R/asyr_pullRaws.R

In JARS3N/asyr: asyr

# pulls entire dataframe of RawVariables
pull_raws<-function(xml,TickTable){
  vars<-c(
    "LedOffReferenceValues",
    "LedOnReferenceValues",
    "LedOnEmissionValues",
    "LedOffEmissionValues"
  )
  replace_names<-function(str,Analyte){
    replacements<-paste0(Analyte,
                         "_",
                         c("DarkRef","LightRef",
                           "LightEmission","DarkEmission")
    )
    q<-setNames(
      c("Tick","Well",replacements),
      c("Tick","Well",vars)
    )[str]
    unname(q)
  }
  merge_raw<-function(x,y){
    merge(x,y,by=c("Tick","Well"))
  }

  grab_raw_analyte<-function(Xml=xml,vars=vars,Analyte){
    a<-lapply(vars,get_raw_var,xml=Xml,analyte=Analyte)
    A<-Reduce('merge_raw',a)
    setNames(A,replace_names(names(A),Analyte))
  }
  OUT<-merge_raw(
    grab_raw_analyte(xml,vars,Analyte='pH'),
    grab_raw_analyte(xml,vars,Analyte='O2')
  )
  OUT<-OUT[order(OUT$Tick,OUT$Well),]
  if(min(OUT$Tick)==1 && min(TickTable$Tick)==0){
  OUT$Tick<-OUT$Tick-1
  }
  row.names(OUT)<-NULL
  OUT
}