1. KEEP THIS TEXT BOX this slide includes some ESRI fonts. when you save this presentation, use File > Save As > Tools (upper right) > Save Options > Embed TrueType Fonts (all characters) this will allow vector maps created with common ESRI symbols to show on computers that do not have ESRI software loaded a a a a a a a a a a a a a a a R, PostGIS, and Sweave: Reproducible Research Philip M. Hurvitz, PhD Urban Form Lab College of Built Environments University of Washington 1 of 12

2. Acknowledgments  NIH 5R01HL091881-04 (PI B. Saelens) 2 of 12

3. Disclaimers  I rarely make maps  I use GIS for analytics (usually I want numbers and tables at the end of analyses) So this talk might not be for you... 3 of 12

4. Background  Analysis is fun  Writing is not fun  Documentation is the most important, yet the most difficult part of research  Typical workflows are not conducive to efficient documentation 4 of 12

5. The way most of us work  Perform a bunch of analysis  Generate summary tables as files  Spreadsheet  SQL database  Programming (e.g., MATLAB, R, NumPy)  Generate graphics as files  ArcGIS  Mapserver, QGIS, OpenJUMP  Compile files in a word processed document  “If it works,” don’t fix it. 5 of 12

6. But does it really work?  What if you need to change something (who has ever needed to do that)?  …Lather, rinse, repeat… 6 of 12

7. But does it really work?  What if you need to revisit your analysis or results (say, during peer review)?  If your results were copied into Excel & Word, how will you track down what you did?  If you programmed your analyses, your workflow should be stored in scripts … But where are your scripts (“I swear they where here somewhere!”)? Or which version was used? 7 of 12

8. How to fix it? 1. Store your data in a format that can be accessed programmatically  PostGIS (others?) 2. Program your analyses so they are replicable  R with rgdal, RPostgreSQL 3. Use Sweave to run your R code and place results in a(and PDF) document 4. Use RStudio server to streamline the process  Integrated development environment  Persistent sessions  Single-click from Rnw file to PDF file 8 of 12

9. How to do it  Code your analysis in R  Reformat your R code as an Sweave file (“.Rnw”)  R code in “chunks” delimited with >= R code @  Manuscript in syntax  Pass through Sweave and pdflatex R> Sweave(“file.Rnw”) $> pdflatex file.tex; pdflatex file.tex 9 of 12

10. Some details  Use xtable library to format tabular data in format  Generate graphics using native R or the lattice/grid graphical environment  (Optional): Save tables and graphics as separate files (for publication) 10 of 12

11. A sample workflow  Data:  Simulated overlapping polygons (2 classes)  Simulated point observations (2 classes)  Analysis:  Generate point density values for the 2 x 2 combination from intersected data 11 of 12

12. A demo  Rnw code: http://gis.washington.edu/phurvitz/presentations/2012 /cugos_spring_fling/cugos.Rnw  Resultant PDF http://gis.washington.edu/phurvitz/presentations/2012 /cugos_spring_fling/cugos.pdf 12 of 12