MedStat Stutter

Phantasies of a physicist fallen among physicians


Time series from 13C breath test recordings are used as a surrogate indicator for gastric emptying. Gastric emptying half time t50 is computed by fitting the series with an exponential beta or a Gamma function. Often, records are too short to obtain stable estimates of the trailing part. One can easily get unrealistic emptying times when single curves are fitted (Ghoos et al. (1993), Maes et al. (1998)).

Population methods can come to the rescue. When these fail, Bayesian methods provide a robust approach to non-linear curve fitting.

The methods described here are implemented in packages breathtestcore and breathtestshiny, and can be tested online here

Zipped source files and data

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Using vectors for indexed access to ragged arrays in Stan

volume ~ normal(
      v0[record] .* (1+ kappa[record] .* (minute ./ tempt[record])) .*
      exp(-minute ./ tempt[record]), sigma);

Fitting gastric emptying time series

Gastric volume times serie measured by MRI techniques can have an initial volume overshoot due to secretion. To estimate half-times and the degree of overshoot, the author of this blog has introduced the linexp function [@Fruehauf2011] with three parameters to complement the power exponential function used in earlier research [@Elashoff1982, @Elashoff1983b] with scintigraphic data.


v = v0* (1+t*kappa/tempt)*exp(-t/t_{empt})

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