R/concCorrections.R

Defines functions corrFluxLeakage corrFluxDensity corrConcDilution

Documented in corrConcDilution corrFluxDensity corrFluxLeakage

corrConcDilution <- function(
		### Calculate concentration corrected for dilution with water vapor		
		ds 					##<< data frame with each row one observations, and respective columns 
		,colConc="CO2_Avg"	##<< column name of CO2 concentration [ppm]
		,colVapour="H20_Avg"	##<< column name of water vapour concentration [ppt]
		,isUpdateOnNonFiniteVapour=TRUE	##<< set to FALSE to not correct concentrations for records where vapour is not finite
			##<< in the default, the concentration will be NA
){
	##details<< 
	##  If CO2 concentration is measured per moist air, this function will calculate the concentration\
	## per dry air.
	##references<<
	## LI-COR, Application Note 129. The Importance of Water Vapor Measurements and Corrections. LI-COR, Inc., 4421 Superior Street, Lincoln, NE 68504, USA.
	vapourPpm <- ds[[colVapour]]/1000
	if( isTRUE(isUpdateOnNonFiniteVapour) ){
		ds[[colConc]]/(1-vapourPpm)
	} else {
		ans <- ds[[colConc]]
		isFiniteVapour <- is.finite(vapourPpm)
		ans[isFiniteVapour] <- ans[isFiniteVapour]/(1-vapourPpm[isFiniteVapour])
		ans
	}
	### numeric vector (nrow ds):  concentration of CO2 per dry air [ppm]
} 
attr(corrConcDilution,"ex") <- function(){
  #data(chamberLoggerEx1s)
  ds <- chamberLoggerEx1s
  ds$H20_Avg[1L] <- NA
  ds$CO2_dry <- corrConcDilution(ds); head(ds$CO2_dry)	
  ds$CO2_dry <- corrConcDilution(ds, isUpdateOnNonFiniteVapour=FALSE); head(ds$CO2_dry)	
}



corrFluxDensity <- function(
	### Calculate total flux inside the chamber from flux per amount of air
  	CO2_molarFlux 		##<< numeric vector of rate of changes in CO2 dry molar fraction [ppm/s]
	,volume=1			##<< numeric scalar: volume of the chamber in [m3]
	,temp=20	     	##<< numeric vector: temperature inside chamber [degC]  
	,pressure=101325 	##<< numeric vector: pressure inside chamber [Pa]
){
	##details<< 
	## The amount of air or CO2 is determined by the volume, pressure and temperature (universal gas law).
	## Converts concentrations to amount of substance in mol.
	R <- 8.3144621	# universal gas constant in [J/K/mol]  (J=Pa * m3)  
	CO2_molarFlux * pressure * volume  / (temp+273.15) / R 
	### numeric vector (nrow ds):  CO2 flux [mumol CO2 /s]
} 
attr(corrFluxDensity,"ex") <- function(){
	#data(chamberLoggerEx1s)
	ds <- chamberLoggerEx1s
	# here, just to have a column, take concentrations
	# aside fromt teh example, the flux should be calculated properly before
  	CO2_molarFlux <- ds$CO2_Avg   
	ds$CO2_flux <- corrFluxDensity(CO2_molarFlux, pressure=101*1000) #kPa converted to Pa	
  	plot(ds$CO2_flux)
}


corrFluxLeakage <- function(
	### Calculate flux corrected for leakage of the chamber	
	conc 				##<< numeric vector: concentration [Amount of substance]
	,pLeakage=1			##<< numeric scalar: fraction of concentration lost by leakage
){
	##details<< 
	## XX
	conc * pLeakage
	### numeric vector (length conc): corrected concentration [Amount of substance]
} 
attr(corrFluxLeakage,"ex") <- function(){
	#data(chamberLoggerEx1s)
	ds <- chamberLoggerEx1s
	ds$CO2_leakC <- corrFluxLeakage(ds$CO2_Avg)	
}

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RespChamberProc documentation built on June 23, 2017, 3 p.m.