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Episode 12 Show Notes

The basics for version control and Git

• Why it’s important: Backups and reproducibility
• Git is available for all major platforms, see GitHub page for installation instructions for all operating systems
• IDEs RStudio and Eclipse via Egit plugin offer integration of Git for easy usage
• Key commands: git init, git add file.R, git commit -m “my commit message”
• Tell Git what files you don’t want to be tracked with .gitignore file(s)
• GitHub and BitBucket are two excellent remote repository host sites
• Wikipedia article on revision control
• Pro Git book, with electronic copy available for free!
• How do you combine revision control with workflow in R
• R and version control for the solo data analyst
• Jeremy Anglim’s tutorial on Using Git, Egit, Eclipse, and GitHub for version control
• Win-Vector blog on minimal version control lesson
• Top 10 Git Tutorials for Beginners
• Aha moments when learning Git

Listener Feedback

• Daniel provides link to Open Education Database: www.oedb.org/open
• StatisticsBlog: www.statisticsblog.com
• Aron: Big data and parallel processing
• Eric: Questions about data structures
• Adam: Text mining and workflow
• Randall offers first donation for the R-Podcast (thanks, Randall!)

R Community Roundup

• Visualization of season performance of NCAA tournament teams by Rodrigo Zamith
• Plotting lm and glm models with ggplot via strengejacke.wordpress.com

Package pick

• reports: An R package to assist in the workflow of writing academic articles and other reports (via TRinker’s blog)

How to interact with the show

• Submit your questions and comments via the R-Podcast contact page, or send an email to theRcast(at)gmail.com
• Send in an audio comment via audio attachment to theRcast(at)gmail.com, or leave a voicemail on the R-Podcast voicemail hotline: +1-269-849-9780
• Get show updates via our Twitter account: @theRcast
• Follow us on our R-Podcast Google Plus page: gplus.to/thercast
• Provide your favorite R community links at the R-Podcast subreddit: links.r-podcast.org/

Music Credits

• The opening theme is entitled “Super Fighting Robot X” by WillRock from the Megaman X: Maverick Rising Album at ocremix.org
• The closing theme is entitled “Countdown to Infinity” by WillRock from the Megaman X: Maverick Rising Album at ocremix.org

The following resources are mentioned in this episode:

• R-Podcast subreddit: links.r-podcast.org
• Sweave: http://www.stat.uni-muenchen.de/~leisch/Sweave/
• Knitr: http://yihui.name/knitr/
• The Duke Research Trial Saga: http://simplystatistics.org/post/18378666076/the-duke-saga-starter-set
• RStudio Shiny web application: http://www.rstudio.com/shiny/
• Listener Brock’s NHL analysis blog: http://www.brocktibert.com/blog/?s=NHL
• Guide to installing latest version of R on Ubuntu: http://darrenjw.wordpress.com/2012/11/10/keeping-r-up-to-date-on-ubuntu-linux/
• R 2.15.2 release notes: http://blog.revolutionanalytics.com/2012/10/r-2152-now-available.html
• Guide to new theme system in ggplot 0.9.2.1: https://github.com/wch/ggplot2/wiki/New-theme-system
• Plyr package: http://plyr.had.co.nz/
• The opening theme is entitled “Super Fighting Robot X” by WillRock from the Megaman X: Maverick Rising Album at www.ocremix.org
• The closing theme is entitled “Countdown to Infinity” by WillRock from the Megaman X: Maverick Rising Album at www.ocremix.org

Episode 11 Time Stamps

00:00 The R-Podcast #011 Reproducible Analysis Part 1
00:40 Introduction
02:43 Reproducible Research: Introduction
08:18 Sweave overview
16:20 Knitr overview
20:20 The Duke University Research Saga
30:56 What version control can offer
38:34 Presenting results
42:18 Listener feedback
60:55 R community roundup
69:39 Package pick: plyr
72:04 Wrapping up: subscribe at www.r-podcast.org, theRcast@gmail.com, + 1-269-849-9780, Twitter @theRcast, Google Plus, links.r-podcast.org
77:21 End

The following resources are mentioned in this episode:

