Package: gastempt 0.7.0

gastempt: Analyzing Gastric Emptying from MRI or Scintigraphy

Fits gastric emptying time series from MRI or 'scintigraphic' measurements using nonlinear mixed-model population fits with 'nlme' and Bayesian methods with Stan; computes derived parameters such as t50 and AUC.

Authors:Dieter Menne [aut, cre]

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gastempt.pdf |gastempt.html✨
gastempt/json (API)

# Install 'gastempt' in R:

install.packages('gastempt', repos = c('https://dmenne.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dmenne/gastempt/issues

Pkgdown site:https://dmenne.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

5.41 score 3 stars 17 scripts 406 downloads 13 exports 79 dependencies

Last updated 2 months agofrom:5c68a56b54. Checks:2 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 22 2025
R-4.5-win-x86_64	NOTE	Jan 22 2025
R-4.5-linux-x86_64	OK	Jan 22 2025
R-4.4-win-x86_64	NOTE	Jan 22 2025
R-4.4-mac-x86_64	NOTE	Jan 22 2025
R-4.4-mac-aarch64	NOTE	Jan 22 2025
R-4.3-win-x86_64	NOTE	Jan 22 2025
R-4.3-mac-x86_64	NOTE	Jan 22 2025
R-4.3-mac-aarch64	NOTE	Jan 22 2025

Exports:linexp linexp_auc linexp_log linexp_slope nlme_gastempt powexp powexp_log powexp_slope run_shiny simulate_gastempt stan_gastempt stan_model_names t50

Dependencies:abind assertthat backports base64enc BH bslib cachem callr checkmate cli colorspace commonmark crayon desc digest distributional dplyr fansi farver fastmap fontawesome fs generics ggplot2 glue gridExtra gtable htmltools httpuv inline isoband jquerylib jsonlite labeling later lattice lifecycle loo magrittr MASS Matrix matrixStats memoise mgcv mime munsell nlme numDeriv pillar pkgbuild pkgconfig posterior processx promises ps QuickJSR R6 rappdirs RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan sass scales shiny sourcetools StanHeaders stringi stringr tensorA tibble tidyselect utf8 vctrs viridisLite withr xtable

Fitting gastric emptying curves

Dieter Menne

Rendered fromgastempt.Rmdusingknitr::rmarkdownon Jan 22 2025.

Last update: 2024-12-04
Started: 2016-04-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract coefficients from nlme_gastempt result	coef.nlme_gastempt
Extract coefficients from stan_gastempt result	coef.stan_gastempt
Functions for gastric emptying analysis	gastemptfunc linexp linexp_auc linexp_log linexp_slope powexp powexp_log powexp_slope
Simplified population fit of gastric emptying data	nlme_gastempt
Plot data points and fit curve of an nlme_gastempt fit	plot.nlme_gastempt
Plot data points and fit curve of an stan_gastempt fit	plot.stan_gastempt
Run shiny app demonstrating fit strategies with simulated data	run_shiny
Simulate gastric emptying data following a linexp or powexp function	simulate_gastempt
Fit gastric emptying curves with Stan	stan_gastempt
Names and descriptions of precompiled Stan models	stan_model_names
Compute half-emptying time from nlme parameters	t50