Reading and Writing Data

Functions for reading and writing breath test data

read_any_breathtest()

Read breathtest files of any format

read_breathid()

Read BreathID file

read_breathid_xml()

Read new BreathID/Examens XML file

read_breathtest_excel()

Reads breathtest data in Excel format

read_iris()

Read 13C data from IRIS/Wagner Analysen

read_iris_csv()

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

breathtest_data()

Data structure with PDR data and descriptors for breath test records

breathtest_read_function()

Snoop method to read breath test file

extract_id()

Extracts an ID from string IRIS CSV file

btcore_file()

Path to example breath test data file

Data

Simulated and patient data

simulate_breathtest_data()

Simulate 13C breath time series data

usz_13c

Zurich sample set of 13C breath test data

usz_13c_a

Exotic 13C breath test data

usz_13c_d

13C breath test data with MRI emptying for comparison

Cleanup and manipulate

Functions to cleanup and manipulate breath test data

dob_to_pdr()

Convert breath test DOB data to PDR data

cleanup_data()

Transforms 13C breath data into a clean format for fitting

subsample_data()

Decimate densely sampled 13C time series

Fitting time series

Functions to fit time series

nlme_fit()

Mixed-model nlme fit to 13C Breath Data

nls_fit()

Individual curve fit with nls to 13C breath test data

null_fit()

Convert data to class breathtestfit

Extracting parameters

Functions to extract parameters from a fitted model

AIC(<breathtestnlmefit>)

S3 AIC method for breathtestnlmefit

sigma(<breathtestnlmefit>)

S3 method to extract the fit's residual standard deviation

augment(<breathtestfit>)

Augmented prediction for breathtest fit

coef_by_group()

Tabulates per-group breath test parameters

coef_diff_by_group()

Tabulates breath test parameter differences of groups

coef(<breathtestfit>)

S3 coef and summary for breathtestfit

tidy(<breathtestfit>)

Broom-style tidying methods for breathtestfit

cum_exp_beta()

Cumulative exponential beta function

exp_beta()

Exponential beta function for 13C breath data

t50_bluck_coward()

Bluck-Coward self-corrected half-emptying time

t50_maes_ghoos()

Half-emptying time by Maes/Ghoos method

t50_maes_ghoos_scintigraphy()

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

tlag_bluck_coward()

Lag phase for Bluck-Coward self-correcting fit

tlag_maes_ghoos()

So-called lag time from Maes/Ghoos fit

Plotting

Functions to plot data and fits

plot(<breathtestfit>)

S3 plot method for breathtestfit