nlme_gastempt {gastempt} | R Documentation |
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
|
pnlsTol |
The value of pnlsTol at the initial iteration.
See |
model |
|
variant |
For both models, there are 3 variants
|
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
Parameterkappa
formodel = linexp
-
beta
Parameterbeta
formodel = 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 viasummary
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 ofnlme
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