tests”

## Teaching with R

1:30-1:55 Philip Turk “Experiences using R to teach undergraduate statistics courses”

1:55-2:20 Daniel Kaplan “Using R for Introductory Calculus and Statistics”

2:20-2:45 Amy Froelich and Michael D. Larsen “Using R in undergraduate and graduate probability and mathematical statistics courses”

2:45-3:00 Discussion

## GUIs II

1:30-1:55 Michael Lawrence “RGtk2”

1:55-2:20 Suh-Yeon Choi, Michael Lawrence, Dianne Cook, Heike Hofmann, Lauralynn Kourtz, Kristi Snell, Basil J. Nikolau and Eve Syrkin Wurtele “Metabolomic and transcriptomic data analysis of PHB-producing Arabidopsis using R, exploRase and GGobi”

2:20-2:45 John Verzani “pmg: Poor man’s GUI”

2:45-3:00 Discussion

## Electronic documents

3:15-3:50 Paul Hewson “R-books: integrating R into an e-book”

3:50-4:25 Max Kuhn “odfWeave and Data Analysis Platforms”

4:25-4:45 Discussion

## Models II

3:15-3:40 K. M. Mullen, L. J. G. W. van Wilderen, M. L. Groot and I. H. M. van Stokkum “Standard error estimation and multi-dataset modeling with TIMP”

3:40-4:05 Thomas Lumley “Developments in survey analysis in R”

4:05-4:30 Felipe Mendiburu, Reinhard Simon “Agricolae: A Free Statistical Library for Agricultural Research”

4:30-4:45 Discussion

## Large data and Programming Competition Winners

5:00-5:30 Martin Maechler “Sparse Matrices for Large Data Modeling”

5:30-6:00 Doug Bates “Fitting Linear, Generalized Linear and Mixed-effects Models to Large Data Sets”

6:00-6:25 D. Adler, O. Nenadic, W. Zucchini, C. Glaser. “The ff package: Handling Large Data Sets in R with Memory Mapped Pages of Binary Flat Files”.

## Spatial Methods

5:00-5:25 Jonathan M. Lees “SeisR and FocR: Earthquake and Seismic Analysis in R”

5:25-5:50 Jon Hobbs “Manipulating Spatio-temporal Environmental Data in R using the ncdf package”

5:50-6:15 Andrew D. Gelman, Gary King, Andrew C. Thomas “JudgeIt II (for R): A Program for Evaluating Electoral Systems and Redistricting Plans”

6:15-6:30 Discussion

## Banquet (Speaker: Thomas Lumley, 10th Anniversary of R-core)

## R Graphics: New approaches to data exploration and presentation

Chair: Antony Unwin

9:00-9:35 Deepayan Sarkar “lattice”

9:35-10:10 Hadley Wickham “ggplot”

10:10-10:30 Discussion

## Data Mining

9:00-9:25 Jose Guerra, Donald E. Franke “Using Random Forests procedures of R combined with mixed models to analyze animal breeding data”

9:25-9:50 Krishna Kumar “Learning from Currency Crises”

9:50-10:15 Brian Peterson and Peter Carl “PerformanceAnalytics”

10:15-10:30 Discussion

## Panel Session: The Use of R in Clinical Trials and Industry-Sponsored Medical Research

Chair: Marc Schwartz

Panelists:

## Graphical Methods

10:45-11:10 Duncan Murdoch, Daniel Adler “RGL in 2007” (R code)

11:10-11:35 Simon Urbanek “TBA”

11:35-12:00 Heike Hofmann and Dianne Cook “Graphical methods for longitudinal data”

## Genomics

1:30-1:55 Gregg R. Lind and Michael B. Miller “Power Calculations for Genetic Studies”

1:55-2:20 Jason Sinnwell “ibdreg, A package using regression methods to test for genetic linkage with covariates”

2:20-2:45 Jing Hua Zhao “Use of R in Genetic Association Studies”

2:45-3:00 Discussion

## Multivariate Methods and Graphical Models

1:30-1:55 Julie Josse, Sebastien L. and Francois Husson “Multivariate Analysis with the FactoMineR package”

1:55-2:20 James Ramsay, Hadley Wickham, Spencer Graves “Functional Data Analysis in Matlab and R”

2:20-2:45 Søren Højsgaard “Packages for gRaphical modelling in R”

## First session

(1) Jason Owen “The R Guide: A Manual on R for Everyone”

(2) Panayotis Giannakouros and Lihua Chen “A Free Software DVD for statistical computing”

(3) Guennadi Andrianov “A case for the Uncertainty Treatments with R: Generic Approach in Guidelines and Open Source SW”

(4) Dai Feng and Luke Tierney “Misc3D: A Package to Draw 3D Plots”

(5) Stephen Weigand “Some ideas on creating publication-quality tables in R”

(6) Jeffrey Horner “Brewing with RApache”

(7) Michael Lawrence “rsbml: An R package for importing SBML data”

(8) Charlotte Wickham “An exploratory stroll along the beach”

(9) Garrett Dancik and Karin Dorman “mlgp: an R package for maximum likelihood estimation of Gaussian processes”

(10) Chinthaka Kuruwita “A Bayesian Approach for Bandwidth Selection in Kernel Density Estimation”

(11) Jungeun Song “Bayesian Estimation of Curves or Surfaces”

(12) Panayotis Giannakouros and Lihua Chen “An Xgrid oriented R package for prediction-based model combining”

(13) Jeff Ryan “quantmod: Quantitative Financial Modelling Framework for R”

(14) C. Glaser, D. Adler, O. Nenadic, W. Zucchini, S. Sperlich “R General Purpose Computing on Graphics Processing Units”

(15) D. Adler, O. Nenadic, W. Zucchini, C. Glaser “The ff package: Handling Large Data Sets in R with Memory-Mapped Pages of Binary Flat Files”

(16) Mario Pineda-Krch “GillespieSSA: A stochastic simulation package for R”

## Second session

(1) Elaine A. McVey, Perry Haaland, Friedrich Hahn, Megan Gottlieb, Ruiling Yuan “Sample-Size Determination for a Flow Cytometry Assay”

(2) Kyongryun Lee, Michael Lawrence, Julie Dickerson “Cytoscript: Running R in Cytoscape”

(3) Elizabeth Atkinson, Eric Lunde, Patrick Votruba, Mariza de Andrade “An R library for quantitative trait linkage analysis”

(4) Vinay Ravindrakumar, Michael Bauer “Identification of correlated genes in malignant gliomas”

(5) Heather Babka, Suh-Yeon Choi, Michael Lawrence, Di Cook, Beth L. Fatland, Basil J. Nikolau, Eve Syrkin Wurtele “Exploratory Analysis of Transcripmtomic Data from Antisense ATP-Citrase Lyase Arabidopsis thaliana Supplemented with Malonic Acid using R and GGobi ”

(6) Jose Lima-Guerra “Automation of phenotypic analysis with R software”

(7) Lei Yang “ENM: an R package for the computational modelling and analysis of protein dynamics using elastic network models”

(8) Scott Diegel and Erik Iverson “Interim Data Monitoring Reports in Clinical Trials”

(9) Ryan Moore “blocktools: High-dimensional Nonbipartite Matching for Social Science Experiments”

(10) Derek H. Ogle and George R. Spangler “FSA: R Functions for Fisheries Stock Assessment”

(11) Ling Li, Wenxu Zhou, Wengang Zhou, Dan Nettleton, Mark Westgate, Basil Nikolau, and Eve Syrkin Wurtele “Analyses of soybean seed transcriptomics data and metabolomics data using R: A systems biology approach to understanding seed composition”