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breathtestcore (version 0.8.7)

Core Functions to Read and Fit 13c Time Series from Breath Tests

Description

Reads several formats of 13C data (IRIS/Wagner, BreathID) and CSV. Creates artificial sample data for testing. Fits Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'. Methods to fit breath test curves with Bayesian Stan methods are refactored to package 'breathteststan'. For a Shiny GUI, see package 'dmenne/breathtestshiny' on github.

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Install

install.packages('breathtestcore')

Monthly Downloads

291

Version

0.8.7

License

GPL-3

Issues

0

Pull Requests

0

Stars

3

Forks

2

Maintainer

Dieter Menne

Last Published

January 24th, 2024

Functions in breathtestcore (0.8.7)

t50_bluck_coward

Bluck-Coward self-corrected half-emptying time
simulate_breathtest_data

Simulate 13C breath time series data
t50_maes_ghoos_scintigraphy

Half-emptying time t50 from Maes/Ghoos fit with scintigraphic correction
subsample_data

Decimate densely sampled 13C time series
t50_maes_ghoos

Half-emptying time by Maes/Ghoos method
read_iris_csv

Read 13C data from IRIS/Wagner Analysen in CSV Format
read_iris

Read 13C data from IRIS/Wagner Analysen
read_breathtest_excel

Reads breathtest data in Excel format
tidy.breathtestfit

Broom-style tidying methods for breathtestfit
usz_13c_d

13C breath test data with MRI emptying for comparison
sigma.breathtestnlmefit

S3 method to extract the fit's residual standard deviation
tlag_bluck_coward

Lag phase for Bluck-Coward self-correcting fit
tlag_maes_ghoos

So-called lag time from Maes/Ghoos fit
usz_13c

Zurich sample set of 13C breath test data
usz_13c_a

Exotic 13C breath test data
cum_exp_beta

Cumulative exponential beta function
augment.breathtestfit

Augmented prediction for breathtest fit
coef_diff_by_group

Tabulates breath test parameter differences of groups
AIC.breathtestnlmefit

S3 AIC method for breathtestnlmefit
breathtest_read_function

Snoop method to read breath test file
btcore_file

Path to example breath test data file
coef_by_group

Tabulates per-group breath test parameters
coef.breathtestfit

S3 coef and summary for breathtestfit
cleanup_data

Transforms 13C breath data into a clean format for fitting
breathtest_data

Data structure with PDR data and descriptors for breath test records
read_breathid_xml

Read new BreathID/Examens XML file
extract_id

Extracts an ID from string IRIS CSV file
dob_to_pdr

Convert breath test DOB data to PDR data
plot.breathtestfit

S3 plot method for breathtestfit
nlme_fit

Mixed-model nlme fit to 13C Breath Data
read_breathid

Read BreathID file
nls_fit

Individual curve fit with nls to 13C breath test data
read_any_breathtest

Read breathtest files of any format
null_fit

Convert data to class breathtestfit
exp_beta

Exponential beta function for 13C breath data