R/val_TDL_Licor_variables.R
In erikerhardt/isogasex: Isotopic gas exchange using TDL and Licor input. Updated version of package tdllicor
#' Assign TDL and Licor values to val variable names, raw and summarized values
#'
#' Function to assign TDL and Licor values to variable names,
#' summaries and some smart way for individual observations (later for NPBS).
#' If the variable has values, use those, if not then populate with NAs.
#'
#' These are the columns expected from the Licor and TDL.
#' Any columns with headers not listed here will not be used.
#'
#' EXPECTED column names for Licor:
#' \preformatted{
#' (in isogasex) (column from Licor)
#' Obs Obs
#' HHMMSS HHMMSS
#' FTime FTime
#' A Photo
#' E Trmmol
#' temp_air Tair
#' temp_leaf Tleaf
#' temp_block TBlk
#' Ce CO2R
#' Co CO2S
#' xin H2OR
#' xout H2OS
#' rh_ref RH_R
#' rh_sam RH_S
#' uin Flow
#' par_int PARi
#' par_ext PARo
#' Atm_press Press
#' CsMch CsMch
#' HsMch HsMch
#' StableF StableF
#' Status Status
#' gsc Cond
#' Ci Ci
#' VPD VpdL
#' La Area
#' StmRat StmRat
#' gbw BLCond
#' VpdA VpdA
#' Ci_Ca Ci_Ca
#' pi Ci_Pa
#' uc_20_mV uc_20_mV
#' uc_21_mV uc_21_mV
#' U_S X.U.S.
#' Trans Trans
#' CndCO2 CndCO2
#' Ref_mV Ref_mV
#' xTemp1 xTemp1
#' xTemp2 xTemp2
#' TChamAir TChamAir
#' }
#'
#' EXPECTED column names for TDL:
#' \preformatted{
#' (in isogasex) (column from TDL)
#' TIMESTAMP TIMESTAMP
#' RECORD RECORD
#' PrevSite PrevSite
#' SiteOutput SiteOutput
#' StartSeqFlag StartSeqFlag
#' SeqActiveFlag SeqActiveFlag
#' SiteCount SiteCount
#' conc12CO2 ConcA
#' conc13CO2 ConcB
#' ConcC ConcC
#' TGAStatus TGAStatus
#' TGApressure TGApressure
#' MassFlow1 MassFlow1
#' Pressure1 Pressure1
#' MassFlow2 MassFlow2
#' Pressure2 Pressure2
#' PressureProMan PressureProMan
#' }
#'
#' Conventions, put everything in \code{val}.
#' Observed values from TDL or Licor prefix: \code{val$obs$*}
#'
#' Summarized values from TDL or Licor prefix: \code{val$sum$*}
#'
#' @param TDL xxxPARAMxxx
#' @param Licor xxxPARAMxxx
#' @param TDL_cycle xxxPARAMxxx
#' @param val xxxPARAMxxx
#' @param sw xxxPARAMxxx
#'
#' @return val xxxRETURNxxx
#'
val_TDL_Licor_variables <-
function# Assign TDL and Licor values to val variable names, raw and summarized values
###
(TDL
###
, Licor
###
, TDL_cycle
###
, val
###
, sw
###
)
