R/pl_gower.R

In aplantin/pldist: Paired and Longitudinal Ecological Dissimilarities

#' Paired or longitudinal Gower distances 
#'
#' The distances are calculated as follows, where d_k^X is the within-subject 
#'     measure of change appropriate to the setting (paired/longitudinal and 
#'     quantitative/qualitative), as described in the full package documentation 
#'     and vignette. 
#'     
#' \eqn{D_{AB} = (1/m) \sum_k (|d_k^A - d_k^B|)/(\max d_k - \min d_k)} 
#'    
#' @param tsf.data Transformed OTU table and metadata (from function pl.transform)
#' @param binary Logical indicating whether to use the binary version of the distance 
#' @return Returns an n x n distance matrix. 
#'
#' @export
#' 
gower <- function(tsf.data, binary) {
  if (binary) { dat = tsf.data$dat.binary
  } else { dat = tsf.data$dat.quant }
  
  n = nrow(dat); m = ncol(dat) 
  out.D <- matrix(0, n, n) 
  rownames(out.D) = colnames(out.D) = rownames(dat) 
  
  taxmax <- round(apply(dat, 2, max), 8) 
  taxmin <- round(apply(dat, 2, min), 8) 
  idx = which(taxmax != taxmin) 
  
  for (i in 1:(n-1)) {
    for (j in (i+1):n) {
      out.D[i, j] = out.D[j, i] = sum( abs(dat[i,idx] - dat[j,idx]) / (taxmax[idx] - taxmin[idx]) )/m
    }
  }

  return(out.D) 
}