TO 1 Site Report

This report covers enrollment progress, participant demographics, testing results, and a variety of data quality checks.

Here's the overview of how to make the report work:

• Download the files in this repository
• Install R and the required packages
• Use the package to1check to generate cleaned data
• Write a local_facts.csv file.
• Run knit.r to generate the report.
• View the qa_report.html file.

Download Files

You'll need three files to make this report work:

• qa_report.rmd: an R-Markdown file that contains the report template.
• knit.r: a simple R script that converts the .rmd file to HTML
• local_facts.csv: a .csv file containing key information about your site

The first two are included in this repository; you'll need to make the third yourself. See local_facts.csv below.

Install R and Packages

You'll also need to install R (http://cran.r-project.org/) and a few of its packages. After you've installed R, open it and type this into the console:

install.packages(c("knitr", "to1check", "plyr", "xtable", "lubridate"))

Use the package to1check to generate cleaned data

In DMS, download all of the Data Extract tables into a single folder. There's a function called clean_to1 in the to1check package that will convert all of these .csv files into a nice, clean R list. Run that function (and remember where the output goes!)

Create a local_facts.csv

local_facts.csv is just a .csv file that looks like this:

site,enroll_target,period_start,period_end,datapath
Denver,500,2012-11-01,2013-08-30,"G:\StrategicArea\TB_Program\Research\TBESC 2\Data\cleaned\to1clean.rdata"

That is: columns named site, enroll_target, period_start, period_end, and datapath.

• site: the name of your site, e.g., "Denver", "Maricopa County", and so on.
• enroll_target: an integer indicating how many participants you aim to enroll during the period in question
• period_start: the start date of the period in question, in "YYYY-MM-DD" format
• period_end: the end date of the period in question, in "YYYY-MM-DD" format
• datapath: the path to your cleaned data - see the to1check package for R (https://github.com/mmparker/to1check)

Save this into the same directory as qa_report.rmd and knit.r.

Run knit.r to generate the report.

The simplest thing to do is just open R, then open knit.r and paste its commands into the R console.

View the qa_report.html file.

knit.r converts qa_report.rmd into qa_report.html, which you should be able to view in any browser, send in emails, etc.