Curriculum Vitae

Yihui Xie

Contact Information

Email: xie@yihui.name; Homepage: http://yihui.name; Twitter @xieyihui

Research Interest

Statistical computing, statistical graphics, data visualization, reproducible research

Education Background

  • 2009 ~ 2013, PhD in Statistics, Department of Statistics, Iowa State University
  • 2006 ~ 2009, Master of Statistics, School of Statistics, Renmin University of China
  • 2002 ~ 2006, Bachelor of Economics, School of Statistics, Renmin University of China

Honors & Awards

  • Snedecor Award, 2012 (the most outstanding PhD candidate in the Department of Statistics, Iowa State University)
  • Honorable Mention Prize, the Applications of R in Business Competition, 2012
  • Vince Sposito Statistical Computing Award, 2011 (Department of Statistics, Iowa State University)
  • John M. Chambers Statistical Software Award, ASA, 2009 (for the R package animation)
  • Excellent graduate scholarship, Renmin University of China, 2007
  • Successful Participant, Mathematical Contest in Modeling (America), 2006 (paper; certificate”))
  • Excellent graduate of Renmin University of China, 2006
  • “Excellent Worker in Student Media” of Renmin University of China, 2006 (for hosting the website of statistics discussions in http://cos.name)
  • Scholarship for outstanding learning, Renmin University of China, 2005

Publications

In Chinese

Books under development:

  1. R Ninja
  2. Modern Statistical Graphics

Papers:

  1. Yanyun Zhao, Nailin Feng, Yuncheng Zhao, Yihui Xie, Ning Xiao, 2008, Research on the National Quality Competitiveness of China, Statistical Research, 25(3), 12-19
  2. Yihui Xie, 2008. On the Applications of Statistical Graphics in Data Analysis, Statistics Review, Bo Zhang (ed)
  3. Yihui Xie, 2008. Bootstrap Methods: Developments and Frontiers, Statistics & Information Forum, 89, 90-96.
  4. Yihui Xie, 2007. The Application of the Classification and Regression Tree Based on the Package rpart in R, Statistics & Information Forum, 86, 67-70.
  5. Yihui Xie, 2007. Series in International Competitiveness: How Weak is the Financial System of China?, China Statistics, 7, 35.
  6. Yanyun Zhao, Yihui Xie, 2006. Unbalanced growth in top 100 industrial enterprises in China: market expanding outgoes business managing, Talents, 9, 84.
  7. Yanyun Zhao, Yihui Xie, 2005. Who is the champion of growth among top 1000 industrial enterprises in China: analysis on the capability of market expanding and aggregate efficiency, Talents, 9, 72-73.

Besides, I published several articles in the Capital of Statistics in Chinese.

In English

Books and book chapters:

  1. Yihui Xie (2016). bookdown: Authoring Books and Technical Documents with R Markdown. Chapman and Hall/CRC. ISBN 978-1138700109
  2. Yihui Xie (2015). Dynamic Documents with R and knitr. 2nd edition. Chapman and Hall/CRC. ISBN 978-1498716963
  3. Yihui Xie (2014). knitr: A Comprehensive Tool for Reproducible Research in R. In Victoria Stodden, Friedrich Leisch and Roger D. Peng, editors, Implementing Reproducible Computational Research. Chapman and Hall/CRC. ISBN 978-1466561595
  4. Yihui Xie (2013). Dynamic Documents with R and knitr. Chapman and Hall/CRC. ISBN 978-1482203530

Papers:

  1. Yihui Xie, Heike Hofmann, and Xiaoyue Cheng (2014). Reactive Programming for Interactive Graphics. Statistical Science, 29(2), 201-213. (PDF)
  2. Yihui Xie (2013). animation: An R Package for Creating Animations and Demonstrating Statistical Methods. Journal of Statistical Software, 53(1), 1-27. URL http://www.jstatsoft.org/v53/i01/
  3. Yihui Xie and Xiaoyue Cheng, 2008. animation: A Package for Statistical Animations, R News, 8(2). URL: http://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf
  4. Yihui Xie, 2007. Visualization of Data and Statistical Models Using R, Proceedings of the 3rd Conference on Australia-China Free Trade Agreement (ACFTA): Econometric Modeling and Policy in Trade, Investment and Economic Integration (paper)

Professional Experience

I’m currently a software engineer at RStudio, Inc.

