cwm: Community-Weighted Mean values of traits

In alexology/biomonitoR: biomonitoring indices and metrics

Community-Weighted Mean values of traits

Description

This function calculates the community-weighted means of trait categories.

Usage

cwm(x, trait_db = NULL, tax_lev = "Taxa", trans = log1p, traceB = FALSE)

Arguments

x	Result of aggregate_taxa().
trait_db	A trait data.frame with a column Taxa and the other columns containing traits. By default, the data.frame used is the one from Tachet et al. (2010) that can be retrieved from freshwaterecology.info website (Schmidt-Kloiber & Hering, 2015).
tax_lev	Character string giving the taxonomic level used to retrieve trait information. Possible levels are Taxa, Species, Genus, Family as returned by aggregate_taxa().
trans	Function for transforming the abundances, by default log1p.
traceB	When set to TRUE returns a list with the results of the cwm() function and the traits value used for the calculation.

Details

This function first takes the abundance table corresponding to the desired taxonomic level from the x object generated with aggregate_taxa().

The community mean trait values are calculated using the transformed abundances (using the trans function) as weigths.

Value

a table with the CWM values of each trait (trait modality)

References

Tachet, H., Richoux, P., Bournaud, M., & Usseglio-Polatera, P. (2010). Invertebres d'eau douce: systematique, biologie, ecologie. Paris: CNRS editions.

Schmidt-Kloiber, A., & Hering, D. (2015). www. freshwaterecology. info-An online tool that unifies, standardises and codifies more than 20,000 European freshwater organisms and their ecological preferences. Ecological indicators, 53, 271-282.

See Also

aggregate_taxa

Examples

data(macro_ex)

data_bio <- as_biomonitor(macro_ex)
data_agr <- aggregate_taxa(data_bio)
data_ts <- assign_traits(data_agr)

# averaging
data_ts_av <- average_traits(data_ts)

# community specialization index
cwm(x = data_agr, trait_db = data_ts_av, tax_lev = "Taxa", trans = log1p)
cwm(
  x = data_agr, trait_db = data_ts_av, tax_lev = "Taxa",
  trans = function(x) {
    ifelse(x > 0, 1, 0)
  }
)
cwm(x = data_agr, trait_db = data_ts_av, tax_lev = "Genus", trans = log1p)

alexology/biomonitoR documentation built on April 7, 2024, 10:15 a.m.