fast (?) implementations of tanimoto distance calculations

tanimoto.R

#' @title fast_tanimoto 
#' @param mat matrix or data frame of numeric values
#' @param output 'matrix' (default) or 'edge list' (non-redundant and undirected)
#' @param progress TRUE, show progress
#' @imports reshape2
fast_tanimoto<-function(mat,output='matrix',progress=TRUE){
  mat[is.na(mat)]<-0 
  
  #scoring function
  score<-function(x){sum(x==2)/sum(x>0)}
  
  if (progress == TRUE){ pb <- txtProgressBar(min = 0, max = nrow(mat), style = 3)} else {pb<-NULL}
  out<-lapply(1:nrow(mat), function(i){
    tmp.mat<-sweep(mat,2,as.numeric(mat[i,]),"+")
    if (progress == TRUE){setTxtProgressBar(pb, i)}
    apply(tmp.mat,1,score)
  })
  if (progress == TRUE){close(pb)}
  
  res<-do.call("rbind",out)
  rownames(res)<-rownames(mat)
  if(output=='edge list'){ 
    res[upper.tri(res,diag=TRUE)]<-NA
    na.omit(melt(res))
  } else {
    return(res)
  }
}

#' @title fast_tanimoto_par
#' @description parallel implementation of \code{\link{fast_tanimoto}} 
#' @param mat matrix or data frame of numeric values
#' @param output 'matrix' (default) or 'edge list' (non-redundant and undirected)
#' @param progress TRUE, print progress to 'log.txt'
#' @imports reshape2, foreach, doMC
fast_tanimoto_par<-function(mat,output='matrix'){
  mat[is.na(mat)]<-0 
  
  #scoring function
  score<-function(x){sum(x==2)/sum(x>0)}
  
  sink(paste0(getwd(),"/log.txt"), append=TRUE)
  out<-foreach(i=1:nrow(mat)) %dopar% {
    sink(paste0(getwd(),"/log.txt"), append=TRUE)
    cat(paste("Starting iteration",i,"\n"))
    sink()
    tmp.mat<-sweep(mat,2,as.numeric(mat[i,]),"+")
    apply(tmp.mat,1,score)
  }

  res<-do.call("rbind",out) #would have to convert each element to a data frame to use faster data.table::rbindlist
  rownames(res)<-rownames(mat)
  if(output=='edge list'){ 
    res[upper.tri(res,diag=TRUE)]<-NA
    na.omit(melt(res))
  } else {
    return(res)
  }
}