Package: breathtestcore 0.8.11

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

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.

Authors:Dieter Menne [aut, cre], Menne Biomed Consulting Tuebingen [cph], Benjamin Misselwitz [fnd], Mark Fox [fnd], Andreas Steingoetter [dtc], University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]

breathtestcore_0.8.11.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
breathtestcore/json (API)

# Install 'breathtestcore' in R:
install.packages('breathtestcore', repos = c('https://dmenne.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dmenne/breathtestcore/issues

Datasets:
  • 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

On CRAN:

Conda:

13cbreathbreath-testgastroenterologymedicalstan

5.91 score 3 stars 67 scripts 381 downloads 26 exports 69 dependencies

Last updated from:0f09a9db11. Checks:1 ERROR, 8 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR199
source / vignettesOK290
linux-release-x86_64OK220
macos-release-arm64OK118
macos-oldrel-arm64OK171
windows-develOK180
windows-releaseOK151
windows-oldrelOK168
wasm-releaseOK167

Exports:breathtest_databreathtest_read_functionbtcore_filecleanup_datacoef_by_groupcoef_diff_by_groupcum_exp_betadob_to_pdrexp_betaextract_idnlme_fitnls_fitnull_fitread_any_breathtestread_breathidread_breathid_xmlread_breathtest_excelread_irisread_iris_csvsimulate_breathtest_datasubsample_datat50_bluck_cowardt50_maes_ghoost50_maes_ghoos_scintigraphytlag_bluck_cowardtlag_maes_ghoos

Dependencies:assertthatbackportsbitbit64broomcellrangerclicliprcodetoolscommonmarkcpp11crayoncurldplyrfarvergenericsggfittextggplot2gluegridtextgtablehmsisobandjpeglabelinglatticelifecyclelitedownmagrittrmarkdownMASSMatrixmultcompmvtnormnlmepillarpkgconfigpngprettyunitsprogresspurrrR6RColorBrewerRcppreadrreadxlrematchrlangS7sandwichscalesshadessignalstringistringrsurvivalTH.datatibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxfunxml2zoo

Methods and concepts
A heretical view on 13C breath test for gastric emptying | Current concepts | Dieter's soapbox | How to correct for the pharmacological bias? | Why do we need population fits? | Why no Wagner-Nelson (Sanaka)? | Citations
Rendered frommethods_and_concepts.Rmdusingknitr::rmarkdown

Last update: 2026-07-13
Started: 2017-10-07

Data formats
Concepts | Automatic grouping | Simulated data | Built-in data sets | Generic formats | How to use the Excel data formats | Two-column format | Three-column format | Four-column format | DOB instead of PDF | Vendor-specific formats | IRIS-Wagner composite data | IRIS/Wagner CSV format | BreathID composite format | BreathID XML format
Rendered fromdata_formats.Rmdusingknitr::rmarkdown

Last update: 2024-11-20
Started: 2017-10-09

Readme and manuals

Help Manual

Help pageTopics
S3 AIC method for breathtestnlmefitAIC.breathtestnlmefit
Augmented prediction for breathtest fitaugment.breathtestfit
Data structure with PDR data and descriptors for breath test recordsbreathtest_data
Snoop method to read breath test filebreathtest_read_function
Path to example breath test data filebtcore_file
Transforms 13C breath data into a clean format for fittingcleanup_data
Tabulates per-group breath test parameterscoef_by_group
Tabulates breath test parameter differences of groupscoef_diff_by_group
S3 coef and summary for breathtestfitcoef.breathtestfit
Cumulative exponential beta functioncum_exp_beta
Convert breath test DOB data to PDR datadob_to_pdr
Exponential beta function for 13C breath dataexp_beta
Extracts an ID from string IRIS CSV fileextract_id
Mixed-model nlme fit to 13C Breath Datanlme_fit
Individual curve fit with nls to 13C breath test datanls_fit
Convert data to class breathtestfitnull_fit
S3 plot method for breathtestfitplot.breathtestfit
Read breathtest files of any formatread_any_breathtest
Read BreathID fileread_breathid
Read new BreathID/Examens XML fileread_breathid_xml
Reads breathtest data in Excel formatread_breathtest_excel
Read 13C data from IRIS/Wagner Analysenread_iris
Read 13C data from IRIS/Wagner Analysen in CSV Formatread_iris_csv
S3 method to extract the fit's residual standard deviationsigma.breathtestnlmefit
Simulate 13C breath time series datasimulate_breathtest_data
Decimate densely sampled 13C time seriessubsample_data
Bluck-Coward self-corrected half-emptying timet50_bluck_coward
Half-emptying time by Maes/Ghoos methodt50_maes_ghoos
Half-emptying time t50 from Maes/Ghoos fit with scintigraphic correctiont50_maes_ghoos_scintigraphy
Broom-style tidying methods for breathtestfittidy.breathtestfit
Lag phase for Bluck-Coward self-correcting fittlag_bluck_coward
So-called lag time from Maes/Ghoos fittlag_maes_ghoos
Zurich sample set of 13C breath test datausz_13c
Exotic 13C breath test datausz_13c_a
13C breath test data with MRI emptying for comparisonusz_13c_d