R/RssBioGro.R

In serbinsh/biocro: Simulation of Energycane and Sugarcane

## 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
##' Residual sum of squares for BioGro.
##'
##' Computes residual sum of squares for the \code{\link{BioGro}} function.
##'
##'
##' @param obs Observed data.
##' @param sim Simulated data.
##' @export
##' @return Atomic vector with the residual sum of squares.
##' @author Fernando E. Miguez
##' @seealso See Also \code{\link{BioGro}}.
##' @keywords models
##' @examples
##'
##' ## A simple example
##' data(annualDB)
##' data(EngWea94i)
##' res <- BioGro(EngWea94i)
##' RssBioGro(annualDB,res)
##'
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 <- BioCro:::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
}