Ship conference presentation on data quality and coverage reports of routinely collected health data

1. Data quality and coverage assessments
for the Secure Anonymous Information
Linkage databank
J. C. Demmler, C. Brooks, R. A. Lyons
College of Medicine, Swansea University
4th SHIP conference 2013, St. Andrews
29th of August 2013

2. Quality of routinely collected data
historically been collected for administrative purposes
data coverage is different for different datasets
but also changes over time and space
and between variables

3. Need for flexible data documentation
1 Documenting of dataset
2 Project documentation
3 Reproducible publications
4 Support web based enquiry system

4. Other considerations
usable by data analysts with minimum training
import and/or run code on the fly
option to display SQL and statistics coding
reproducible

5. Platform considerations
LaTeX, LyX or Open Office
using listings package
write or import syntax highlighted code
hide using comment package
weave together code and text using reproducible
research principle

6. Reproducible research (literate programming)
Package name Language
Sweave S-plus & R
knitr R
StatWeave STATA & SAS & R
SASweave SAS & R
MATweave Matlab/Octave
Pweave Python
Noweb C, C++, Perl, Java etc.
SPSS could be called through R shell or Noweb

7. STEP 1: Prepare SQL code
Lyx
SQL output if wanted in documentation

8. STEP 2: SQL → R
connect to SAIL database
connect to SHIP example1.sql script
run SHIP example1.sql script and save
results in a table called my.tables
manipulate and reformat table
create some summary statistics for
elements in table

9. STEP 3: R → documentation

10. Create formatted table straight from R object using xtable

11. Years covered by dataset

13. Spatial quality and coverage

14. Taking it further
Publish report online
export from LaTeX or LyX to HTML
create HTML straight from R markdown
Query basic data information through web site
Interactive web applications using R Studio Shiny
HTML form as input variables for LaTeX or R
markdown file

15. Thank you ...
LaTeX
Joanne Demmler www.latex-project.org
Email: j.demmler@swansea.ac.uk LyX
www.lyx.org
SAIL databank R
URL: www.SAILDatabank.com www.r-project.org
Email: SAILDatabank@swansea.ac.uk R Studio
www.rstudio.com