Package: breathtestcore 0.8.6

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]

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breathtestcore.pdf |breathtestcore.html✨
breathtestcore/json (API)

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

Peer review:

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:

13cbreathbreath-testgastroenterologymedicalstan

26 exports 2 stars 1.27 score 71 dependencies 1 dependents 57 scripts 416 downloads

Last updated 8 months agofrom:fdd4a4c773. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 18 2024
R-4.5-winNOTESep 18 2024
R-4.5-linuxNOTESep 18 2024
R-4.4-winNOTESep 18 2024
R-4.4-macNOTESep 18 2024
R-4.3-winOKSep 18 2024
R-4.3-macOKSep 18 2024

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:assertthatbackportsbitbit64broomcellrangerclicliprcodetoolscolorspacecommonmarkcpp11crayoncurldplyrfansifarvergenericsggfittextggplot2gluegridtextgtablehmsisobandjpeglabelinglatticelifecyclemagrittrmarkdownMASSMatrixmgcvmultcompmunsellmvtnormnlmepillarpkgconfigpngprettyunitsprogresspurrrR6RColorBrewerRcppreadrreadxlrematchrlangsandwichscalesshadessignalstringistringrsurvivalTH.datatibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxfunxml2zoo

Data formats

Dieter Menne, [email protected]

Rendered fromdata_formats.Rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2020-01-28
Started: 2017-10-09

Methods and concepts

Dieter Menne, Menne Biomed Consulting Tuebingen, [email protected]

Rendered frommethods_and_concepts.Rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2022-04-06
Started: 2017-10-07

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