R/convert_to_vegan.R

In alexology/biomonitoR: biomonitoring indices and metrics

#' @title convert data to other formats
#'
#' @description
#' Utility functions to export data to other formats.
#'
#' @param x Result of `aggregate_taxa()`.
#' @param tax_lev The taxonomic level of interest. Possible choices are Phylum, Class, Subclass, Order, Family, Subfamily, Tribus, Genus, Species, Subspecies, Taxa
#'
#' @keywords convert_to_vegan
#' @details `convert_to_vegan()` converts data to the `vegan` package style, with sites on rows and taxa on columns. `convert_to_biotic()` converts data to
#' the format of `biotic` package. This function will extract information at the family level, with an exception for Oligochaeta.
#' In `convert_to_biotic()` if both family and above family level taxonomic information of Oligochaeta are concurrently present,
#' information will be provided for Oligochaeta level only.
#' `biomonitoR` automatically identify the taxonomic level at which Oligochaeta are stored (subclass is the default in `biomonitoR`).
#' Be careful, for all the other taxa entered at taxonomic level higher than family will be discarded (e.g. Trombidiformes).
#' @export
#' @export convert_to_biotic
#' @seealso \code{\link{aggregate_taxa}}
#' @examples
#' data(macro_ex)
#' data_bio <- as_biomonitor(macro_ex)
#' data_agr <- aggregate_taxa(data_bio)
#' data_cv <- convert_to_vegan(data_agr, tax_lev = "Family")
convert_to_vegan <- function(x, tax_lev = "Family") {

  # check if the object x is of class "biomonitoR"
  classCheck(x)

  # useful for transforming data to 0-1 later
  if (inherits(x, "bin")) {
    BIN <- TRUE
  } else {
    BIN <- FALSE
  }

  # vector of possible taxonomic levels
  taxa.vec <- c(
    "Phylum", "Class", "Subclass", "Order", "Family", "Subfamily", "Tribus",
    "Genus", "Species", "Subspecies", "Taxa"
  )

  # tax_lev must be one of the tax.vec levels
  if (!tax_lev %in% taxa.vec) {
    stop("Please provide a valid tax_lev")
  }

  # get the data.frame at the specified taxonomic level
  x <- x[[tax_lev]]
  st.names <- names(x)[-1]
  taxa.names <- x[, 1]

  # transform the data.frame from abundance to presence-absence if needed
  if (BIN) {
    x <- to_bin(x)
  }

  # if unassigned are present remove them, otherwise return the x after having changed column names
  if ("unassigned" %in% taxa.names) {
    # position of unassigned
    un.numb <- which("unassigned" %in% taxa.names)
    x <- x[-un.numb, ]
    x.t <- as.data.frame(t(x[, st.names]))
    names(x.t) <- taxa.names[-un.numb]
    x.t
  }

  else {
    x.t <- as.data.frame(t(x[, st.names]))
    names(x.t) <- taxa.names
    x.t
  }
}