R/muotu.R

In yewei369/clotu: Classification of OTUs

#' Mean of OTU
#' 
#' Calculate mean value of target groups
#' 
#' @param da, dataset
#' @param esti.mode, digits for covariance estimating method, 0 for Kaul's method, 1/2/3 for Jun Li's 1st/2nd/3rd method
#' @return mean values for each OTU
#' 


muotu<-function(da,esti.mode=0){

  d<-dim(da)[1]
  if(esti.mode %in% c(0,1)){
    pres<-present(da)
    mu<-sapply(as.data.frame(t(da)),sum)/(pres$blood*dim(da)[2])
    return (mu)}
  
  else if(esti.mode %in% c(2,3)){
    mu<-array(0,dim=c(2,d,d))
    for(i in 1:d)
      for(j in 1:d){
        ind<-which(da[i,]!=0 & da[j,]!=0)
        mu[,i,j]<-ifelse(length(ind)==0,0,c(sum(da[i,ind])/length(ind)  , sum(da[j,ind])/length(ind)  ) ) } }
  if(esti.mode==2) return (mu)
  else if(esti.mode==3) {
    mu1<-rep(0,d)
    for(i in 1:d) mu1[i]<-mean(mu[1,i,])
    return (mu1)}}