Internship

  1. Summer 2012, AT&T Labs Research, Florham, NJ (mentor: Simon Urbanek)
  2. Summer 2013, Fred Hutchinson Cancer Research Center (mentor: Raphael Gottardo)

Website Management

Sept 2003 - Present

I created and maintained web pages for:

  • The School of Statistics, Renmin University of China (Sept 2003 - Jun 2009)
  • The Center for Applied Statistics, Renmin University of China (Apr 2004 - Jun 2009)
  • The Center for Risk Management and Actuarial Studies (Jun 2004 - Apr 2006); Data Mining Center of Renmin University of China (Jul 2004 - Apr 2006), etc
  • The “Great Expectation Society”, a student society in Renmin University (Mar 2005 - Jul 2006)

I founded and have been maintaining:

I worked in these web studios:

  • The English web studio of Renmin University of China (for the construction of English website of the university) (Sept 2006 - Jun 2009)
  • The web club of the School of Statistics (as the founder & leader) (Apr 2006 - 2008)

My personal projects:

Conference Organization

Feb 2005 - Present

I initiated the Chinese R conference in 2008, and organized

  • the 1st Chinese R conference (in Beijing), Dec 13~14, 2008

I helped organize these conferences:

  • the 3rd Chinese R conference (Beijing), Jun 12~13, 2010
  • the 2nd Chinese R conference (Beijing & Shanghai), December 2009
  • Second Conference on Micro Evidence on Innovation in Developing Economies, April 22 ~ 23, 2008 (an international conference; I was also the Chair for the last session on April 22)
  • the 2nd Conference on Australia-China Free Trade Agreement (ACFTA): Econometric Modeling and Policy in Trade, Investment and Economic Integration, April 17th ~ 18th, 2006
  • the 15th International Conference on Input-Output Techniques, June 27th ~ July 1st, 2005
  • the Data Mining and Business Intelligence Conference 2006
  • the International Statistics Forum 2006

Statistical Consulting

May 2005 - Present

I offer statistical consulting by email and I have been answering questions in the Capital of Statistics almost every day. I’m particularly interested in these topics:

  • data analysis and visualization
  • theoretical problems without measure theory
  • linear models, generalized linear models and nonlinear models
  • R packages that I maintain (other questions on R should be asked on StackOverflow)
  • statistics in other disciplines (e.g. biology) in which I can also learn something from you
  • real world data mining and machine learning
  • simulation
  • teaching

I ignore any questions on Structural Equation Modeling (SEM) or factor analysis, as I do not believe their usefulness at all. I know little about time series and do not like econometrics. I have little interest in quantitative research in social science.

Other Work Experience

Sep 2004 - present

Duties in associations & centers:

  • Program chair, Section on Statistical Graphics, American Statistical Association (2015)
  • Data Sharing and Reproducibility Committee, American Statistical Association (2013)
  • Column editor of the ICSA bulletin for its R column (2012 - 2013)
  • Webmaster of the Center for Applied Statistics, Renmin University of China (2004 - 2009)
  • Vice-chairman of the “Great Expectation Society” (a student association, Apr 2005 - Jul 2006)

Projects participated:

  • Google Summer of Code 2012: Dynamic report generation on the web with R (I was the mentor);
  • Translation of R for beginners by Emmanuel Paradis (Collaborated with some colleagues on the translation) (Nov 2005 - Feb 2006);
  • Performance Evaluation of Taxation Management of the China Customs (designed several R programs for sampling databases using R) (Sept 2006 - Jun 2009);
  • Important Projects in Social Science of the Ministry of Education: Research on the Industry Competitiveness of China (Apr 2007 - May 2007);
  • A research project on statistical quality control co-operated with China National Research Institute of Food and Fermentation Industries, National Standardization Centre of Food & Fermentation Industry, P.R.C.; R (D)COM was used in developing programs (May 2007 - Jun 2009)
  • Cooperative project with the Office of 1% Population Sampling Survey of the State Department: Research on the National Population Competitiveness of China (Jun 2007 - Nov 2007)

