R/DistContinuous.R

In laura20vg/permanova: MANOVA and PERMANOVA

DistContinuous <- function(x, y=NULL,  coef = "Pythagorean", r = 1) {
  # We sould change this function to avoid loops
  distances = c("Pythagorean", "Taxonomic", "City", "Minkowski", "Divergence", "dif_sum", "Camberra", "Bray_Curtis", "Soergel", "Ware_Hedges", "Gower")
  if (is.numeric(coef)) coef = distances[coef]
  if (!is.matrix(x)) x=as.matrix(x)
  if (is.null(y)) y=x
  if (!is.matrix(y)) y=as.matrix(y)
  n = nrow(x)
  p = ncol(x)
  s = nrow(y)
  q=ncol(y)
  NamesX=rownames(x)
  NamesY=rownames(y)

  if (coef=="Gower") rank=apply(rbind(y,x),2,max)-apply(rbind(y,x),2,min)
  if (!(p==q)) stop("The matrices should have the same number of columns")

  dis=matrix(0,s,n)
  for (i in 1:s) for (j in 1:n) {
    switch(coef, Pythagorean = {
      dis[i, j] = sqrt(sum((y[i, ] - x[j, ])^2))
    },Taxonomic = {
      dis[i,j]=sqrt(sum(((y[i,]-x[j,])^2)/r^2))
    },City = {
      dis[i,j]=sum(abs(y[i,]-x[j,]))
    },Minkowski = {
      dis[i,j]=(sum(abs(y[i,]-x[j,])^r))^(1/r)
    },Divergence = {
      dis[i,j]=sqrt(sum((y[i,]-x[j,])^2/(y[i,]+x[j,])^2))
    },dif_sum = {
      dis[i,j]=sum(abs(y[i,]-x[j,])/abs(y[i,]+x[j,]))
    },Camberra = {
      dis[i,j]=sum(abs(y[i,]-x[j,])/(abs(y[i,])+abs(x[j,])))
    },Bray_Curtis = {
      dis[i,j]=sum(abs(y[i,]-x[j,]))/sum(y[i,]+x[j,])
    },Soergel = {
      dis[i,j]=sum(abs(y[i,]-x[j,]))/sum(apply(rbind(y[i,],x[j,]),2,max))
    },Ware_Hedges = {
      dis[i,j]=sum(1-apply(rbind(y[i,],x[j,]),2,min)/apply(rbind(y[i,],x[j,]),2,max))
    },Gower = {
      dis[i,j]=sum(abs(y[i,]-x[j,])/rank)
    })
  }

  rownames(dis)=NamesY
  colnames(dis)=NamesX
  distances=list(Data=x, D=dis, Coefficient=coef)
  class(distances) = "proximities"
  return(distances)
}