R/GetValue_GXcurve.R

In KevinCrab/Instant-Gas-Exchange-Measurements: Instant Gas Exchange Analysis

# Calculate mean values for each parameter
GetValue = function(table, ...){
  UseMethod("GetValue",table)
}

GetValue.GXcurve = function(table, first.minute = TRUE, last.minute = TRUE, ...){
  # set emply vectors
  plot_name <- vector(mode="character", length=0)
  leaf_name <- vector(mode="numeric", length=0)
  name <- vector(mode="character", length=0)
  genotype <- vector(mode="character", length=0)
  range <- vector(mode="character", length=0)
  row <- vector(mode="character", length=0)
  block <- vector(mode="character", length=0)
  # decide output parameter numbers
  if(first.minute){
    Photo_first <- vector(mode="numeric", length=0)
    Cond_first <- vector(mode="numeric", length=0)
    Ci.Ca_first = vector(mode="numeric", length=0)
  }
  if(last.minute){
    Photo_last <- vector(mode="numeric", length=0)
    Cond_last <- vector(mode="numeric", length=0)
    Ci.Ca_last = vector(mode="numeric", length=0)
  }
  nameslist = unique(table$name)
  # get parameters
  for (x in 1:length(nameslist)){
    sub = table[which(table$name == nameslist[x]),]
    plot_name = c(plot_name,sub[1,"plot"])
    leaf_name = c(leaf_name,sub[1,"leaf"])
    name = c(name,sub[1,"name"])
    genotype = c(genotype,sub[1,"genotype"])
    range = c(range,sub[1,"range"])
    row = c(row,sub[1,"row"])
    block = c(block,sub[1,"block"])
    if(first.minute){
      subfirstone = sub[c(1:min(which(sub$FTime > sub$FTime[1] +60))),]
      Photo_first = c(Photo_first, subfirstone$Photo[which.max(subfirstone$Cond)])
      Cond_first = c(Cond_first, max(subfirstone$Cond))
      Ci.Ca_first = c(Ci.Ca_first, subfirstone$Ci.Ca[which.max(subfirstone$Cond)])
    }
    if(last.minute){
      sublastone = sub[c(max(which(sub$FTime < sub$FTime[length(sub$FTime)]-60)):length(sub$FTime)),]
      Photo_last = c(Photo_last,mean(sublastone$Photo))
      Cond_last = c(Cond_last, mean(sublastone$Cond))
      Ci.Ca_last = c(Ci.Ca_last,mean(sublastone$Ci.Ca))
    }
    cat(x,"getting value for ----",nameslist[x],"\n")
  }
  #combining and assigning new class
  ps = data.frame(plot_name, leaf_name, name,genotype,range,row,block,stringsAsFactors = FALSE)
  if(first.minute) ps = cbind(ps,Photo_first,Cond_first,Ci.Ca_first)
  if(last.minute) ps = cbind(ps,Photo_last,Cond_last,Ci.Ca_last)
  class(ps) <- c("GXvalue", class(ps))
  return(ps)
}