Presentations & Tutorials

  • Yihui Xie, 2017, The R Markdown Ecosystem: Reproducible Reports, Papers, Books, Websites, and Presentations, a seminar in the Department of Plant Pathology, Kansas State University, Manhattan, KS (slides)
  • Yihui Xie, 2017, Customizing & Extending R Markdown, a talk at rstudio::conf, Kissimmee, FL (slides)
  • Yihui Xie, 2017, Making Websites with R Markdown, a talk at rstudio::conf, Kissimmee, FL (slides)
  • Yihui Xie, 2017, Advanced R Markdown, a tutorial at rstudio::conf, Kissimmee, FL (slides)
  • Yihui Xie, 2016, bookdown: Authoring Books with R Markdown, Department of Statistics, Colorado State University (slides)
  • Yihui Xie, 2016, Sharing the Fun of Using/Developing A Few R Packages, Department of Statistics, Colorado State University
  • Yihui Xie, 2016, Authoring Books with R Markdown, a webinar at RStudio (slides; video)
  • Yihui Xie, 2016, Reproducibility in Statistics and Data Science (Discussion), JSM 2016, Chicago (slides)
  • Yihui Xie, 2016, HTML Widgets: Interactive Visualizations from R Made Easy!, JSM 2016, Chicago (slides)
  • Yihui Xie and Hadley Wickham, 2016, Authoring Books with R Markdown, useR! 2016, Stanford University (slides)
  • Yihui Xie, Karl Broman, and Ian Lyttle, 2016, Dynamic Documents with R Markdown, a tutorial at useR! 2016, Stanford University (slides)
  • Yihui Xie, 2016, Pleasant Book Writing with bookdown, the 9th China-R conference, Beijing (slides)
  • Yihui Xie, 2016, CosPlay R, the 9th China-R conference, Beijing
  • Yihui Xie, 2016, R Markdwon: A Convenient Toolset for Academic Writing and Data Analysis, Ocean University of China, Qingdao (slides)
  • Yihui Xie, 2016, Some Interesting Packages for Interactive Graphics, School of Economics, Qingdao University, Qingdao
  • Yihui Xie, 2016, Shiny and HTML Widgets in R, Greater Omaha Tableau User Group, University of Nebraska at Omaha (slides)
  • Yihui Xie, 2016, Authoring Books with R Markdown, the Chicago chapter of ASA, Chicago (slides)
  • Yihui Xie, 2016, Get Ready to Write A Book Now
    • 03/31, University of Chicago (slides)
    • 02/17, Department of Statistics, University of Nebraska at Lincoln (slides)
  • Yihui Xie, 2016, Complex Application Layouts with Grid Style Sheets, Shiny Developer Conference, Stanford University (slides)
  • Yihui Xie, 2016, Interfacing DataTables, Shiny Developer Conference, Stanford University (slides)
  • Yihui Xie, 2015, Reflections on R Package Developemnt a Software Engineer, the 8th China-R conference, Nanchang, China (slides in Chinese)
  • Yihui Xie, 2015, Reproducible Reports with Big Data, Strata, New York City (slides)
  • Yihui Xie, 2015, A Quick Dream in Ten Years, Renmin University of China, Beijing (slides in Chinese
  • Yihui Xie, 2015, Escape the Land of LaTeX/Word for Statistical Reporting: The Ecosystem of R Markdown
    • 03/13, Wright State University, Dayton, Ohio (slides)
    • 07/14, Central Iowa R User Group
    • 09/03, ASA webinar (slides)
    • 1028, RStudio webinar (slides; video)
  • Yihui Xie, 2015, Boosting R Skills and Automating Statistical Reports, New England Statistical Symposium, UConn
  • Yihui Xie, 2015, Automatic reporting and interactive applications with R, 58.com Inc, Beijing (slides in Chinese)
  • Yihui Xie, 2015, HTML Widgets, LA R User Group (slides; video)
  • Yihui Xie & Dirk Eddelbuettel, 2014, An R Workshop at the Warren Center of UPenn, Philadelphia, PA
  • JJ Allaire & Yihui Xie, 2014, _Reproducible R Reports with Packrat and Rmarkdown _, R Day at Strata New York
  • Yihui Xie, 2014, Reproducible Research Is Dead, Long Live Reproducible Research!, a talk given at JSM 2014, Boston, MA (slides)
  • Yihui Xie, 2014, Knitr Ninja, a talk given at UseR! 2014, UCLA (slides)
  • Yihui Xie, 2014, Dynamic Documents with R and knitr, a tutorial given at UseR! 2014, UCLA (slides; examples)
  • Yihui Xie, 2014, The Next Generation of Dynamic Documents with R Markdown, Great Plains R-Users Group Conference, Sioux Center, Iowa (slides)
  • Yihui Xie, 2014, How I Managed to Find Time to Play Badminton Three Times A Week, a talk in the Department of Animal Science, ISU (slides)
  • Yihui Xie, 2014, New developments in knitr and R Markdown v2, LA R user group (slides)