{
### !!!!!
### Note, the variable names used below were from the CalculationsFile.xls
### in cases in the calculations, variables are referred to by their column header name
### Look at the variable names again and decide whether to use var name or col name.
## Function to assign TDL and Licor values to variable names,
## summaries and some smart way for individual observations (later for NPBS).
## If the variable has values, use those, if not then populate with NAs.
## These are the columns expected from the Licor and TDL.
## Any columns with headers not listed here will not be used.
##
## EXPECTED column names for Licor:
## \preformatted{
## (in isogasex) (column from Licor)
## Obs Obs
## HHMMSS HHMMSS
## FTime FTime
## A Photo
## E Trmmol
## temp_air Tair
## temp_leaf Tleaf
## temp_block TBlk
## Ce CO2R
## Co CO2S
## xin H2OR
## xout H2OS
## rh_ref RH_R
## rh_sam RH_S
## uin Flow
## par_int PARi
## par_ext PARo
## Atm_press Press
## CsMch CsMch
## HsMch HsMch
## StableF StableF
## Status Status
## gsc Cond
## Ci Ci
## VPD VpdL
## La Area
## StmRat StmRat
## gbw BLCond
## VpdA VpdA
## Ci_Ca Ci_Ca
## pi Ci_Pa
## uc_20_mV uc_20_mV
## uc_21_mV uc_21_mV
## U_S X.U.S.
## Trans Trans
## CndCO2 CndCO2
## Ref_mV Ref_mV
## xTemp1 xTemp1
## xTemp2 xTemp2
## TChamAir TChamAir
## }
##
## EXPECTED column names for TDL:
## \preformatted{
## (in isogasex) (column from TDL)
## TIMESTAMP TIMESTAMP
## RECORD RECORD
## PrevSite PrevSite
## SiteOutput SiteOutput
## StartSeqFlag StartSeqFlag
## SeqActiveFlag SeqActiveFlag
## SiteCount SiteCount
## conc12CO2 ConcA
## conc13CO2 ConcB
## ConcC ConcC
## TGAStatus TGAStatus
## TGApressure TGApressure
## MassFlow1 MassFlow1
## Pressure1 Pressure1
## MassFlow2 MassFlow2
## Pressure2 Pressure2
## PressureProMan PressureProMan
## }
## Conventions, put everything in \code{val}.
## Observed values from TDL or Licor prefix: \code{val$obs$*}
val$obs <- list();
val$obs$TDL <- list();
val$obs$Licor <- list();
## Summarized values from TDL or Licor prefix: \code{val$sum$*}
val$sum <- list();
val$sum$TDL <- list();
val$sum$Licor <- list();
#Licor$data:
if (sw$use_Licor) {
temp_n_Licor <- length(Licor$data[,1]); # "Obs"
} else {
temp_n_Licor <- 0;
}
# Variables in calculations
if (sum(colnames(Licor$data)=="Obs" )) { val$obs$Licor$Obs <- Licor$data[,"Obs" ]; } else {val$obs$Licor$Obs <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="HHMMSS" )) { val$obs$Licor$HHMMSS <- Licor$data[,"HHMMSS" ]; } else {val$obs$Licor$HHMMSS <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="FTime" )) { val$obs$Licor$FTime <- Licor$data[,"FTime" ]; } else {val$obs$Licor$FTime <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Photo" )) { val$obs$Licor$A <- Licor$data[,"Photo" ]; } else {val$obs$Licor$A <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Trmmol" )) { val$obs$Licor$E <- Licor$data[,"Trmmol" ]; } else {val$obs$Licor$E <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Tair" )) { val$obs$Licor$temp_air <- Licor$data[,"Tair" ]; } else {val$obs$Licor$temp_air <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Tleaf" )) { val$obs$Licor$temp_leaf <- Licor$data[,"Tleaf" ]; } else {val$obs$Licor$temp_leaf <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="TBlk" )) { val$obs$Licor$temp_block <- Licor$data[,"TBlk" ]; } else {val$obs$Licor$temp_block <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="CO2R" )) { val$obs$Licor$Ce <- Licor$data[,"CO2R" ]; } else {val$obs$Licor$Ce <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="CO2S" )) { val$obs$Licor$Co <- Licor$data[,"CO2S" ]; } else {val$obs$Licor$Co <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="H2OR" )) { val$obs$Licor$xin <- Licor$data[,"H2OR" ]; } else {val$obs$Licor$xin <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="H2OS" )) { val$obs$Licor$xout <- Licor$data[,"H2OS" ]; } else {val$obs$Licor$xout <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="RH_R" )) { val$obs$Licor$rh_ref <- Licor$data[,"RH_R" ]; } else {val$obs$Licor$rh_ref <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="RH_S" )) { val$obs$Licor$rh_sam <- Licor$data[,"RH_S" ]; } else {val$obs$Licor$rh_sam <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Flow" )) { val$obs$Licor$uin <- Licor$data[,"Flow" ]; } else {val$obs$Licor$uin <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="PARi" )) { val$obs$Licor$par_int <- Licor$data[,"PARi" ]; } else {val$obs$Licor$par_int <- matrix(NA,temp_n_Licor,1)}; # PAR or PPFD These two are defined in the same way at top of CalculationsFile.xls
if (sum(colnames(Licor$data)=="PARo" )) { val$obs$Licor$par_ext <- Licor$data[,"PARo" ]; } else {val$obs$Licor$par_ext <- matrix(NA,temp_n_Licor,1)}; # PAR or PPFD
if (sum(colnames(Licor$data)=="Press" )) { val$obs$Licor$Atm_press <- Licor$data[,"Press" ]; } else {val$obs$Licor$Atm_press <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="CsMch" )) { val$obs$Licor$CsMch <- Licor$data[,"CsMch" ]; } else {val$obs$Licor$CsMch <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="HsMch" )) { val$obs$Licor$HsMch <- Licor$data[,"HsMch" ]; } else {val$obs$Licor$HsMch <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="StableF" )) { val$obs$Licor$StableF <- Licor$data[,"StableF" ]; } else {val$obs$Licor$StableF <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Status" )) { val$obs$Licor$Status <- Licor$data[,"Status" ]; } else {val$obs$Licor$Status <- matrix(NA,temp_n_Licor,1)};
# Variables NOT in calculations
if (sum(colnames(Licor$data)=="Cond" )) { val$obs$Licor$gsc <- Licor$data[,"Cond" ]; } else {val$obs$Licor$gsc <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Ci" )) { val$obs$Licor$Ci <- Licor$data[,"Ci" ]; } else {val$obs$Licor$Ci <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="VpdL" )) { val$obs$Licor$VPD <- Licor$data[,"VpdL" ]; } else {val$obs$Licor$VPD <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Area" )) { val$obs$Licor$La <- Licor$data[,"Area" ]; } else {val$obs$Licor$La <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="StmRat" )) { val$obs$Licor$StmRat <- Licor$data[,"StmRat" ]; } else {val$obs$Licor$StmRat <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="BLCond" )) { val$obs$Licor$gbw <- Licor$data[,"BLCond" ]; } else {val$obs$Licor$gbw <- matrix(NA,temp_n_Licor,1)};
