You can use this script with the following example:
  Rscript inst/scripts/prepare_libraries_sop_merged.R --fil-lib-sop-pre data/interim/libraries/sop/lotus_prepared.tsv.gz --fil-lib-sop-mer bitter_db.tsv.gz --org-fil-mod TRUE --org-fil-lev family --org-fil-val 'Simaroubaceae|Gentianaceae'

Usage:
  prepare_libraries_sop_merged.R [--fil-lib-sop-pre=<fil-lib-sop-pre>] [--fil-lib-sop-mer=<fil-lib-sop-mer>] [--org-fil-mod=<org-fil-mod>] [--org-fil-lev=<org-fil-lev>] [--org-fil-val=<org-fil-val>]

Arguments:
  fil-lib-sop-pre            List of prepared structure organism pairs libraries. STRING
  fil-lib-sop-mer            Merged structure organism pairs library. STRING
  
  org-fil-mod                Filter library to restrict it to a portion of organisms only. BOOLEAN
  org-fil-lev                Level at which the library will be filtered. Must be one of "domain", "phylum", "class", "order", "family", "tribe", "genus", "species", "varietas" . STRING
  org-fil-val                Value to be applied for filtering. "OR" can be used as "|". Example: "Simaroubaceae|Gentianaceae". STRING

Options:
  -h --help                  Shows this screen.
  -v --version               Shows version.