  • Yihui Xie, 2014, Dynamic and Interactive Statistical Reporting, a talk in the Department of Statistics, UCLA (slides)
  • Yihui Xie, 2014, How to Save More Time from Your Homework and Projects, a guest lecture for Stat 416 at Iowa State University (slides)
  • Yihui Xie, 2014, An Introduction to knitr, a remote talk for the Orange County R User Group (slides)
  • Yihui Xie, 2014, R Markdown v2, Seattle R User Meetup, Seattle, WA (slides)
  • Yihui Xie, 2013, You Can Save More Time from Homework/Projects/Data Analysis for Beer/Fun/Whatever, Iowa Chapter of ASA poster session with mixer (poster)
  • Yihui Xie, 2013, knitr for ninja, a distance talk at the New York R Users Group (slides)
  • Yihui Xie, 2013, A tour through knitr, Raphael Gottardo’s research lab, Fred Hutchinson Cancer Research Center, Seattle, WA (slides; same talk given to the stats group)
  • Yihui Xie, 2013, An Introduction to knitr, Bioconductor 2013, Seattle, WA (slides, R Markdown)
  • Yihui Xie, 2013, The Development of R in China, and One Sentence Summaries of My R Projects, Revolution Analytics, Seattle, WA (slides)
  • Yihui Xie, 2013, Doing Reproducible Research Unconsciously: Higher Standard But Less Work, The 36th annual Midwest Biopharmaceutical Statistics Workshop, Muncie, IN (slides)
  • Yihui Xie, 2013, Lessons Learned in Developing R Packages, The 6th Chinese R Conference, Beijing (slides)
  • Yihui Xie, 2013, knitr: A General-purpose Tool for Dynamic Report Generation in R, ENAR 2013, Orlando, FL (slides)
  • Yihui Xie, 2013, Reproducible Research on the Web: From Homework, Blogging to Open Journals, SIAM CSE13, Boston, MA (slides)
  • Yihui Xie, 2012, knitr: Starting From Reproducible Homework, Workshop on Reproducibility in Computational and Experimental Mathematics, ICERM, Brown University, Providence, RI (slides)
  • Yihui Xie, 2012, Can You Reproduce Your Homework?, Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (slides)
  • Yihui Xie, 2012, I web, therefore I am, ISU Computing Working Group (slides)
  • Yihui Xie, 2012, Dynamic Report Generation and Interactive Graphics on the Web, End of Summer talk at AT&T Labs as a summer intern, Florham Park, NJ
  • Yihui Xie, 2012, cranvas: A New Package for Interactive Statistical Graphics in R, Joint Statistical Meetings at San Diego, CA
  • Yihui Xie, 2012, cranvas: Interactive statistical graphics in R based on Qt, useR! 2012, Nashville, TN (R code)
  • Yihui Xie and JJ Allaire, 2012, New Tools for Reproducible Research with R (slides)
    • 05/30 Iowa State University
    • 05/30 Minneapolis UseR Group
    • 06/05 New York UseR Group
    • 06/14 invited talk at the 8th International useR! Conference
  • Yihui Xie, 2012, Go social coding! Make open source more open!, lightning talk at useR! 2012 (slides)
  • Yihui Xie, 2012, cranvas: Building from Plumbing and Painting, Interface 2012, Houston TX (slides)
  • Yihui Xie, 2012, Generating beautiful statistical reports quickly and faithfully, ISU Graphics Working Group (slides)
  • Yihui Xie, 2011, How I See Bootstrap, Tests and KDE, Stat546 presentation at ISU (slides)
  • Yihui Xie, 2011, An Introduction to R, tutorial workshops in the Econ department of ISU (slides)
  • Yihui Xie, 2011, Lessons Learned in Developing R Packages, ISU Computational Statistics working group (slides)
  • Yihui Xie, 2011, cranvas: Interactive Statistical Graphics in R via Qt, AT&T Research Labs, New Jersey (slides)
  • Yihui Xie, 2011, Interactive Parallel Coordinates Plot Based on Qt, Joint Statistical Meetings at Miami Beach, Florida (slides)
  • Yihui Xie, 2011, New Features and Enhancements of the animation Package, ISU Graphics Working Group (slides)
  • Yihui Xie, 2010, LaTeX and Sweave without Tears, ISU Graphics Working Group (slides)
  • Yihui Xie, 2010, Creating Animations with R, the useR! 2010 conference at NIST, Gaithersburg, MD (slides; R code)
  • Yihui Xie, 2010, Creating GUI with the gWidgets package, the 3rd Chinese R conference, Beijing (slides in Chinese; R code)
  • Yihui Xie, 2010, Modern Statistical Graphics, tutorial lecture on the 3rd Chinese R conference, Beijing (slides in Chinese)
  • Yihui Xie, 2009, Creating R Packages, Working Group in Statistical Computing and Computationally-intensive Statistical Methods, Department of Statistics, ISU (slides; C code)