• New additions to the RStudio team: blog.rstudio.org/2012/08/20/welcome-hadley-winston-and-garrett/
• Over 4,000 packages on CRAN: http://blog.revolutionanalytics.com/2012/08/two-r-community-milestones.html
• NHL Analysis web-scraping scripts on GitHub: https://github.com/thercast/nhl_analysis/tree/master/web-scraping
• XML package: http://cran.r-project.org/web/packages/XML/index.html
• RCurl package: http://cran.r-project.org/web/packages/RCurl/
• Hockey-Reference data: http://www.hockey-reference.com
• Using R for Scraping Data Presentation at UseR! 2012: http://www.slideshare.net/rtelmore/user-2012-talk
• Using RMySQL tutorial: http://playingwithr.blogspot.com/2011/05/accessing-mysql-through-r.html
• Jeroen Ooms’ lme4 web application: http://www.stat.ucla.edu/~jeroen/lme4.html
• Coursera Course on R: https://www.coursera.org/course/compdata
• RPubs: http://rpubs.com/
• Theme music provided by WillRock from the Return All Robots Remix Album at ocremix.org
• The closing theme is entitled “The Way” and provided by Jewbei from the Wild Arms: ARMed and Dangerous album at ocremix.org

Episode 10 Time Stamps

00:00 The R-Podcast #010 Adventures in Data Munging Part 2
00:33 Introduction
01:50 Wrapping up season 1 ... wait, what?
03:30 Rstudio team expands
05:41 R Community milestone
07:53 Discovering hockey-reference.com 
10:54 Tips for readHTMLtable
21:10 Checking for valid data first
29:23 Minor processing needed
35:18 Saving data to MySQL database
45:26 Listener Feedback: Andrew
54:58 Frans: Pitfalls of R segment 2
63:40 Wrapping up: subscribe to the podcast, theRcast@gmail.com, + 1-269-849-9780, Twitter @theRcast
69:14 End

The following resources are mentioned in this episode:

• Summary of UserR! 2012 conference: http://pairach.com/2012/06/24/user2012/
• R 2.15.1 release notes: http://cran.r-project.org/src/base/NEWS
• NHL Analysis GitHub Repo: https://github.com/thercast/nhl_analysis
• plyr package: http://plyr.had.co.nz/
• car package: http://cran.r-project.org/web/packages/car/index.html
• ProjectTemplate: http://www.projecttemplate.net/
• Hockey Summary Project: http://hsp.flyershistory.com/
• Pitfalls of R blog post: http://pitfalls-r-us.blogspot.nl/2012/07/time-zones.html

Episode 9 Time Stamps

00:00 The R-Podcast #009: Adventures in Data Munging Part 1
00:31 Introduction
01:38 Big news: +1
03:53 R 2.15.1 released
04:26 UseR! 2012
07:20 Hockey Summary Project
10:30 Dealing with empty files
15:18 Importing inconsistent data files
28:15 Recoding using car package
35:08 Useful functions for pinpointing issues
44:55 Listener Feedback
45:14 Daniel: Advice on data munging
55:01 Frans: Pitfalls of R
66:28 Wrapping up: subscribe to the podcast, theRcast@gmail.com, + 1-269-849-9780, Twitter @theRcast, Google Plus
71:22 End

The following resources are mentioned in this episode:

• Hockey Summary Project: http://hsp.flyershistory.com/
• Plot Code on GitHub: https://github.com/thercast/nhl_analysis/blob/master/src/plot_demo_code.R
• Cookbook for R by Winston Chang: http://wiki.stdout.org/rcookbook
• ggplot2 0.90 Transition Guide: http://cloud.github.com/downloads/hadley/ggplot2/guide-col.pdf
• ggplot2 online reference: http://had.co.nz/ggplot2/
• ggplot2 GitHub wiki: https://github.com/hadley/ggplot2/wiki/
• ggplot2 blog: http://blog.ggplot2.org/
• ggplot2 mailing list: https://groups.google.com/forum/?fromgroups#!forum/ggplot2
• Kaplan-Meier Survival Plot with ggplot2: http://mcfromnz.wordpress.com/2011/11/06/kaplan-meier-survival-plot-with-at-risk-table/
• Learning R Series: http://learnr.wordpress.com/2009/06/28/ggplot2-version-of-figures-in-lattice-multivariate-data-visualization-with-r-part-1/
• Code A La Mode ggplot2 articles: http://codealamode.blogspot.com/search/label/ggplot2
• ggplot2 textbook by Hadley Wickham: http://tinyurl.com/ggplot2-book
• Theme music provided by WillRock from the Return All Robots Remix Album at ocremix.org

