Rapid_aci_correction: Rapid_aci_correction function
In ManuelLamothe/RapidACi: Automated Rapid A-Ci curve correction for Li-Cor system

Description Usage Arguments Value

View source: R/Rapid_aci_correction_fct.r

Main function of the package. From a list of files, as produced by the buid_list function, the function will first extract recalculated gas exchange values when new leaf surface areas are provided (or original values if leafArea_mm2 = NA). The values will then be corrected according to the paired matching empty chamber measurements. Finally, data are prepared for further modelling analysis in an R list object.

1 2	Rapid_aci_correction(list_files, delta_max = 0.05, max_degree = 3, priority_curve = "positive")

`list_files`	A dataframe as generated by the build_list function
`delta_max`	Difference between two measure points below which we consider measurements to be at steady state. If not sure, verify with the diagnostic plots produced by the diagnose_sample function.
`max_degree`	The maximum polynomial order to consider for fitting the empty chamber measurement curve in order to correct the Rapid A-Ci measurements. This parameter takes an integer value from 1 up to 5 (as suggested by Stinziano _et al._, 2017). Default max_degree = 3.
`priority_curve`	For the very specific case when coefficients were retrieved from both an up and down ramp of the empty chamber A-Ci curve, a priority can be set. This argument can only take "positive" or "negative" (default = "postive").

The function returns a list of elements per A-Ci measurement file that contains the sample ID, the leaf area used, the timestamp, the paths to the A-Ci and empty chamber file used, important data variables from these files (recalculated variables if leaf area was provided), the coefficients of the fitted curve(s) used to correct values, as well as corrected A and Ci. The formatted data for plantecophys can be found under the Raci element.

ManuelLamothe/RapidACi documentation built on Sept. 16, 2020, 9:53 p.m.