  • Yihui Xie, 2009, R in Stat500: Demonstration, Computing, and Graphics (with An Introduction to the R Package ISU.Stat500), RTG Seminar, Department of Statistics, ISU (slides)
  • Yihui Xie, 2009, Turning Statistical Ideas into Animations, VIGRE Graphics Seminar, Department of Statistics, ISU (slides; R code)
  • Yihui Xie, 2009, Reproducible Research and An Introduction to LaTeX, R and Sweave, a report for PhD students in the School of Statistics, RUC (slides in Chinese)
  • Yihui Xie, 2008, (1) The History of R Language and Current Developments (slides) (2) animation: An R Package for Statistical Animations with Applications in Teaching and Data Analysis (slides) (3) Explore Irregular Data with R (slides, R code), the 1st Chinese R Conference, Beijing, 2008.12.13~14 (introduction to the conference, R code)
  • Yihui Xie, 2008, Tutorial Lectures on R Basics, a four-day tutorial lecture series given at the Institute of Botany, Chinese Academy of Sciences (slides in Chinese: 1, 2, 3, 4)
  • Yihui Xie, 2008, See? (escaping the math world via animations…), a talk in the School of Statistics, Renmin University of China (slides)
  • Yihui Xie, 2008, Statistical Animations Using R, useR! 2008 in Dortmund (abstract; slides; slides in PDF)
  • Yihui Xie, 2008, Computer Animations for Demonstrating Statistical Procedures: Methods and Implementations, a talk at the workshop “Statistical Graphics: Data and Information Visualization in Today’s Multimedia Society (Data Viz VI)” in Jacobs University, Bremen, Germany (slides)
  • Yihui Xie, 2008, The Influence of Population Quality Competitiveness to Regional Innovation: the China Case, a presentation at the 2nd MEIDE conference (slides)
  • Yihui Xie, 2008, A Training Course on EViews and Examples in Macroeconomic Statistics, a lecture in the National Development and Reform Commission (NDRC) of People’s Republic of China (slides in Chinese)
  • Yihui Xie, 2007, Animation in Statistics: Dynamic Graphics for Statistical Models and Practical Applications, an invited talk in the 2nd postgraduate forum on statistics for universities in Beijing (slides)
  • Yihui Xie, 2007, Classification Tree Ensembles with Applications to the Prognostic Analysis of Cerebral Infarction, a report in “The Seminar for the Statistical Methods in Clinical Research” held in Renmin University of China (slides in Chinese )
  • Yihui Xie, 2007, Jokes in Statistics, an invited lecture in the Capital University of Economics and Business (slides)
  • Yihui Xie, 2007, A Leisure Look on Some Tools for Statistics, an invited lecture in the Capital University of Economics and Business (slides in Chinese; R code)
  • Yihui Xie, 2007, Bootstrap Methods: A Review, a report in the class of “Frontiers in Statistics” (slides)
  • Yihui Xie, 2007, An Introduction to Support Vector Machine and Implementation in R, an article for a presentation of the class “Data Mining and Machine Learning” (slides)
  • Yihui Xie, 2007, A Framework for Statistical Programming and An Introduction to Basic Statistical Analysis Using R, a lecture given to the members of the “Capital of Statistics” (slides in Chinese)
  • Yihui Xie, 2007, A Brief Introduction to Java, a lecture in the School of Statistics (slides)
  • Yihui Xie, 2007, A Guide to Stata, a lecture in People’s Bank of China (slides in Chinese)
  • Yihui Xie, 2007, Visualization of Data and Statistical Models Using R, 3rd Conference on Australia-China Free Trade Agreement (ACFTA): Econometric Modeling and Policy in Trade, Investment and Economic Integration (paper; slides)
  • Yihui Xie, 2006, Thoughts of Statistics, an invited talk in the 1st postgraduate forum on statistics for universities in Beijing (slides)
  • Yihui Xie, 2006, Typesetting and LATEX, a lecture in the School of Statistics (slides)
  • Yihui Xie, 2006, Statistical Programming & R Basics, a lecture in the School of Statistics (slides)
  • Yihui Xie, 2006, An Introduction to Structural Equation Modeling, A small seminar on SEM in Renmin University (slides)
  • Yanyun Zhao, Guirong Li, Xuanxuan Chen, Yihui Xie, 2006, The Industrial Structure and Foreign Investment Introduction Policy in Shanghai and Its Adjacency, 2nd Conference on Australia-China Free Trade Agreement (ACFTA): Econometric Modeling and Policy in Trade, Investment and Economic Integration (slides)

