usz_13c_d: 13C breath test data with MRI emptying for comparison

In dmenne/breathtestcore: Core Functions to Read and Fit 13c Time Series from Breath Tests

13C breath test data with MRI emptying for comparison

Description

13C time series PDR data from normals and three different meals in a cross-over design from the division of Gastroenterology and Hepatology, University Hospital Zurich. See Kuyumcu et al., Gastric secretion does not affect....

Data are formatted as described in usz_13c. In addition, half emptying times from MRI measurements are attached to the data as attribute mri_t50. The example below shows how to analyze the data and present half emptying times from MRI and 13C in diagrams.

Usage

data(usz_13c_d)

Examples

library(dplyr)
library(ggplot2)
data(usz_13c_d)
mri_t50 = attr(usz_13c_d, "mri_t50")
d = usz_13c_d %>% 
  cleanup_data() %>% # recommended to test for validity
  nlme_fit()
plot(d) +
  geom_vline(data = mri_t50, aes(xintercept = t50), linetype = 2)

# Maes-Ghoos t50
dd = mri_t50 %>% 
  inner_join(
    coef(d) %>% filter(parameter=="t50", method == "maes_ghoos"),
    by = c("patient_id", "group")) %>% 
  mutate(
    t50_maes_ghoos = value
 )

ggplot(dd, aes(x=t50, y = t50_maes_ghoos, color = group)) +  
  geom_point() +
  facet_wrap(~group) +
  geom_abline(slope = 1, intercept = 0) +
  xlim(45,205) +
  ylim(45,205) 

# Bluck-Coward t50
dd = mri_t50 %>% 
  inner_join(
    coef(d) %>% filter(parameter=="t50", method == "bluck_coward"),
    by = c("patient_id", "group")) %>% 
  mutate(
    t50_bluck_coward = value
 )

ggplot(dd, aes(x=t50, y = t50_bluck_coward, color = group)) +  
  geom_point() +
  facet_wrap(~group) +
  geom_abline(slope = 1, intercept = 0) +
  xlim(0,205) +
  ylim(0,205) 

dmenne/breathtestcore documentation built on Feb. 2, 2024, 6:12 p.m.