R/sub.sp.matrix.R

In helixcn/spaa: SPecies Association Analysis

sub.sp.matrix <- function(spmatrix, freq = 0.5, common = NULL) {
  if (!is.null(common)) {
    freq <- NULL
    if ((!is.null(freq)) & (!is.null(common))) {
      stop(
        "Contradiction in argument freq and common,
                 try to specify only one argument.\n"
      )
    }
    if (common > ncol(spmatrix)) {
      stop("There are fewer species than you want to subset.\n")
    }
    freq.spmatrix <- freq.calc(spmatrix)
    names.spmatrix <- colnames(spmatrix)
    sort.freq <- sort(freq.spmatrix, decreasing = TRUE)
    names.freq <- names(sort.freq)
    nn <- names.freq[1:common]
    wii <- c()
    for (i in 1:length(nn)) {
      wii <- append(wii, which(nn[i] == names.spmatrix))
    }
    submatrix <- spmatrix[, wii]
  } else {
    if (!is.null(freq)) {
      freq.spmatrix <- freq.calc(spmatrix)
      sel <- freq.spmatrix > freq
      base <- 1:length(sel)
      se <- base[sel]
      submatrix <- spmatrix[, se]
    }
  }

  return(submatrix)
}