R/RssBioGro.R

In BioCro: Simulation of Biomass Crops

## Very simple function to compare the distance between simulated
## and observed data for the BioGro function
## Need to add an argument such as pc.sigmas "plant component sigmas"
## If variability of the plant component is known

RssBioGro <- function(obs,sim){

    simDat <- data.frame(TT = sim$ThermalT, Stem = sim$Stem, Leaf = sim$Leaf,
                         Root = sim$Root, Rhiz = sim$Rhizome, 
                         Grain = sim$Grain, LAI = sim$LAI)

    indx <- indfun(obs[,1],simDat[,1])
    simDat2 <- simDat[indx,]
    obs2 <- obs[1:length(indx),]

    dobs2 <- dim(obs2)
    dSimDat2 <- dim(simDat2)
    
    if((dobs2[1] != dSimDat2[1]) || (dobs2[2] != dSimDat2[2])){
      cat("dim obs: ",dim(obs),"\n")
      cat("dim simDat2: ",dim(simDat2),"\n")
       stop("dim(obs) should be equal to dim(sim)")
    }

    resid <- obs2[,-1] - simDat2[,-1]
    resid[is.na(resid)] <- 0
    rss <- sum(resid^2)
    rss
  }