# additional columns
if (sum(colnames(Licor$data)=="VpdA" )) { val$obs$Licor$VpdA <- Licor$data[,"VpdA" ]; } else {val$obs$Licor$VpdA <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Ci_Ca" )) { val$obs$Licor$Ci_Ca <- Licor$data[,"Ci_Ca" ]; } else {val$obs$Licor$Ci_Ca <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Ci_Pa" )) { val$obs$Licor$pi <- Licor$data[,"Ci_Pa" ]; } else {val$obs$Licor$pi <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="uc_20_mV" )) { val$obs$Licor$uc_20_mV <- Licor$data[,"uc_20_mV" ]; } else {val$obs$Licor$uc_20_mV <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="uc_21_mV" )) { val$obs$Licor$uc_21_mV <- Licor$data[,"uc_21_mV" ]; } else {val$obs$Licor$uc_21_mV <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="X.U.S." )) { val$obs$Licor$U_S <- Licor$data[,"X.U.S." ]; } else {val$obs$Licor$U_S <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Trans" )) { val$obs$Licor$Trans <- Licor$data[,"Trans" ]; } else {val$obs$Licor$Trans <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="CndCO2" )) { val$obs$Licor$CndCO2 <- Licor$data[,"CndCO2" ]; } else {val$obs$Licor$CndCO2 <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Ref_mV" )) { val$obs$Licor$Ref_mV <- Licor$data[,"Ref_mV" ]; } else {val$obs$Licor$Ref_mV <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="xTemp1" )) { val$obs$Licor$xTemp1 <- Licor$data[,"xTemp1" ]; } else {val$obs$Licor$xTemp1 <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="xTemp2" )) { val$obs$Licor$xTemp2 <- Licor$data[,"xTemp2" ]; } else {val$obs$Licor$xTemp2 <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="TChamAir" )) { val$obs$Licor$TChamAir <- Licor$data[,"TChamAir" ]; } else {val$obs$Licor$TChamAir <- matrix(NA,temp_n_Licor,1)};
#TDL$data:
val$obs$TDL$TIMESTAMP <- TDL$data [,"TIMESTAMP" ];
val$obs$TDL$RECORD <- TDL$data [,"RECORD" ];
val$obs$TDL$PrevSite <- TDL$data [,"PrevSite" ];
val$obs$TDL$SiteOutput <- TDL$data [,"SiteOutput" ];
val$obs$TDL$StartSeqFlag <- TDL$data [,"StartSeqFlag" ];
val$obs$TDL$SeqActiveFlag <- TDL$data [,"SeqActiveFlag" ];
val$obs$TDL$SiteCount <- TDL$data [,"SiteCount" ];
val$obs$TDL$conc12CO2 <- TDL$data [,"ConcA" ];
val$obs$TDL$conc13CO2 <- TDL$data [,"ConcB" ];
val$obs$TDL$ConcC <- TDL$data [,"ConcC" ];
val$obs$TDL$TGAStatus <- TDL$data [,"TGAStatus" ];
val$obs$TDL$TGApressure <- TDL$data [,"TGApressure" ];
val$obs$TDL$MassFlow1 <- TDL$data [,"MassFlow1" ];
val$obs$TDL$Pressure1 <- TDL$data [,"Pressure1" ];
val$obs$TDL$MassFlow2 <- TDL$data [,"MassFlow2" ];
val$obs$TDL$Pressure2 <- TDL$data [,"Pressure2" ];
val$obs$TDL$PressureProMan <- TDL$data [,"PressureProMan" ];
val$obs$TDL$interp_tank_hi_12 <- TDL$interp[,"tank_hi_12" ];
val$obs$TDL$interp_tank_hi_13 <- TDL$interp[,"tank_hi_13" ];
val$obs$TDL$interp_tank_low_12 <- TDL$interp[,"tank_low_12" ];
val$obs$TDL$interp_tank_low_13 <- TDL$interp[,"tank_low_13" ];
val$obs$TDL$interp_reference_12 <- TDL$interp[,"reference_12" ];
val$obs$TDL$interp_reference_13 <- TDL$interp[,"reference_13" ];
val$obs$TDL$chamber_12 <- val$obs$TDL$conc12CO2; val$obs$TDL$chamber_12[!(val$obs$TDL$PrevSite == TDL_cycle$number_chamber)] <- NA;
val$obs$TDL$chamber_13 <- val$obs$TDL$conc13CO2; val$obs$TDL$chamber_13[!(val$obs$TDL$PrevSite == TDL_cycle$number_chamber)] <- NA;
if (sw$use_Licor==0) {
Licor$summary$n <- 0;
}
#Licor$summary:
#val$sum$Licor$Obs <- Licor$summary[,"Obs"];
#val$sum$Licor$HHMMSS <- Licor$summary[,"HHMMSS"];
val$sum$Licor$n <- Licor$summary$n;
val$sum$Licor$first_ind <- Licor$summary$first_ind;
val$sum$Licor$ind <- Licor$summary$ind;
val$sum$Licor$site <- Licor$summary$site;
val$sum$Licor$n_sam <- Licor$summary$n_sam;
val$sum$Licor$time <- Licor$summary$time;
# Variables in calculations
if (sum(colnames(Licor$summary$mean)=="FTime" )) { val$sum$Licor$FTime <- Licor$summary$mean[,"FTime" ]; } else {val$sum$Licor$FTime <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Photo" )) { val$sum$Licor$A <- Licor$summary$mean[,"Photo" ]; } else {val$sum$Licor$A <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Trmmol" )) { val$sum$Licor$E <- Licor$summary$mean[,"Trmmol" ]; } else {val$sum$Licor$E <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Tair" )) { val$sum$Licor$temp_air <- Licor$summary$mean[,"Tair" ]; } else {val$sum$Licor$temp_air <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Tleaf" )) { val$sum$Licor$temp_leaf <- Licor$summary$mean[,"Tleaf" ]; } else {val$sum$Licor$temp_leaf <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="TBlk" )) { val$sum$Licor$temp_block <- Licor$summary$mean[,"TBlk" ]; } else {val$sum$Licor$temp_block <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="CO2R" )) { val$sum$Licor$Ce <- Licor$summary$mean[,"CO2R" ]; } else {val$sum$Licor$Ce <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="CO2S" )) { val$sum$Licor$Co <- Licor$summary$mean[,"CO2S" ]; } else {val$sum$Licor$Co <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="H2OR" )) { val$sum$Licor$xin <- Licor$summary$mean[,"H2OR" ]; } else {val$sum$Licor$xin <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="H2OS" )) { val$sum$Licor$xout <- Licor$summary$mean[,"H2OS" ]; } else {val$sum$Licor$xout <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="RH_R" )) { val$sum$Licor$rh_ref <- Licor$summary$mean[,"RH_R" ]; } else {val$sum$Licor$rh_ref <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="RH_S" )) { val$sum$Licor$rh_sam <- Licor$summary$mean[,"RH_S" ]; } else {val$sum$Licor$rh_sam <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Flow" )) { val$sum$Licor$uin <- Licor$summary$mean[,"Flow" ]; } else {val$sum$Licor$uin <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="PARi" )) { val$sum$Licor$par_int <- Licor$summary$mean[,"PARi" ]; } else {val$sum$Licor$par_int <- matrix(NA,Licor$summary$n,1)}; # PAR or PPFD These two are defined in the same way at top of CalculationsFile.xls
if (sum(colnames(Licor$summary$mean)=="PARo" )) { val$sum$Licor$par_ext <- Licor$summary$mean[,"PARo" ]; } else {val$sum$Licor$par_ext <- matrix(NA,Licor$summary$n,1)}; # PAR or PPFD
