R/asyr_parse.R

In JARS3N/asyr: asyr

parse<-function(X){
  require(XML)
  require(asyr)
  E<-list(
    file = asyr::getFile(X))
  E$SW = asyr::swversion(X)
  E$PH_COEF = asyr::pH_coefs(X)
  E$O2_COEF = asyr::O2_coefs(X)
  E$Inst = asyr::getInst(X)
  E$sn = asyr::getSn(X)
  E$Lot = asyr::getLot(X)
  E$TickTable<-asyr::tick_table(X)
  E$CAL <- asyr::CalData(X)
  E$LVL <- asyr::get_lvls(X,E$TickTable)
  E$cal_temp <- asyr::cal_temp(X)
  E$O2_COEF$F0<-asyr::f0(E$O2_COEF$Ksv,E$O2_COEF$target,E$cal_temp)
  E$LVL$mmHgO2<-(1/E$O2_COEF$Ksv) * ((E$O2_COEF$F0/E$LVL$O2_CorrectedEmission)-1)
  E$LVL<-merge(E$LVL,E$CAL[c('Well','pH.CalEmission')],by='Well')
  E$LVL$pH<-(7400 - ((E$LVL$pH.CalEmission - E$LVL$pH_CorrectedEmission)/E$PH_COEF$gain))*1000^-1
  E$LVL<-E$LVL[order(E$LVL$Tick),]
  E$LVL$file<-E$file
  E
}