Project: s41467-024-44813-2 | Function: commDD (r)

system: You are an expert R programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow R best practices and maintain consistent code style.
Return **only** the complete R function code.

user: Complete this R function:

**DESCRIPTION:** Calculates phylogenetic diversity metrics (DD, MPD, MNTD) for dissolved organic matter molecular data using dendrogram distances. Core analytical method for DOM assemblage characterization.

**KEY TERMS:** {
  "mol.data": "molecular data matrix",
  "mol.dendrogram": "molecular phylogenetic tree",
  "DD": "phylogenetic diversity",
  "MPD": "mean pairwise distance",
  "MNTD": "mean nearest taxon distance"
}

**CONTEXT CODE:** 
#' @title Calculate Molecular Dendrogram-based Diversity
#' @description This function calculates various Dendrogram-based diversity indices for molecular data.
#' @param mol.data Data frame containing molecular data where rows represent different samples or conditions, and columns represent individual molecules. Default: mol.data.
#' @param mol.dendrogram The dendrogram object representing the relationships among molecules.
#' @param type A character vector specifying the types of diversity indices to calculate. Default: c("DD", "MPD", "MNTD").
#' @return A data frame with the calculated diversity indices for each sample.
#' @seealso 
#'  \code{\link[vegan]{decostand}}
#'  \code{\link[picante]{pd}}, \code{\link[picante]{mpd}}, \code{\link[picante]{mntd}}
#' @rdname commDD
#' @export 
#' @importFrom vegan decostand
#' @importFrom picante pd mpd mntd

commDD <- function(mol.data, mol.dendrogram, type = c("DD", "MPD", "MNTD")){
  stop("Function implementation has been masked")
}


Complete the function implementation replacing "stop("Not implemented")".