R/mod_FPD.R

In levisc8/Fun_Phylo_Package: Helpers to Power the Fun Phylo Shiny App

#' @title Functional-Phylogenetic Distances (FPD)
#' 
#' @description Calculate hybrid functional phylogenetic distance matrices
#' based on the method of Cadotte et al 2013
#'
#' @param FDist A matrix of functional trait distances
#' @param PDist A matrix of phylogenetic distances
#' @param phyloWeight The phylogenetic scaling parameter \emph{a} as
#' described in Cadotte et al 2013. A value of 1 denotes only phylogenetic
#' information while a value of 0 indicates only functional trait 
#' information. The value must be between 0 and 1. 
#' @param p the power to raise each matrix to when combining the two 
#' distance matrices. 
#' @param ... Ignored here 
#' 
#' @return A matrix with weighted interspecific distances
#' 
#' @note The function does not check to make sure names in 
#' \code{FDist} and \code{PDist match}. Additionally, if
#' NAs or NaNs in the distance matrix are generated by missing data,
#' they will be replaced with matrix level mean distance values and
#' a warning message will be generated. 
#' 
#' @seealso \code{\link{rarefy_FPD}}
#' @author Sam Levin
#' @export


func_phy_dist <- function (FDist, PDist, phyloWeight, p, ...)
{
  if (phyloWeight < 0 | phyloWeight > 1)
    stop("'phyloWeight' must be between 0 and 1")
  if (!is.numeric(p))
    stop("'p' must be a numeric")
  
  if(any(is.na(FDist)) | any(is.na(PDist))){
    FDist[is.na(FDist)] <- mean(FDist, na.rm = T)
    PDist[is.na(PDist)] <- mean(PDist, na.rm = T)
    warning('NAs/NaNs detected in distance matrix. Values are being filled in\n,',
            'by matrix level mean values. Check data if this is problematic.')
  }
  
  if(phyloWeight < 1 & phyloWeight > 0){
    FDist <- FDist/max(FDist)
    PDist <- PDist/max(PDist)
  }
  (phyloWeight * PDist^p + (1 - phyloWeight) * FDist^p)^(1/p)
}