Export taxon abundances in a format suitable for CoNet

If provided, metadata are exported into a CoNet feature file. Prior to the export, categoric metadata are binarised, such that the resulting feature file only contains binary (as 0/1) and numeric features, since CoNet cannot handle categoric features. Constant metadata are removed. If binary metadata are provided as strings, the strings encoding 0 (no) and 1 (yes) have to be indicated. If lineages are provided, they are exported into a CoNet metadata file, which can be used for all group-specific data sets, in case groups are provided. Either the last column or the row names of the lineage matrix have to match the row names of the abundance matrix.

exportToCoNet(
  abundances,
  metadata = NULL,
  lineages = NULL,
  groups = c(),
  export.folder = "",
  root.name = "conet",
  metadata.to.skip = c(),
  omitNeg = TRUE,
  yes = "Y",
  no = "N",
  date.items = c(),
  date.format = "%d/%m/%y",
  taxa.are.rownames = FALSE
)

Arguments

abundances	a matrix with taxa as rows and samples as columns
metadata	an optional data frame with metadata items as columns where sample names match sample names in abundances; data types (factor vs numeric) are supposed to be correct
lineages	an optional lineage matrix where row names match row names of taxa; taxa must be provided in the same order as in abundances; first column gives kingdom, following columns give phylum, class, order, family, genus and species (not all are required)
groups	an optional group membership vector with as many entries as abundances has samples; if provided, data are exported separately for each group
export.folder	the export folder into which files should be saved
root.name	a name included in all exported files
metadata.to.skip	names of metadata items that should not be exported
omitNeg	if true, metadata with negative values are removed, since CoNet run with Bray Curtis or Kullback Leibler dissimilarity cannot handle them
yes	the string encoding 1 in a binary metadata item
no	the string encoding 0 in a binary metadata item
date.items	names of metadata items that are dates (they will be converted into days since 1/1/1900)
date.format	the date format (an example date fitting the default format is 26/1/80)
taxa.are.rownames	if true, row names instead of the last column of the lineage matrix provide the lowest-level taxa (e.g. for OTUs or sequencing variants)