breathteststan (version 0.4.7)

stan_group_fit: Bayesian Stan fit to 13C Breath Data in Multiple Groups

Description

Fits exponential beta curves to 13C breath test series data using Bayesian Stan methods, by assuming fixed between group effects. This model is overly parsiomonious. Do not use it unless you check the results carefully and understand why fits can be very bad.

Usage

stan_group_fit(data, dose = 100, sample_minutes = 15,
  student_t_df = 10, chains = 2, iter = 1000,
  model = "breath_test_group_1")

Arguments

data

Data frame or tibble as created by cleanup_data, with mandatory columns patient_id, group, minute and pdr. It is recommended to run all data through cleanup_data which will insert dummy columns for patient_id and minute if the data are distinct, and report an error if not. Since the Bayesian method is stabilized by priors, it is possible to fit single curves.

dose

Dose of acetate or octanoate. Currently, only one common dose for all records is supported.

sample_minutes

If mean sampling interval is < sampleMinutes, data are subsampled using a spline algorithm

student_t_df

When student_t_df < 10, the student distribution is used to model the residuals. Recommended values to model typical outliers are from 3 to 6. When student_t_df >= 10, the normal distribution is used.

chains

Number of chains for Stan

iter

Number of iterations for each Stan chain

model

Name of model; use names(stanmodels) for other models.

Value

A list of classes "breathteststangroupfit", "breathteststanfit" and "breathtestfit" with elements

• coef Estimated parameters as data frame in a key-value format with columns patient_id, group, parameter, method and value. Has an attribute AIC.

• data The effectively analyzed data. If density of points is too high, e.g. with BreathId devices, data are subsampled before fitting.

• stan_fit The Stan fit for use with shinystan::launch_shiny or extraction of chains.

See Also

Base methods coef, plot, print; methods from package broom: tidy, augment.

Examples

# NOT RUN {
library(breathtestcore)
library(dplyr)
data("usz_13c", package = "breathtestcore")
data = usz_13c %>%
  dplyr::filter( patient_id %in%
       c("norm_001", "norm_002", "norm_003", "norm_004",
         "pat_001", "pat_002","pat_003")) %>%
  breathtestcore::cleanup_data()
fit = stan_group_fit(data, chains = 1, iter = 100)
plot(fit) # calls plot.breathtestfit
coef(fit)
# }
# NOT RUN {
# }