countyreports

R code for creating POC's County Reports.

Installation Requirements

You will need to have installed

• R
• The following R packages:
  • pocr (see the pocr git repository)
  • extrafont
  • knitr
  • brew
  • xtable
• TeX (with XeLaTeX compiler)

You will also need to have an ODBC connection set up to annie (or test_annie or review_annie if you're building from there). For production annie, you may need to set up a pipe (e.g., via Putty) to allow R to talk to the db.

First time set-up or recently updated R

If you haven't used the extrafont package before, you will need to load it in an R session and import the system fonts. This will take some time (between 10 and 30 minutes) but only needs to be done once per base R installation. The code is as follows:

library(extrafont)
font_import()

# verify that it worked
loadfonts()

Creating county reports

In the reports/ directory, open the file template_write_reports.R. It has some reminders at the top which shouldn't require any action unless you're updating the report template. Simply run the code in template_write_reports.R to produce the county report PDFs and clean up the intermediate files.

Check that all the PDFs are about the right size (400-500 KB), and open a few of them to verify nothing's amiss, then they can be uploaded to data/pocweb/www-*/county_reports/ with the * filled in with the appropriate version of the website.

Technical overview

The tempalate is separated into two files: template.Rnw contains all the text and TeX code to produce the formatting, as well as placeholders for R code. The R code is externalized to county_reports.R, where the code chunks are named with a ## @knitr chunk_name comment for placement into the .Rnw file. (See the knitr manual for details on Rnw documents with externalized R code.) Many of the graphs are produced by functions defined in the pocr package. At some point, they should probably be put into their own countyreports package...

To write a report (this is done with the write_report function in template_write_reports.R), we loop through each county, use brew::brew to create the individual county .Rnw file, knit the .Rnw file into .tex and .PDF files, and re-compile the PDF from the .tex file to fix internal references (this is supposed to happen automatically with knit2pdf, but it seems to need one more nudge).

There is code there to auto-upload the files, but I've had mixed success with it in the past so I generally transfer the files manually.