R/bic.select.best.mode.R

In antagomir/netresponse: Functional Network Analysis

#' @title Select best mode with BIC
#' @description Select optimal number of mixture components by adding components until 
#' the increase in objective function is below threshold.
#' @param x  dat vector (for univariate analysis) or a matrix (for multivariate analysis)
#' @param max.modes Maximum number of modes to be checked for mixture model selection
#' @param bic.threshold BIC threshold which needs to be exceeded before a new mode is added to the mixture.
#' @param min.modes Optional. Minimum number of modes.
#' @return Fitted latent class model (parameters and free energy)
#' @author Contact: Leo Lahti \email{leo.lahti@@iki.fi}
#' @references See citation('netresponse')
bic.select.best.mode <- function(x, max.modes = 1, bic.threshold = 1, min.modes = 1) {


    # Cost for single mode BIC : smaller is better mclustBIC returns the value for
    # -BIC, to be exact
    nc <- min.modes
    if (is.vector(x)) {
        # univariate
        m <- -mclustBIC(x, G = nc)[, "V"]
    } else {
        # multivariate
        m <- -mclustBIC(x, G = nc)[, "VVV"]  # BIC : smaller is better
    }
    
    # ----------------------------------------------------------------
    
    add.component <- TRUE
    best.mode <- min.modes
    if (max.modes == min.modes) {
        add.component <- FALSE
    }
    
    while (add.component && nc < max.modes) {
        
        nc <- nc + 1
        
        # BIC : smaller is better univariate
        if (is.vector(x)) {
            m.new <- try(-mclustBIC(x, G = nc)[, "V"])
        } else {
            # multivariate
            m.new <- try(-mclustBIC(x, G = nc)[, "VVV"])
        }
        if (is.na(m.new)) 
            {
                m.new <- Inf
            }  # infinitely bad = Inf
        
        # FIXME: compressing data with PCA after dimensionality gets otherwise too high?
        # with around ncol(x) = 30 the mclustBIC is starting to produce NAs
        
        # FIXME: remove this when code works ok if (is.na(m.new)) {save(x, nc, file =
        # 'm.new.RData')}
        
        bic.delta <- m.new - m
        
        if (bic.delta < -bic.threshold) {
            best.mode <- nc
            m <- m.new
        } else {
            add.component <- FALSE
        }
    }
    
    best.mode
    
}