inst/shiny/include/details.md

In dmenne/breathtestshiny: Shiny Web App to Fit 13c Time Series from Breath Tests

The Details panel displays per-curve fit results. To perform your own statistical analysis, you can download the displayed parameters as Excel file or to the clipboard.

By default, the Search box in the top right corner contains the text t50 which filters the table to show values for gastric emptying half-time only, computed by different methods. If you want to further restrict the table to show only t50 computed by the Maes/Ghoos method, use the drop-down filter box in column method.

• To sort by the values in one column, click the up/down arrows in the column header.
• To download or print the currently displayed parameter table, use the buttons in the top-left corner.
• To display all parameters, clear the text in Search box.

Primary fit parameters

Each curve has 3 primary fit parameter for the exponential beta function labeled as method exp_beta.

• m: Effectively metabolized fraction of 13C as percentage, computed from the area under the PDF curve from 0 to infinity. This parameter depends on body weight and height, and may be badly defined if these are not given. Since some of the assumptions on metabolics are not well defined, it is rarely interpreted. The half-emptying time does not depend on m, but only on beta and k. In the current implementation, it is also assumed that the dose is 100 mg for all records.
• k: Time constant of the beta-exponential in units of 1/min; 1/k is sometimes quoted as the emptying time tempt. Both k and tempt are rarely interpreted directly, because the derived quantities t50 and tlag have a better defined meaning.
• beta: A dimensionless quantity, typically in the range from 1 to 3. (beta-1) is the degree of polynomial at minute = 0. For beta = 2, the function starts with a linear slope, for beta = 3 as a quadratic parabola with slope = 0. For higher values of beta, this results in a lag-like behaviour, most pronounced in the peak position that shifts to higher values.
• deviance: Deviance quantifies the goodness of fit, i.e. the average deviation of the measured data points from the fit; smaller values indicate better fit. By sorting for deviance, outlier curves can be identified.

Derived parameters

The most important derived parameter is the half-emptying time t50. It can be computed from the primary fit parameters by different methods; see the documentation for references.

• maes_ghoos The classical method by Maes/Ghoos (often called Ghoos-method); compared to the half-emptying time from MRI or scintigraphy, the values of t50 are much to high.
• maes_ghoos_scint The Maes/Ghoos half-emptying time, with a linear correction so that emptying times are closer to those from MRI or scintigraphy. This is a purely ad-hoc correction that might work for some special meal, but demonstrates one of the heroic attempts to obtain realistic estimates for a method that does only badly reflect real gastric processing. Don't use it.
• bluck_coward A version proposed by Bluck and Coward to correct the estimated half emptying times. While the theory is has a sound pharmcological basis, in practice the estimate does not correlate better with the results from MRI than those from maes_ghoos.

A second parameter often used to describe the lag in gastric emptying is tlag, in the same method variants as for t50. maes_ghoos tlag is given as the position of the peak of the PDR time series. It is only indirectly related to a real lag in gastric emptying, which would be represented by a time shift without deformation, but it is a reasonable surrogate. bluck_coward This estimate is not very useful, it can be negative. Don't use it.

Where is the Wagner-Nelson method?

The Wagner-Nelson method is semi-parametric fit that seemingly does not require a fit, so it was used for PDR time series for which the single-curve fit failed. The approach is valid for the rising slope of the PDR curve, but uses a fixed value for the trailing part of the curve which has little basis. In the legacy package d13cbreath I have implemented a method to replace the fixed estimate for the trailing slope by a Bluck-Coward fit, but I do not recommend the method any longer.

With the population-based methods and the Bayesian (Stan) method, all curves can be fitted successfully. Do not use the Wagner-Nelson method, it does not give any 'better' values. Double-peaked excretion curves for which the Wagner-Nelson method was introduced cannot be meaningfully quantified by half-times. The problems of using ^13^C PDR time series as surrogates for gastric emptying are much more basic.

Sanaka, Yamamoto, Tsutsumi, Abe, Kuyama (2005) Wagner-Nelson method for analysing the atypical double-peaked excretion curve in the [13c]-octanoate gastric emptying breath test in humans. Clinical and experimental pharmacology and physiology 32, 590-594.

dmenne/breathtestshiny documentation built on July 21, 2022, 3:41 a.m.