Processing data from respiration chambers.
Main method is calcClosedChamberFlux
,
to calculate flux and its uncertainty from a time series of measurements.
A first set of functions correct measured CO2 concentrations and fluxes for environmental and chamber properties.
Dilution with water vapor: corrConcDilution
Changing air density with pressure and temperature: corrFluxDensity
Leakage of the chamber: corrFluxLeakage
A second set of functions estimates the flux and its uncertainty from the concentrations.
Aggregating estimates: calcClosedChamberFlux
Select the subset of data after lagTime: selectDataAfterLag
Estimate the initial flux by polynomial regression: regressFluxExp
Estimate uncertainty of regression due to leverage of starting and end points: sigmaBootLeverage
Convert from mumol CO2/s to g C/day: convert_mumolPers_to_gPerday
Further misc functionality:
Reading files generated by data-loggers into R: readDat
and read81x
Plotting the time series and the resulting best fit: plotResp
Plotting measurement time versus resulting standard error of the flux estimate: plotDurationUncertainty
Working with a time series of several measurement cycles (see vignette)
identifying contiguous measurement cycles: subsetContiguous
apply the fitting to all measurement cycles: calcClosedChamberFluxForChunks
Plotting all time series and fits: plotCampaignConcSeries
Thomas Wutzler, Oscar Perez Priego
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