R/asyr_CalData.R

In JARS3N/asyr: asyr

getACal<-function(xml,var,analyte){
  xstr<-"//AssayDataSet//AnalyteCalibrationsByAnalyteName//Item[Key='"
  vars<-c("LED"="']//Value//AnalyteCalibration//LedValues//ArrayOfInt//int",
          "CalEmission"="']//Value//AnalyteCalibration//CalibrationEmissionValues//ArrayOfDouble//double",
          "IntialReferenceDelta"="']//Value//AnalyteCalibration//IntialReferenceDeltaValues//ArrayOfInt//int",
          "Status"="']//Value//AnalyteCalibration//LedStatusValues//ArrayOfCalibrationQuality//CalibrationQuality"
  )
  type<-list(
    "LED"=as.numeric,
    "CalEmission"=as.numeric,
    "IntialReferenceDelta"=as.numeric,
    "Status"=as.character
  )
  type[[var]](xpathSApply(xml,paste0(xstr,analyte,vars[var]),xmlValue))
}


CalData<-function(xml){
  anCal<-function(xml,analyte){
    var_names<-c("LED","CalEmission","IntialReferenceDelta","Status")
    setNames(data.frame(lapply(var_names,getACal,xml=xml,analyte=analyte)),
             paste(analyte,var_names,sep="."))
  }
  pH<-anCal(xml,'pH')
  O2<-anCal(xml,'O2')
  Well<-seq_along(pH[,1])
  cbind(Well,pH,O2)
}