Computer Skills

I like playing with computer tools for building web pages and statistical computation & graphics. I often try to improve the efficiency of my work by creating software tools (i.e. work hard to be lazy).

  • Statistical Packages: R (OpenBUGS, S-Plus, SPSS, Eviews, SAS, MatLab, STATA, AMOS and LISREL)
  • Languages: R, HTML/CSS, JavaScript, PHP, SQL (Visual Basic, VBA, VBScript, ASP, Java, C)
  • Applications: LaTeX via LyX, Markdown via Pandoc, databases (e.g. MySQL), SVN and GIT
  • Operating Systems: 95% macOS, 2.5% Ubuntu, and 2.5% Windows (the latter two mostly for purposes of testing software)

Listed above are what I’m familiar with, and the ones being crossed out are due to my brain stack overflow and I do garbage collection in my brain once in a while.

Software Packages

I support open source software, and below is a list of open source packages that I’m involved with.

R packages:

I’m the creator and main author of:

  • knitr: a general-purpose package for dynamic report generation in R
  • bookdown: authoring books and technical documents with R Markdown
  • xaringan: presentation ninja
  • blogdown: create blogs and websites with R Markdown
  • tufte: Tufte styles for R Markdown documents
  • servr: a simple HTTP server to serve static files or dynamic documents
  • animation: a gallery of animations in statistics and utilities to create animations
  • testit: a simple package for testing R packages
  • formatR: format R code automatically
  • DT: a wrapper of the JavaScript library DataTables
  • mime: map filenames to MIME types
  • highr: syntax highlighting for R source code
  • printr: some printing methods for knitr
  • Rd2roxygen: convert Rd to roxygen documentation
  • R2SWF, MSG, iBUGS, fun, and so on

I have contributed to:

  • rmarkdown: dynamic documents for R
  • shiny: web application framework for R
  • evaluate: parsing and evaluation tools that provide more details than the default
  • htmlwidgets: HTML widgets for R
  • leaflet: create interactive web maps with the JavaScript leaflet library
  • htmltools: tools for HTML
  • roxygen2: in-source documentation for R
  • tikzDevice: R graphics output in LaTeX format
  • cranvas, the next generation of GGobi for interactive statistical graphics

PHP applications:

  • Wordpress plugin UTF-8 DB Converter (June 2009)
  • Dokuwiki plugin animation to insert animations into wiki pages; written in PHP and JavaScript (Jun 2008)

Misc

  • the Sweave and knitr modules in LyX