Add phytoplankton nutrient-uptake traits (Edwards et al.)

Joins species-level phytoplankton nutrient physiology (Droop/Monod uptake and growth parameters for ammonium, nitrate and phosphorus, plus cell size and carbon content) to a taxify() result by looking up accepted_name.

Usage

add_edwards_phyto(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:

edwards_taxon_group

Coarse phytoplankton group (diatom, green, ...).

edwards_habitat_system

Habitat (marine/freshwater).

edwards_cell_volume

Cell volume (micron^3).

edwards_carbon_per_cell

Carbon content per cell (pg C).

edwards_mu_inf_nit

Maximum growth rate on nitrate (per day).

edwards_k_nit

Half-saturation constant for growth on nitrate.

edwards_qmin_nit

Minimum cell nitrogen quota.

edwards_mu_inf_p

Maximum growth rate on phosphorus (per day).

edwards_k_p

Half-saturation constant for growth on phosphorus.

edwards_qmin_p

Minimum cell phosphorus quota.

With cols = "all" the full set of ammonium/nitrate/phosphorus uptake and quota parameters (vmax_amm, mu_nit, vmax_p, qmax_p, ...) is attached under their source names. All uptake/quota traits are joined on accepted_name.

Details

Source: Edwards et al. (2015, Ecology, CC BY 4.0), a compilation of phytoplankton nutrient-utilization traits for ~130 species. Single-source physiological data with no cross-source analogue, so it is surfaced through this door rather than the cross-source add_trait() verb.

References

Edwards KF, Thomas MK, Klausmeier CA, Litchman E (2015) Phytoplankton growth and the interaction of light and temperature: A synthesis at the species and community level. Ecology 96(9):2554-2564. doi:10.1890/14-2252.1

Examples

if (FALSE) { # \dontrun{
taxify("Thalassiosira pseudonana", backbone = "gbif") |>
  add_edwards_phyto()
} # }