if (sum(colnames(Licor$summary$mean)=="Press" )) { val$sum$Licor$Atm_press <- Licor$summary$mean[,"Press" ]; } else {val$sum$Licor$Atm_press <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="CsMch" )) { val$sum$Licor$CsMch <- Licor$summary$mean[,"CsMch" ]; } else {val$sum$Licor$CsMch <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="HsMch" )) { val$sum$Licor$HsMch <- Licor$summary$mean[,"HsMch" ]; } else {val$sum$Licor$HsMch <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="StableF" )) { val$sum$Licor$StableF <- Licor$summary$mean[,"StableF" ]; } else {val$sum$Licor$StableF <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Status" )) { val$sum$Licor$Status <- Licor$summary$mean[,"Status" ]; } else {val$sum$Licor$Status <- matrix(NA,Licor$summary$n,1)};
# Variables NOT in calculations
if (sum(colnames(Licor$summary$mean)=="Cond" )) { val$sum$Licor$gsc <- Licor$summary$mean[,"Cond" ]; } else {val$sum$Licor$gsc <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Ci" )) { val$sum$Licor$Ci <- Licor$summary$mean[,"Ci" ]; } else {val$sum$Licor$Ci <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="VpdL" )) { val$sum$Licor$VPD <- Licor$summary$mean[,"VpdL" ]; } else {val$sum$Licor$VPD <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Area" )) { val$sum$Licor$La <- Licor$summary$mean[,"Area" ]; } else {val$sum$Licor$La <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="StmRat" )) { val$sum$Licor$StmRat <- Licor$summary$mean[,"StmRat" ]; } else {val$sum$Licor$StmRat <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="BLCond" )) { val$sum$Licor$gbw <- Licor$summary$mean[,"BLCond" ]; } else {val$sum$Licor$gbw <- matrix(NA,Licor$summary$n,1)};
# additional columns
if (sum(colnames(Licor$summary$mean)=="VpdA" )) { val$sum$Licor$VpdA <- Licor$summary$mean[,"VpdA" ]; } else {val$sum$Licor$VpdA <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Ci_Ca" )) { val$sum$Licor$Ci_Ca <- Licor$summary$mean[,"Ci_Ca" ]; } else {val$sum$Licor$Ci_Ca <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Ci_Pa" )) { val$sum$Licor$pi <- Licor$summary$mean[,"Ci_Pa" ]; } else {val$sum$Licor$pi <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="uc_20_mV" )) { val$sum$Licor$uc_20_mV <- Licor$summary$mean[,"uc_20_mV" ]; } else {val$sum$Licor$uc_20_mV <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="uc_21_mV" )) { val$sum$Licor$uc_21_mV <- Licor$summary$mean[,"uc_21_mV" ]; } else {val$sum$Licor$uc_21_mV <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="X.U.S." )) { val$sum$Licor$U_S <- Licor$summary$mean[,"X.U.S." ]; } else {val$sum$Licor$U_S <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Trans" )) { val$sum$Licor$Trans <- Licor$summary$mean[,"Trans" ]; } else {val$sum$Licor$Trans <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="CndCO2" )) { val$sum$Licor$CndCO2 <- Licor$summary$mean[,"CndCO2" ]; } else {val$sum$Licor$CndCO2 <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Ref_mV" )) { val$sum$Licor$Ref_mV <- Licor$summary$mean[,"Ref_mV" ]; } else {val$sum$Licor$Ref_mV <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="xTemp1" )) { val$sum$Licor$xTemp1 <- Licor$summary$mean[,"xTemp1" ]; } else {val$sum$Licor$xTemp1 <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="xTemp2" )) { val$sum$Licor$xTemp2 <- Licor$summary$mean[,"xTemp2" ]; } else {val$sum$Licor$xTemp2 <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="TChamAir" )) { val$sum$Licor$TChamAir <- Licor$summary$mean[,"TChamAir" ]; } else {val$sum$Licor$TChamAir <- matrix(NA,Licor$summary$n,1)};
#TDL$summary:
val$sum$TDL$n <- TDL$summary$n;
val$sum$TDL$first_ind <- TDL$summary$first_ind;
val$sum$TDL$ind <- TDL$summary$ind;
val$sum$TDL$site <- TDL$summary$site;
val$sum$TDL$n_sam <- TDL$summary$n_sam;
val$sum$TDL$time <- TDL$summary$time;
val$sum$TDL$conc12CO2 <- TDL$summary$mean[,"ConcA" ];
val$sum$TDL$conc13CO2 <- TDL$summary$mean[,"ConcB" ];
val$sum$TDL$TGApressure <- TDL$summary$mean[,"TGApressure" ];
val$sum$TDL$MassFlow1 <- TDL$summary$mean[,"MassFlow1" ];
val$sum$TDL$Pressure1 <- TDL$summary$mean[,"Pressure1" ];
val$sum$TDL$MassFlow2 <- TDL$summary$mean[,"MassFlow2" ];
val$sum$TDL$Pressure2 <- TDL$summary$mean[,"Pressure2" ];
val$sum$TDL$PressureProMan <- TDL$summary$mean[,"PressureProMan" ];
val$sum$TDL$interp_tank_hi_12 <- TDL$summary$mean[,"interp_tank_hi_12" ];
val$sum$TDL$interp_tank_hi_13 <- TDL$summary$mean[,"interp_tank_hi_13" ];
val$sum$TDL$interp_tank_low_12 <- TDL$summary$mean[,"interp_tank_low_12" ];
val$sum$TDL$interp_tank_low_13 <- TDL$summary$mean[,"interp_tank_low_13" ];
val$sum$TDL$interp_reference_12 <- TDL$summary$mean[,"interp_reference_12" ];
val$sum$TDL$interp_reference_13 <- TDL$summary$mean[,"interp_reference_13" ];
val$sum$TDL$chamber_12 <- val$sum$TDL$conc12CO2; val$sum$TDL$chamber_12[!(val$sum$TDL$site == TDL_cycle$number_chamber)] <- NA;
val$sum$TDL$chamber_13 <- val$sum$TDL$conc13CO2; val$sum$TDL$chamber_13[!(val$sum$TDL$site == TDL_cycle$number_chamber)] <- NA;
## "Which values to use" switches 9/5/2012
# val$obs$Licor
if (sw$val_const_override_Licor_flow_rate ) { val$obs$Licor$uin <- rep(val$const$flow_rate , length(val$obs$Licor$uin )); };
if (sw$val_const_override_Licor_leaf_area ) { val$obs$Licor$La <- rep(val$const$leaf_area , length(val$obs$Licor$La )); };
if (sw$val_const_override_Licor_boundary_layer_cond_to_water ) { val$obs$Licor$gbw <- rep(val$const$boundary_layer_cond_to_water, length(val$obs$Licor$gbw )); };
if (sw$val_const_override_Licor_H2OS ) { val$obs$Licor$xout <- rep(val$const$H2OS , length(val$obs$Licor$xout )); };
if (sw$val_const_override_Licor_StmRat ) { val$obs$Licor$StmRat <- rep(val$const$StmRat , length(val$obs$Licor$StmRat)); };
# val$sum$Licor
if (sw$val_const_override_Licor_flow_rate ) { val$sum$Licor$uin <- rep(val$const$flow_rate , length(val$sum$Licor$uin )); };
if (sw$val_const_override_Licor_leaf_area ) { val$sum$Licor$La <- rep(val$const$leaf_area , length(val$sum$Licor$La )); };
if (sw$val_const_override_Licor_boundary_layer_cond_to_water ) { val$sum$Licor$gbw <- rep(val$const$boundary_layer_cond_to_water, length(val$sum$Licor$gbw )); };
if (sw$val_const_override_Licor_H2OS ) { val$sum$Licor$xout <- rep(val$const$H2OS , length(val$sum$Licor$xout )); };
if (sw$val_const_override_Licor_StmRat ) { val$sum$Licor$StmRat <- rep(val$const$StmRat , length(val$sum$Licor$StmRat)); };
return( val );
### val
}
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#' Assign TDL and Licor values to val variable names, raw and summarized values
#'
#' Function to assign TDL and Licor values to variable names,
#' summaries and some smart way for individual observations (later for NPBS).
