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breathtestcore: 13C breath test to analyze gastric emptying

Dieter Menne
Menne Biomed Consulting Tübingen, Germany
http://www.menne-biomed.de

dieter.menne@menne-biomed.de

This is a reboot of R package dmenne/d13cbreath which is partially obsolete.

What it does

Sponsors and supporters

The software is being developed in cooperation with the Department of Gastroenterology of the University Hospital of Zürich and Claraspital Basel. Thanks to Benjamin Misselwitz, Mark Fox and Werner Schwizer. And special thanks to Andreas Steingötter for constantly reminding me that better statistics does necessarily make a method physiologically relevant.

How to install

To install the functions, use

devtools::install_github("breathtestcore","dmenne")
# In case you want to use the fancy Stan-based methodes
devtools::install_github("breathteststan","dmenne")
# And here the still rudimentary web GUI
devtools::install_github("breathtestshiny","dmenne")

Usage example

This example is from the documentation of function nlme_fit.

library(breathtestcore)    
d = simulate_breathtest_data(n_records = 3, noise = 0.2, seed = 4711)
data = cleanup_data(d$data)
fit = nlme_fit(data)
plot(fit) # calls plot.breathtestfit

For additional examples, see the folder tests/testthat of the source package.

Previous and planned work

The core fitting functions and the Stan variants are quite stable and can be used to analyze your breath test data with R. For the Stan variants, additional models that give credible intervals for differences between groups are planned. The Shiny web app with reporting is work in progress; online demo, source code.

Reference: