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Add host-virus association breadth (VIRION)

Source: R/add-virion.R
add_virion.Rd

Joins per-host counts of recorded virus associations to a taxify() result.

Usage

add_virion(x, cols = NULL, verbose = TRUE)

Arguments

x

A data.frame returned by taxify().

cols

Which columns to attach: NULL (default) all, or a character vector of names. See enrichment_cols.

verbose

Logical. Default TRUE.

Value

The same data.frame with virion_ columns: virus_richness, virus_family_count, virus_record_count, host_class.

Details

Source: Carlson et al. (2022), 4223 vertebrate hosts and 9833 viruses. ODbL-1.0. As with add_globi() and add_invacost(), only the derived per-host counts are redistributed, not the association records.

These counts measure how much a host has been looked at as much as what infects it. Homo sapiens leads with 936 distinct viruses across 633,053 records, and the ordering below it tracks livestock and laboratory species. virus_record_count travels alongside so the effort behind a richness is visible; treat richness as association breadth as recorded, not as a biological property of the host.

References

Carlson CJ, Gibb RJ, Albery GF, et al. (2022) The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations. mBio 13:e0298521. doi:10.1128/mbio.02985-21

Examples

if (FALSE) { # \dontrun{
taxify(c("Sus scrofa", "Myotis lucifugus")) |>
  add_virion()
} # }