gastempt: Fitting gastric emptying curves

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

A package and a Shiny web application to create simulated gastric emptying data, and to analyze gastric emptying from clinical studies using a population fit with R and package nlme. In addition,Bayesian fits with Stan to handle critical cases are implemented.

Part of the work has been supported by section GI MRT, Klinik für Gastroenterologie und Hepatologie, Universitätsspital Zürich; thanks to Werner Schwizer and Andreas Steingötter for their contributions.

Download

The package is available from CRAN and github (source, documentation). To install, use:

devtools::install_github("dmenne/gastempt")

Compilation of the Stan models needs several minutes.

Shiny online interface

The web interface can be installed on your computer, or run as web app.

Two models are implemented in the web interface

Methods with variants

Data entry:

Example

Program with simulated data (needs about 40 seconds till plot shows):

library(gastempt)
dd = simulate_gastempt(n_records = 6, seed = 471)
d = dd$data
ret = stan_gastempt(d)
print(ret$coef)
print(ret$plot)
Screenshot

Docker image

The image cannot be compiled on the Docker hub because the build runs out of memory in the standard configuration.

Installing Docker

Installing gastempt

docker run --name gastempt  --restart unless-stopped -p 3838:3838 -d dmenne/gastempt