gastempt
A package and a Shiny web application to create simulated gastric emptying data, and to analyze experimental gastric emptying data using population fit with R and package nlme. Use the Docker image (https://hub.docker.com/u/dmenne) for easy installation. Documentation:
Science Score: 26.0%
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Low similarity (15.6%) to scientific vocabulary
Repository
A package and a Shiny web application to create simulated gastric emptying data, and to analyze experimental gastric emptying data using population fit with R and package nlme. Use the Docker image (https://hub.docker.com/u/dmenne) for easy installation. Documentation:
Basic Info
- Host: GitHub
- Owner: dmenne
- Language: R
- Default Branch: main
- Homepage: http://dmenne.github.io/gastempt/
- Size: 4.41 MB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 3
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
gastempt: Fitting gastric emptying curves
Dieter Menne\ Menne Biomed Consulting Tübingen, Germany\ https://www.menne-biomed.de\ dieter.menne\@menne-biomed.de{.email}
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
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linexp, vol = v0 * (1 + kappa * t / tempt) * exp(-t / tempt):Recommended for gastric emptying curves with an initial volume overshoot from secretion. With parameter kappa > 1, there is a maximum after t=0. When all emptying curves start with a steep drop, this model can be difficult to fit. -
powexp, vol = v0 * exp(-(t / tempt) ^ beta):The power exponential function introduced by Elashof et. al. to fit scintigraphic emptying data; this type of data does not have an initial overshoot by design. Compared to thelinexpmodel, fittingpowexpis more reliable and rarely fails to converge in the presence of noise and outliers. The power exponential can be useful with MRI data when there is an unusual late phase in emptying.
Methods with variants
- Population fits based on function
nlmein package Rnlme. - Stan-based fits, both without and with covariance estimation. Thanks to priors, fitting with Bayesian methods also works for single records, even if stability strongly improves with more data sets available; see stan_gastempt. Some details can be found in my blog. The rationale for using Stan to fit non-linear curves is discussed here for 13C breath test data, but is equally valid for gastric emptying data.
Data entry:
- Data can be entered directly from the clipboard copied from Excel, or can be simulated using a Shiny app.
- Several preset simulations are provided in the Shiny app, with different amounts of noise and outliers
- Robustness of models can be tested by manipulating noise quality and between-subject variance.
- Fits are displayed with data.
- The coefficients of the analysis including half-emptying time t50 and the slope at time t50 can be downloaded in .csv format.
Example
Program with simulated data (needs about 10 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)
Installing Docker
- For Windows 10, you can get the installer from the Docker store. For installation details, see here.\
- Linux users know how to install Docker anyway.
Installing gastempt
- From the command line, enter the following to start the container
docker run --name gastempt --restart unless-stopped -p 3838:3838 -d dmenne/gastempt
- The first startup needs some time because 1 GB has to be downloaded. Subsequent startups require only a few seconds.
- Connect to the app with your browser via
localhost:3838.
Owner
- Name: Dieter Menne
- Login: dmenne
- Kind: user
- Location: 72144 Dusslingen, Germany
- Company: Menne Biomed Consulting
- Website: http://www.menne-biomed.de
- Repositories: 6
- Profile: https://github.com/dmenne
Started as a nuclear physicist, PhD in genetics/biophysics. Signal processing in bat echolocation (Marburg, Tübingen, Singapore) Since 1989: Freelance
GitHub Events
Total
- Issues event: 2
- Issue comment event: 1
- Push event: 11
Last Year
- Issues event: 2
- Issue comment event: 1
- Push event: 11
Committers
Last synced: over 3 years ago
All Time
- Total Commits: 288
- Total Committers: 3
- Avg Commits per committer: 96.0
- Development Distribution Score (DDS): 0.201
Top Committers
| Name | Commits | |
|---|---|---|
| Dieter Menne | d****e@m****e | 230 |
| Dieter Menne | d****e@m****r | 56 |
| Jeffrey Pullin | j****n@g****m | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 2
- Total pull requests: 3
- Average time to close issues: 7 days
- Average time to close pull requests: 12 months
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 2.0
- Average comments per pull request: 1.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: 3 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 2.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- MRWUR (1)
- esbenbolvig (1)
Pull Request Authors
- jeffreypullin (1)
- andrjohns (1)
- bgoodri (1)
Top Labels
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Packages
- Total packages: 1
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Total downloads:
- cran 257 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 10
- Total maintainers: 1
cran.r-project.org: gastempt
Analyzing Gastric Emptying from MRI or Scintigraphy
- Homepage: https://github.com/dmenne/gastempt
- Documentation: http://cran.r-project.org/web/packages/gastempt/gastempt.pdf
- License: GPL (≥ 3)
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Latest release: 0.7.0
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.2.0 depends
- Rcpp >= 1.0.3 imports
- assertthat * imports
- dplyr * imports
- ggplot2 >= 3.3.0 imports
- methods * imports
- nlme * imports
- rstan >= 2.21.0 imports
- shiny * imports
- stringr * imports
- tibble >= 3.1.0 imports
- utf8 * imports
- covr * suggests
- knitr * suggests
- ragg * suggests
- rmarkdown * suggests
- rstantools * suggests
- testthat >= 2.99 suggests
- vdiffr * suggests
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- JamesIves/github-pages-deploy-action v4.4.1 composite
- actions/checkout v3 composite
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- rocker/r-base latest build