#' If the variable has values, use those, if not then populate with NAs.
#'
#' These are the columns expected from the Licor and TDL.
#' Any columns with headers not listed here will not be used.
#'
#' EXPECTED column names for Licor:
#' \preformatted{
#' (in isogasex) (column from Licor)
#' Obs Obs
#' HHMMSS HHMMSS
#' FTime FTime
#' A Photo
#' E Trmmol
#' temp_air Tair
#' temp_leaf Tleaf
#' temp_block TBlk
#' Ce CO2R
#' Co CO2S
#' xin H2OR
#' xout H2OS
#' rh_ref RH_R
#' rh_sam RH_S
#' uin Flow
#' par_int PARi
#' par_ext PARo
#' Atm_press Press
#' CsMch CsMch
#' HsMch HsMch
#' StableF StableF
#' Status Status
#' gsc Cond
#' Ci Ci
#' VPD VpdL
#' La Area
#' StmRat StmRat
#' gbw BLCond
#' VpdA VpdA
#' Ci_Ca Ci_Ca
#' pi Ci_Pa
#' uc_20_mV uc_20_mV
#' uc_21_mV uc_21_mV
#' U_S X.U.S.
#' Trans Trans
#' CndCO2 CndCO2
#' Ref_mV Ref_mV
#' xTemp1 xTemp1
#' xTemp2 xTemp2
#' TChamAir TChamAir
#' }
#'
#' EXPECTED column names for TDL:
#' \preformatted{
#' (in isogasex) (column from TDL)
#' TIMESTAMP TIMESTAMP
#' RECORD RECORD
#' PrevSite PrevSite
#' SiteOutput SiteOutput
#' StartSeqFlag StartSeqFlag
#' SeqActiveFlag SeqActiveFlag
#' SiteCount SiteCount
#' conc12CO2 ConcA
#' conc13CO2 ConcB
#' ConcC ConcC
#' TGAStatus TGAStatus
#' TGApressure TGApressure
#' MassFlow1 MassFlow1
#' Pressure1 Pressure1
#' MassFlow2 MassFlow2
#' Pressure2 Pressure2
#' PressureProMan PressureProMan
#' }
#'
#' Conventions, put everything in \code{val}.
#' Observed values from TDL or Licor prefix: \code{val$obs$*}
#'
#' Summarized values from TDL or Licor prefix: \code{val$sum$*}
#'
#' @param TDL xxxPARAMxxx
#' @param Licor xxxPARAMxxx
#' @param TDL_cycle xxxPARAMxxx
#' @param val xxxPARAMxxx
#' @param sw xxxPARAMxxx
#'
#' @return val xxxRETURNxxx
#'
val_TDL_Licor_variables <-
function# Assign TDL and Licor values to val variable names, raw and summarized values
###
(TDL
###
, Licor
###
, TDL_cycle
###
, val
###
, sw
###
)