The following resources are mentioned in this episode:

• The Going Linux Podcast: http://www.goinglinux.com
• Hockey Summary Project: http://hsp.flyershistory.com/
• Plot Code on GitHub: https://github.com/thercast/nhl_analysis/blob/master/src/plot_demo_code.R
• The R Inferno: http://www.burns-stat.com/pages/Tutor/R_inferno.pdf
• Cookbook for R by Winston Chang: http://wiki.stdout.org/rcookbook
• ggplot2 0.90 Transition Guide: http://cloud.github.com/downloads/hadley/ggplot2/guide-col.pdf
• ggplot2 online reference: http://had.co.nz/ggplot2/
• ggplot2 GitHub wiki: https://github.com/hadley/ggplot2/wiki/
• ggplot2 blog: http://blog.ggplot2.org/
• ggplot2 mailing list: https://groups.google.com/forum/?fromgroups#!forum/ggplot2
• Kaplan-Meier Survival Plot with ggplot2: http://mcfromnz.wordpress.com/2011/11/06/kaplan-meier-survival-plot-with-at-risk-table/
• Learning R Series: http://learnr.wordpress.com/2009/06/28/ggplot2-version-of-figures-in-lattice-multivariate-data-visualization-with-r-part-1/
• Code A La Mode ggplot2 articles: http://codealamode.blogspot.com/search/label/ggplot2
• ggplot2 textbook by Hadley Wickham: http://tinyurl.com/ggplot2-book
• Theme music provided by WillRock from the Return All Robots Remix Album at ocremix.org
• The closing theme is entitled “The Way” and provided by Jewbei from the Wild Arms: ARMed and Dangerous album at ocremix.org

Episode 8 Time Stamps

00:00 The R-Podcast #008 Visualization with ggplot2
00:34 Introduction
01:45 Thank you Going Linux
05:01 Listener feedback
14:14 ggplot2 background and philosophy
23:00 Description of data 
30:20 Setting up our plot with ggplot function
38:15 Adding boxplot layer
44:31 Customizing appearance
60:35 Facet by era
67:02 Making code reproducible
73:03 Helpful ggplot2 resources
85:30 Wrapping up: subscribe to the podcast, theRcast@gmail.com, + 1-269-849-9780, Twitter @theRcast
89:29 End

P.S. From our Google Plus page, Darren pointed out that I switched forward slashes with backward slashes in my discussion about file paths in Episode 6. Thanks Darren!

The following resources are mentioned in this episode:

• The new R-Podcast forums: http://www.r-podcast.org/forums/
• RStudio v0.96 release notes: http://blog.rstudio.org/2012/05/14/rstudio-v096/
• Cookbook for R by Winston Chang: http://wiki.stdout.org/rcookbook
• Stack Overflow post on workflow: http://stackoverflow.com/a/1434424/315664
• ProjectTemplate package: http://www.projecttemplate.net/index.html
• RStudio Project feature: http://rstudio.org/docs/using/projects
• Version control in RStudio: http://rstudio.org/docs/version_control/overview
• Stack Overflow discussion on version control: http://stackoverflow.com/questions/2712421/r-and-version-control-for-the-solo-data-analyst
• Setting up Git: http://help.github.com/
• Theme music provided by WillRock from the Return All Robots Remix Album at ocremix.org
• The closing theme is entitled “The Way” and provided by Jewbei from the Wild Arms: ARMed and Dangerous album at ocremix.org

Episode 7 Time Stamps

00:00 The R-Podcast #007 Best Practices for Workflow Management
00:31 Introduction
01:07 No more TV recording for now
03:40 New forums!
08:25 RStudio update v0.96
12:50 Listener feedback
19:35 Using source(), save(), save.image(), and load()
25:00 load.R, clean.R, func.R, do.R
29:50 ProjectTemplate
40:06 Version Control with Git, RStudio
46:30 Wrapping up: subscribe to the podcast, theRcast@gmail.com, + 1-269-849-9780, Twitter @theRcast
52:44 End

