nlme_gastempt: Simplified population fit of gastric emptying data

In gastempt: Analyzing Gastric Emptying from MRI or Scintigraphy

Simplified population fit of gastric emptying data

Description

Compute coefficients v0, tempt and kappa of a mixed model fit to a linexp function with one grouping variable

Usage

nlme_gastempt(d, pnlsTol = 0.001, model = linexp, variant = 1)

Arguments

d	A data frame with columns record Record descriptor as grouping variable, e.g. patient ID minute Time after meal or start of recording. vol Volume of meal or stomach
pnlsTol	The value of pnlsTol at the initial iteration. See nlmeControl When the model does not converge, pnlsTol is multiplied by 5 and the iteration repeated until convergence or pnlsTol >= 0.5. The effective value of pnlsTol is returned in a separate list item. When it is known that a data set converges badly, it is recommended to set the initial pnlsTol to a higher value, but below 0.5, for faster convergence.
model	linexp (default) or powexp
variant	For both models, there are 3 variants variant = 1 The most generic version with independent estimates of all three parameters per record (random = v0 + tempt + kappa ~ 1 | record). The most likely to fail for degenerate cases. If this variant converges, use it. variant = 2 Diagonal random effects (random = pdDiag(v0 + tempt + kappa) ~ 1; groups = ~record ). Better convergence in critical cases. Note: I never found out why I have to use the groups parameter instead of the |; see also p. 380 of Pinheiro/Bates. variant = 3 Since parameters kappa and beta respectively are the most difficult to estimate, these are fixed in this variant (random = v0 + tempt ~ 1). This variant converges in all reasonable cases, but the estimates of kappa and beta cannot be use for secondary between-group analysis. If you are only interested in t50, you can use this safe version.

Value

A list of class nlme_gastempt with elements coef, summary, plot, pnlsTol, message

• coef is a data frame with columns:

  • record Record descriptor, e.g. patient ID

  • v0 Initial volume at t=0

  • tempt Emptying time constant

  • kappa Parameter kappa for model = linexp

  • beta Parameter beta for model = powexp

  • t50 Half-time of emptying

  • slope_t50 Slope in t50; typically in units of ml/minute

  On error, coef is NULL

• nlme_result Result of the nlme fit; can be used for addition processing, e.g. to plot residuals or via summary to extract AIC. On error, nlme_result is NULL.

• plot A ggplot graph of data and prediction. Plot of raw data is returned even when convergence was not achieved.

• pnlsTol Effective value of pnlsTo after convergence or failure.

• message String "Ok" on success, and the error message of nlme on failure.

Examples

suppressWarnings(RNGversion("3.5.0"))
set.seed(4711)
d = simulate_gastempt(n_record = 10, kappa_mean = 0.9, kappa_std = 0.3,
                      model = linexp)$data
fit_d = nlme_gastempt(d)
# fit_d$coef # direct access
coef(fit_d) # better use accessor function
coef(fit_d, signif = 3) # Can also set number of digits
# Avoid ugly ggplot shading (not really needed...)
library(ggplot2)
theme_set(theme_bw() + theme(panel.spacing = grid::unit(0,"lines")))
# fit_d$plot  # direct access is possible
plot(fit_d) # better use accessor function

gastempt documentation built on May 2, 2022, 9:09 a.m.