{
### !!!!!
### Note, the variable names used below were from the CalculationsFile.xls
### in cases in the calculations, variables are referred to by their column header name
### Look at the variable names again and decide whether to use var name or col name.
## Function to assign TDL and Licor values to variable names,
## summaries and some smart way for individual observations (later for NPBS).
## If the variable has values, use those, if not then populate with NAs.
## These are the columns expected from the Licor and TDL.
## Any columns with headers not listed here will not be used.
##
## EXPECTED column names for Licor:
## \preformatted{
## (in isogasex) (column from Licor)
## Obs Obs
## HHMMSS HHMMSS
## FTime FTime
## A Photo
## E Trmmol
## temp_air Tair
## temp_leaf Tleaf
## temp_block TBlk
## Ce CO2R
## Co CO2S
## xin H2OR
## xout H2OS
## rh_ref RH_R
## rh_sam RH_S
## uin Flow
## par_int PARi
## par_ext PARo
## Atm_press Press
## CsMch CsMch
## HsMch HsMch
## StableF StableF
## Status Status
## gsc Cond
## Ci Ci
## VPD VpdL
## La Area
## StmRat StmRat
## gbw BLCond
## VpdA VpdA
## Ci_Ca Ci_Ca
## pi Ci_Pa
## uc_20_mV uc_20_mV
## uc_21_mV uc_21_mV
## U_S X.U.S.
## Trans Trans
## CndCO2 CndCO2
## Ref_mV Ref_mV
## xTemp1 xTemp1
## xTemp2 xTemp2
## TChamAir TChamAir
## }
##
## EXPECTED column names for TDL:
## \preformatted{
## (in isogasex) (column from TDL)
## TIMESTAMP TIMESTAMP
## RECORD RECORD
## PrevSite PrevSite
## SiteOutput SiteOutput
## StartSeqFlag StartSeqFlag
## SeqActiveFlag SeqActiveFlag
## SiteCount SiteCount
## conc12CO2 ConcA
## conc13CO2 ConcB
## ConcC ConcC
## TGAStatus TGAStatus
## TGApressure TGApressure
## MassFlow1 MassFlow1
## Pressure1 Pressure1
## MassFlow2 MassFlow2
## Pressure2 Pressure2
## PressureProMan PressureProMan
## }
## Conventions, put everything in \code{val}.
## Observed values from TDL or Licor prefix: \code{val$obs$*}
val$obs <- list();
val$obs$TDL <- list();
val$obs$Licor <- list();
## Summarized values from TDL or Licor prefix: \code{val$sum$*}
val$sum <- list();
val$sum$TDL <- list();
val$sum$Licor <- list();
#Licor$data:
if (sw$use_Licor) {
temp_n_Licor <- length(Licor$data[,1]); # "Obs"
} else {
temp_n_Licor <- 0;
}
# Variables in calculations
if (sum(colnames(Licor$data)=="Obs" )) { val$obs$Licor$Obs <- Licor$data[,"Obs" ]; } else {val$obs$Licor$Obs <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="HHMMSS" )) { val$obs$Licor$HHMMSS <- Licor$data[,"HHMMSS" ]; } else {val$obs$Licor$HHMMSS <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="FTime" )) { val$obs$Licor$FTime <- Licor$data[,"FTime" ]; } else {val$obs$Licor$FTime <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Photo" )) { val$obs$Licor$A <- Licor$data[,"Photo" ]; } else {val$obs$Licor$A <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Trmmol" )) { val$obs$Licor$E <- Licor$data[,"Trmmol" ]; } else {val$obs$Licor$E <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Tair" )) { val$obs$Licor$temp_air <- Licor$data[,"Tair" ]; } else {val$obs$Licor$temp_air <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Tleaf" )) { val$obs$Licor$temp_leaf <- Licor$data[,"Tleaf" ]; } else {val$obs$Licor$temp_leaf <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="TBlk" )) { val$obs$Licor$temp_block <- Licor$data[,"TBlk" ]; } else {val$obs$Licor$temp_block <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="CO2R" )) { val$obs$Licor$Ce <- Licor$data[,"CO2R" ]; } else {val$obs$Licor$Ce <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="CO2S" )) { val$obs$Licor$Co <- Licor$data[,"CO2S" ]; } else {val$obs$Licor$Co <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="H2OR" )) { val$obs$Licor$xin <- Licor$data[,"H2OR" ]; } else {val$obs$Licor$xin <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="H2OS" )) { val$obs$Licor$xout <- Licor$data[,"H2OS" ]; } else {val$obs$Licor$xout <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="RH_R" )) { val$obs$Licor$rh_ref <- Licor$data[,"RH_R" ]; } else {val$obs$Licor$rh_ref <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="RH_S" )) { val$obs$Licor$rh_sam <- Licor$data[,"RH_S" ]; } else {val$obs$Licor$rh_sam <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Flow" )) { val$obs$Licor$uin <- Licor$data[,"Flow" ]; } else {val$obs$Licor$uin <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="PARi" )) { val$obs$Licor$par_int <- Licor$data[,"PARi" ]; } else {val$obs$Licor$par_int <- matrix(NA,temp_n_Licor,1)}; # PAR or PPFD These two are defined in the same way at top of CalculationsFile.xls
if (sum(colnames(Licor$data)=="PARo" )) { val$obs$Licor$par_ext <- Licor$data[,"PARo" ]; } else {val$obs$Licor$par_ext <- matrix(NA,temp_n_Licor,1)}; # PAR or PPFD
if (sum(colnames(Licor$data)=="Press" )) { val$obs$Licor$Atm_press <- Licor$data[,"Press" ]; } else {val$obs$Licor$Atm_press <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="CsMch" )) { val$obs$Licor$CsMch <- Licor$data[,"CsMch" ]; } else {val$obs$Licor$CsMch <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="HsMch" )) { val$obs$Licor$HsMch <- Licor$data[,"HsMch" ]; } else {val$obs$Licor$HsMch <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="StableF" )) { val$obs$Licor$StableF <- Licor$data[,"StableF" ]; } else {val$obs$Licor$StableF <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Status" )) { val$obs$Licor$Status <- Licor$data[,"Status" ]; } else {val$obs$Licor$Status <- matrix(NA,temp_n_Licor,1)};
# Variables NOT in calculations
if (sum(colnames(Licor$data)=="Cond" )) { val$obs$Licor$gsc <- Licor$data[,"Cond" ]; } else {val$obs$Licor$gsc <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Ci" )) { val$obs$Licor$Ci <- Licor$data[,"Ci" ]; } else {val$obs$Licor$Ci <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="VpdL" )) { val$obs$Licor$VPD <- Licor$data[,"VpdL" ]; } else {val$obs$Licor$VPD <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Area" )) { val$obs$Licor$La <- Licor$data[,"Area" ]; } else {val$obs$Licor$La <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="StmRat" )) { val$obs$Licor$StmRat <- Licor$data[,"StmRat" ]; } else {val$obs$Licor$StmRat <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="BLCond" )) { val$obs$Licor$gbw <- Licor$data[,"BLCond" ]; } else {val$obs$Licor$gbw <- matrix(NA,temp_n_Licor,1)};
