Broom-method tidy to streamline the results of class
breathttestfit as generated by nls_fit or nlme_fit. Returns
the fit coefficients and half-emptying time t50 with the Maes/Ghoos method;
additional parameters should be extracted with coef.
Usage
# S3 method for breathtestfit
tidy(x, ...)Value
A tibble/data frame with columns
- patient_id
Patient Id (character)
- group
Treatment or patient group (character)
- m
Fraction metabolized
- k
Time constant (1/minutes)
- beta
The so-called lag parameters, no dimension
- t50
Emptying half time in minutes as calculated following Maes/Ghoos
Examples
library(broom)
# Generate simulated data
data = cleanup_data(simulate_breathtest_data()$data)
# Fit with the population method
fit = nlme_fit(data)
# Output coefficients
tidy(fit)
#> # A tibble: 10 × 6
#> patient_id group m k beta t50
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 rec_01 A 42.9 0.00605 1.50 164.
#> 2 rec_02 A 62.8 0.00772 1.97 157.
#> 3 rec_03 A 47.7 0.00943 1.38 98.5
#> 4 rec_04 A 34.5 0.0135 1.59 77.4
#> 5 rec_05 A 49.8 0.00916 2.41 151.
#> 6 rec_06 A 38.1 0.0101 2.16 127.
#> 7 rec_07 A 31.9 0.0139 2.32 97.2
#> 8 rec_08 A 43.6 0.00824 2.12 155.
#> 9 rec_09 A 40.3 0.00865 2.32 156.
#> 10 rec_10 A 14.5 0.00711 1.87 165.
# All coefficients in the long form
coef(fit)
#> # A tibble: 80 × 5
#> patient_id group parameter method value
#> <chr> <chr> <chr> <chr> <dbl>
#> 1 rec_01 A m exp_beta 42.9
#> 2 rec_01 A k exp_beta 0.00605
#> 3 rec_01 A beta exp_beta 1.50
#> 4 rec_01 A t50 bluck_coward 21.2
#> 5 rec_01 A t50 maes_ghoos 164.
#> 6 rec_01 A t50 maes_ghoos_scintigraphy 87.6
#> 7 rec_01 A tlag bluck_coward -47.5
#> 8 rec_01 A tlag maes_ghoos 66.9
#> 9 rec_02 A m exp_beta 62.8
#> 10 rec_02 A k exp_beta 0.00772
#> # … with 70 more rows