Add bacterial and archaeal traits (Madin et al.)

Joins species-level bacterial and archaeal phenotypic and genome traits to a taxify() result by looking up accepted_name.

Usage

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

Arguments

x

A data.frame returned by taxify().

cols

Which columns to attach: NULL (default) the curated set, "all" every column the source carries, or a character vector of names. See enrichment_cols.

verbose

Logical. Default TRUE.

Value

The same data.frame with additional columns:

madin_gram_stain

Gram stain (positive/negative).

madin_metabolism

Metabolism (aerobic/anaerobic/facultative/...).

madin_cell_shape

Cell shape (bacillus/coccus/spiral/...).

madin_motility

Motility (yes/no/flagella/gliding/...).

madin_sporulation

Sporulation (yes/no).

madin_isolation_source

Isolation source category.

madin_growth_temp_c

Recorded growth temperature (degrees Celsius).

madin_optimum_temp_c

Optimum growth temperature (degrees Celsius).

madin_optimum_ph

Optimum growth pH.

madin_genome_size_bp

Genome size (base pairs).

madin_gc_content_pct

Genomic G+C content (percent).

Details

Source: Madin et al. (2020, Scientific Data, CC BY 4.0). Coverage: ~14.9k bacterial and archaeal species.

References

Madin JS et al. (2020) A synthesis of bacterial and archaeal phenotypic trait data. Scientific Data 7:170. doi:10.1038/s41597-020-0497-4

Examples

if (FALSE) { # \dontrun{
taxify("Escherichia coli", backbone = "gbif") |>
  add_madin()
} # }