The following resources are mentioned in this episode:

• R Data Import/Export Manual: http://cran.r-project.org/doc/manuals/R-data.html
• XLConnect Package: http://cran.r-project.org/web/packages/XLConnect/index.html
• XLConnect Website: http://miraisolutions.wordpress.com/2012/02/16/xlconnect-0-1-8/
• RMySQL Package: http://cran.r-project.org/web/packages/RMySQL/
• Accessing MySQL through R: http://playingwithr.blogspot.com/2011/05/accessing-mysql-through-r.html
• XML Package: http://cran.r-project.org/web/packages/XML/index.html
• foreign Package: http://cran.r-project.org/web/packages/foreign/index.html
• sas7bdat Package: http://cran.r-project.org/web/packages/sas7bdat/index.html
• sas7bdat on GitHub: https://github.com/biostatmatt/sas7bdat
• ESPN NHL playoff statistics table: http://espn.go.com/nhl/statistics/team/_/stat/scoring/year/2012/seasontype/3
• MythTV: http://www.mythtv.org/
• R script used in this episode: https://github.com/thercast/importing-data/blob/master/importing-data-basics.R
• Theme music provided by WillRock from the Return All Robots Remix Album at ocremix.org
• The Closing theme is entitled Crysis Crystal and provided by K-wix from the Mega Man 9: Back in Blue album at ocremix.org

Episode 6 Time Stamps

00:00 The R-Podcast #006 Importing Data from External Sources
00:34 Introduction
01:46 Listener Feedback
07:45 Description of delimited text files
09:18 Using read.table and key arguments
18:17 R Data Import-Export Manual
19:10 Importing spreadsheet data considerations
21:10 XLConnect package advantages
25:20 Importing HTML tables using XML package
33:55 Using RMySQL with MySQL databases
43:52 Data from other statistical software
44:18 The foreign package
45:45 sas7bdat package
49:13 Wrapping up: subscribe to the podcast, theRcast@gmail.com, + 1-269-849-9780
53:54 End

The following resources are mentioned in this episode:

• R version 2.15.0 release notes: http://cran.r-project.org/src/base/NEWS.html
• “R Fell on Alabama Last Night” presentation by Kent: https://www.youtube.com/watch?v=W8d54ThS37Q
• R script used in this episode: https://github.com/thercast/package_admin/blob/master/basic-package-management.R
• R packages included by default: http://cran.r-project.org/doc/manuals/R-FAQ.html#Which-add_002don-packages-exist-for-R_003f
• CRAN Task Views: http://cran.r-project.org/web/views/
• R-Forge: https://r-forge.r-project.org
• RSeek: http://www.rseek.org
• Crantastic: http://www.crantastic.org
• unknownR R package list: http://unknownr.r-forge.r-project.org/toppkgs.html
• Rtools: http://cran.r-project.org/bin/windows/Rtools
• R Administration Manual-Updating packages: http://cran.r-project.org/doc/manuals/R-admin.html#Updating-packages
• Upgrading R on Windows and updating packages: http://www.r-statistics.com/2010/04/changing-your-r-upgrading-strategy-and-the-r-code-to-do-it-on-windows/
• UCLA R FAQ on managing packages: http://www.ats.ucla.edu/stat/r/faq/packages.htm
• Theme music provided by WillRock from the Return All Robots Remix Album at ocremix.org
• The Closing theme is entitled Crysis Crystal and provided by K-wix from the Mega Man 9: Back in Blue album at ocremix.org

Episode 5 Time Stamps

00:00 The R-Podcast #005 Basic Package Management
00:32 Introduction
01:06 R 2.15.0 "Easter Beagle" released
02:01 Listener Feedback
09:02 What is a package?
12:00 Libraries
13:33 What packages do you have?
19:36 Finding packages
33:26 Installing packages
46:12 Using packages
51:08 Updating packages
58:12 Wrapping up: subscribe to the podcast, theRcast(at)gmail.com, + 1-269-849-9780
61:14 End