# additional columns
if (sum(colnames(Licor$data)=="VpdA" )) { val$obs$Licor$VpdA <- Licor$data[,"VpdA" ]; } else {val$obs$Licor$VpdA <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Ci_Ca" )) { val$obs$Licor$Ci_Ca <- Licor$data[,"Ci_Ca" ]; } else {val$obs$Licor$Ci_Ca <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Ci_Pa" )) { val$obs$Licor$pi <- Licor$data[,"Ci_Pa" ]; } else {val$obs$Licor$pi <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="uc_20_mV" )) { val$obs$Licor$uc_20_mV <- Licor$data[,"uc_20_mV" ]; } else {val$obs$Licor$uc_20_mV <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="uc_21_mV" )) { val$obs$Licor$uc_21_mV <- Licor$data[,"uc_21_mV" ]; } else {val$obs$Licor$uc_21_mV <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="X.U.S." )) { val$obs$Licor$U_S <- Licor$data[,"X.U.S." ]; } else {val$obs$Licor$U_S <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Trans" )) { val$obs$Licor$Trans <- Licor$data[,"Trans" ]; } else {val$obs$Licor$Trans <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="CndCO2" )) { val$obs$Licor$CndCO2 <- Licor$data[,"CndCO2" ]; } else {val$obs$Licor$CndCO2 <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="Ref_mV" )) { val$obs$Licor$Ref_mV <- Licor$data[,"Ref_mV" ]; } else {val$obs$Licor$Ref_mV <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="xTemp1" )) { val$obs$Licor$xTemp1 <- Licor$data[,"xTemp1" ]; } else {val$obs$Licor$xTemp1 <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="xTemp2" )) { val$obs$Licor$xTemp2 <- Licor$data[,"xTemp2" ]; } else {val$obs$Licor$xTemp2 <- matrix(NA,temp_n_Licor,1)};
if (sum(colnames(Licor$data)=="TChamAir" )) { val$obs$Licor$TChamAir <- Licor$data[,"TChamAir" ]; } else {val$obs$Licor$TChamAir <- matrix(NA,temp_n_Licor,1)};
#TDL$data:
val$obs$TDL$TIMESTAMP <- TDL$data [,"TIMESTAMP" ];
val$obs$TDL$RECORD <- TDL$data [,"RECORD" ];
val$obs$TDL$PrevSite <- TDL$data [,"PrevSite" ];
val$obs$TDL$SiteOutput <- TDL$data [,"SiteOutput" ];
val$obs$TDL$StartSeqFlag <- TDL$data [,"StartSeqFlag" ];
val$obs$TDL$SeqActiveFlag <- TDL$data [,"SeqActiveFlag" ];
val$obs$TDL$SiteCount <- TDL$data [,"SiteCount" ];
val$obs$TDL$conc12CO2 <- TDL$data [,"ConcA" ];
val$obs$TDL$conc13CO2 <- TDL$data [,"ConcB" ];
val$obs$TDL$ConcC <- TDL$data [,"ConcC" ];
val$obs$TDL$TGAStatus <- TDL$data [,"TGAStatus" ];
val$obs$TDL$TGApressure <- TDL$data [,"TGApressure" ];
val$obs$TDL$MassFlow1 <- TDL$data [,"MassFlow1" ];
val$obs$TDL$Pressure1 <- TDL$data [,"Pressure1" ];
val$obs$TDL$MassFlow2 <- TDL$data [,"MassFlow2" ];
val$obs$TDL$Pressure2 <- TDL$data [,"Pressure2" ];
val$obs$TDL$PressureProMan <- TDL$data [,"PressureProMan" ];
val$obs$TDL$interp_tank_hi_12 <- TDL$interp[,"tank_hi_12" ];
val$obs$TDL$interp_tank_hi_13 <- TDL$interp[,"tank_hi_13" ];
val$obs$TDL$interp_tank_low_12 <- TDL$interp[,"tank_low_12" ];
val$obs$TDL$interp_tank_low_13 <- TDL$interp[,"tank_low_13" ];
val$obs$TDL$interp_reference_12 <- TDL$interp[,"reference_12" ];
val$obs$TDL$interp_reference_13 <- TDL$interp[,"reference_13" ];
val$obs$TDL$chamber_12 <- val$obs$TDL$conc12CO2; val$obs$TDL$chamber_12[!(val$obs$TDL$PrevSite == TDL_cycle$number_chamber)] <- NA;
val$obs$TDL$chamber_13 <- val$obs$TDL$conc13CO2; val$obs$TDL$chamber_13[!(val$obs$TDL$PrevSite == TDL_cycle$number_chamber)] <- NA;
if (sw$use_Licor==0) {
Licor$summary$n <- 0;
}
#Licor$summary:
#val$sum$Licor$Obs <- Licor$summary[,"Obs"];
#val$sum$Licor$HHMMSS <- Licor$summary[,"HHMMSS"];
val$sum$Licor$n <- Licor$summary$n;
val$sum$Licor$first_ind <- Licor$summary$first_ind;
val$sum$Licor$ind <- Licor$summary$ind;
val$sum$Licor$site <- Licor$summary$site;
val$sum$Licor$n_sam <- Licor$summary$n_sam;
val$sum$Licor$time <- Licor$summary$time;
# Variables in calculations
if (sum(colnames(Licor$summary$mean)=="FTime" )) { val$sum$Licor$FTime <- Licor$summary$mean[,"FTime" ]; } else {val$sum$Licor$FTime <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Photo" )) { val$sum$Licor$A <- Licor$summary$mean[,"Photo" ]; } else {val$sum$Licor$A <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Trmmol" )) { val$sum$Licor$E <- Licor$summary$mean[,"Trmmol" ]; } else {val$sum$Licor$E <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Tair" )) { val$sum$Licor$temp_air <- Licor$summary$mean[,"Tair" ]; } else {val$sum$Licor$temp_air <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Tleaf" )) { val$sum$Licor$temp_leaf <- Licor$summary$mean[,"Tleaf" ]; } else {val$sum$Licor$temp_leaf <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="TBlk" )) { val$sum$Licor$temp_block <- Licor$summary$mean[,"TBlk" ]; } else {val$sum$Licor$temp_block <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="CO2R" )) { val$sum$Licor$Ce <- Licor$summary$mean[,"CO2R" ]; } else {val$sum$Licor$Ce <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="CO2S" )) { val$sum$Licor$Co <- Licor$summary$mean[,"CO2S" ]; } else {val$sum$Licor$Co <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="H2OR" )) { val$sum$Licor$xin <- Licor$summary$mean[,"H2OR" ]; } else {val$sum$Licor$xin <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="H2OS" )) { val$sum$Licor$xout <- Licor$summary$mean[,"H2OS" ]; } else {val$sum$Licor$xout <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="RH_R" )) { val$sum$Licor$rh_ref <- Licor$summary$mean[,"RH_R" ]; } else {val$sum$Licor$rh_ref <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="RH_S" )) { val$sum$Licor$rh_sam <- Licor$summary$mean[,"RH_S" ]; } else {val$sum$Licor$rh_sam <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Flow" )) { val$sum$Licor$uin <- Licor$summary$mean[,"Flow" ]; } else {val$sum$Licor$uin <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="PARi" )) { val$sum$Licor$par_int <- Licor$summary$mean[,"PARi" ]; } else {val$sum$Licor$par_int <- matrix(NA,Licor$summary$n,1)}; # PAR or PPFD These two are defined in the same way at top of CalculationsFile.xls
if (sum(colnames(Licor$summary$mean)=="PARo" )) { val$sum$Licor$par_ext <- Licor$summary$mean[,"PARo" ]; } else {val$sum$Licor$par_ext <- matrix(NA,Licor$summary$n,1)}; # PAR or PPFD
