Add marine protist functional traits (Ramond et al.)

Joins genus-level morphological, behavioural and ecological traits of marine protists to a taxify() result by looking up genus, so any species in a covered genus is annotated.

Usage

add_ramond(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. The curated set:

ramond_shape

Cell shape (round, elongated, amoeboid, ...).

ramond_motility

Motility mode (swimmer, floater, gliding, ...).

ramond_ingestion

Ingestion / trophic mode (phagotrophic, ...).

ramond_chloroplast

Chloroplast presence (1 = present).

ramond_symbiontic

Symbiotic relationship (parasite, mutualist, ...).

ramond_colony

Colony form.

ramond_salinity

Salinity preference.

ramond_size_min_um

Minimum cell size (micrometres).

ramond_size_max_um

Maximum cell size (micrometres).

With cols = "all" the full set of behavioural, ecological and symbiosis descriptors is attached under their source names.

Details

Source: Ramond et al. (SEANOE, CC BY 4.0), functional traits of marine protists. Traits are genus-level; numeric cell size is aggregated by median, categorical traits by mode.

References

Ramond P, Siano R, Sourisseau M (2018) Functional traits of marine protists. SEANOE. doi:10.17882/51662

Examples

if (FALSE) { # \dontrun{
taxify("Alexandrium", backbone = "gbif") |>
  add_ramond()
} # }