if (sum(colnames(Licor$summary$mean)=="Press" )) { val$sum$Licor$Atm_press <- Licor$summary$mean[,"Press" ]; } else {val$sum$Licor$Atm_press <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="CsMch" )) { val$sum$Licor$CsMch <- Licor$summary$mean[,"CsMch" ]; } else {val$sum$Licor$CsMch <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="HsMch" )) { val$sum$Licor$HsMch <- Licor$summary$mean[,"HsMch" ]; } else {val$sum$Licor$HsMch <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="StableF" )) { val$sum$Licor$StableF <- Licor$summary$mean[,"StableF" ]; } else {val$sum$Licor$StableF <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Status" )) { val$sum$Licor$Status <- Licor$summary$mean[,"Status" ]; } else {val$sum$Licor$Status <- matrix(NA,Licor$summary$n,1)};
# Variables NOT in calculations
if (sum(colnames(Licor$summary$mean)=="Cond" )) { val$sum$Licor$gsc <- Licor$summary$mean[,"Cond" ]; } else {val$sum$Licor$gsc <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Ci" )) { val$sum$Licor$Ci <- Licor$summary$mean[,"Ci" ]; } else {val$sum$Licor$Ci <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="VpdL" )) { val$sum$Licor$VPD <- Licor$summary$mean[,"VpdL" ]; } else {val$sum$Licor$VPD <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Area" )) { val$sum$Licor$La <- Licor$summary$mean[,"Area" ]; } else {val$sum$Licor$La <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="StmRat" )) { val$sum$Licor$StmRat <- Licor$summary$mean[,"StmRat" ]; } else {val$sum$Licor$StmRat <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="BLCond" )) { val$sum$Licor$gbw <- Licor$summary$mean[,"BLCond" ]; } else {val$sum$Licor$gbw <- matrix(NA,Licor$summary$n,1)};
# additional columns
if (sum(colnames(Licor$summary$mean)=="VpdA" )) { val$sum$Licor$VpdA <- Licor$summary$mean[,"VpdA" ]; } else {val$sum$Licor$VpdA <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Ci_Ca" )) { val$sum$Licor$Ci_Ca <- Licor$summary$mean[,"Ci_Ca" ]; } else {val$sum$Licor$Ci_Ca <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Ci_Pa" )) { val$sum$Licor$pi <- Licor$summary$mean[,"Ci_Pa" ]; } else {val$sum$Licor$pi <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="uc_20_mV" )) { val$sum$Licor$uc_20_mV <- Licor$summary$mean[,"uc_20_mV" ]; } else {val$sum$Licor$uc_20_mV <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="uc_21_mV" )) { val$sum$Licor$uc_21_mV <- Licor$summary$mean[,"uc_21_mV" ]; } else {val$sum$Licor$uc_21_mV <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="X.U.S." )) { val$sum$Licor$U_S <- Licor$summary$mean[,"X.U.S." ]; } else {val$sum$Licor$U_S <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Trans" )) { val$sum$Licor$Trans <- Licor$summary$mean[,"Trans" ]; } else {val$sum$Licor$Trans <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="CndCO2" )) { val$sum$Licor$CndCO2 <- Licor$summary$mean[,"CndCO2" ]; } else {val$sum$Licor$CndCO2 <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="Ref_mV" )) { val$sum$Licor$Ref_mV <- Licor$summary$mean[,"Ref_mV" ]; } else {val$sum$Licor$Ref_mV <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="xTemp1" )) { val$sum$Licor$xTemp1 <- Licor$summary$mean[,"xTemp1" ]; } else {val$sum$Licor$xTemp1 <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="xTemp2" )) { val$sum$Licor$xTemp2 <- Licor$summary$mean[,"xTemp2" ]; } else {val$sum$Licor$xTemp2 <- matrix(NA,Licor$summary$n,1)};
if (sum(colnames(Licor$summary$mean)=="TChamAir" )) { val$sum$Licor$TChamAir <- Licor$summary$mean[,"TChamAir" ]; } else {val$sum$Licor$TChamAir <- matrix(NA,Licor$summary$n,1)};
#TDL$summary:
val$sum$TDL$n <- TDL$summary$n;
val$sum$TDL$first_ind <- TDL$summary$first_ind;
val$sum$TDL$ind <- TDL$summary$ind;
val$sum$TDL$site <- TDL$summary$site;
val$sum$TDL$n_sam <- TDL$summary$n_sam;
val$sum$TDL$time <- TDL$summary$time;
val$sum$TDL$conc12CO2 <- TDL$summary$mean[,"ConcA" ];
val$sum$TDL$conc13CO2 <- TDL$summary$mean[,"ConcB" ];
val$sum$TDL$TGApressure <- TDL$summary$mean[,"TGApressure" ];
val$sum$TDL$MassFlow1 <- TDL$summary$mean[,"MassFlow1" ];
val$sum$TDL$Pressure1 <- TDL$summary$mean[,"Pressure1" ];
val$sum$TDL$MassFlow2 <- TDL$summary$mean[,"MassFlow2" ];
val$sum$TDL$Pressure2 <- TDL$summary$mean[,"Pressure2" ];
val$sum$TDL$PressureProMan <- TDL$summary$mean[,"PressureProMan" ];
val$sum$TDL$interp_tank_hi_12 <- TDL$summary$mean[,"interp_tank_hi_12" ];
val$sum$TDL$interp_tank_hi_13 <- TDL$summary$mean[,"interp_tank_hi_13" ];
val$sum$TDL$interp_tank_low_12 <- TDL$summary$mean[,"interp_tank_low_12" ];
val$sum$TDL$interp_tank_low_13 <- TDL$summary$mean[,"interp_tank_low_13" ];
val$sum$TDL$interp_reference_12 <- TDL$summary$mean[,"interp_reference_12" ];
val$sum$TDL$interp_reference_13 <- TDL$summary$mean[,"interp_reference_13" ];
val$sum$TDL$chamber_12 <- val$sum$TDL$conc12CO2; val$sum$TDL$chamber_12[!(val$sum$TDL$site == TDL_cycle$number_chamber)] <- NA;
val$sum$TDL$chamber_13 <- val$sum$TDL$conc13CO2; val$sum$TDL$chamber_13[!(val$sum$TDL$site == TDL_cycle$number_chamber)] <- NA;
## "Which values to use" switches 9/5/2012
# val$obs$Licor
if (sw$val_const_override_Licor_flow_rate ) { val$obs$Licor$uin <- rep(val$const$flow_rate , length(val$obs$Licor$uin )); };
if (sw$val_const_override_Licor_leaf_area ) { val$obs$Licor$La <- rep(val$const$leaf_area , length(val$obs$Licor$La )); };
if (sw$val_const_override_Licor_boundary_layer_cond_to_water ) { val$obs$Licor$gbw <- rep(val$const$boundary_layer_cond_to_water, length(val$obs$Licor$gbw )); };
if (sw$val_const_override_Licor_H2OS ) { val$obs$Licor$xout <- rep(val$const$H2OS , length(val$obs$Licor$xout )); };
if (sw$val_const_override_Licor_StmRat ) { val$obs$Licor$StmRat <- rep(val$const$StmRat , length(val$obs$Licor$StmRat)); };
# val$sum$Licor
if (sw$val_const_override_Licor_flow_rate ) { val$sum$Licor$uin <- rep(val$const$flow_rate , length(val$sum$Licor$uin )); };
if (sw$val_const_override_Licor_leaf_area ) { val$sum$Licor$La <- rep(val$const$leaf_area , length(val$sum$Licor$La )); };
if (sw$val_const_override_Licor_boundary_layer_cond_to_water ) { val$sum$Licor$gbw <- rep(val$const$boundary_layer_cond_to_water, length(val$sum$Licor$gbw )); };
if (sw$val_const_override_Licor_H2OS ) { val$sum$Licor$xout <- rep(val$const$H2OS , length(val$sum$Licor$xout )); };
if (sw$val_const_override_Licor_StmRat ) { val$sum$Licor$StmRat <- rep(val$const$StmRat , length(val$sum$Licor$StmRat)); };
return( val );
### val
}
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