Skip to contents

Functional diversity from trait probability densities

Source: R/tpd-phylo.R
trait_tpd.Rd

The trait probability density (TPD) approach (Carmona et al. 2016, 2019) describes each species by the probability density of its trait values, estimated from individual measurements, so intraspecific variability is part of every index. Community TPDs are the abundance-weighted sums of species TPDs. From them, trait_tpd() returns functional richness, evenness and divergence (TPD::REND()) and functional redundancy (TPD::redundancy()) per site, and trait_tpd_dissim() returns pairwise functional dissimilarity between sites, split into shared and non-shared parts (TPD::dissim()).

Usage

trait_tpd(
  data,
  traits,
  site = site,
  species = species,
  abundance = NULL,
  cols,
  alpha = 0.95,
  n_divisions = NULL
)

trait_tpd_dissim(
  data,
  traits,
  site = site,
  species = species,
  abundance = NULL,
  cols,
  alpha = 0.95,
  n_divisions = NULL
)

Arguments

data

A data frame in long format, with one row per record.

traits

A data frame with one row per measured individual: a species column (named as in data) and one to four numeric trait columns. Traits are often log-transformed first.

site, species

<tidy-select> The column holding site identifiers and the column holding species names.

abundance

<tidy-select> The column holding counts. If NULL (the default), a column called abundance is used when present, otherwise every row counts as one individual.

cols

<tidy-select> The trait columns (one to four).

alpha

Proportion of the probability density kept for each species (removes outliers).

n_divisions

Number of grid divisions per trait axis; defaults to those of TPD::TPDs().

Value

trait_tpd(): a tibble with the site column, FRic, FEve, FDiv and redundancy. trait_tpd_dissim(): a tibble of site pairs with dissimilarity, its parts due to shared (p_shared) and non-shared (p_nonshared) trait space.

References

Carmona, C. P. et al. (2016). Traits without borders: integrating functional diversity across scales. Trends in Ecology & Evolution, 31, 382-394. doi:10.1016/j.tree.2016.02.003

Carmona, C. P. et al. (2019). Trait probability density (TPD): measuring functional diversity across scales based on TPD with R. Ecology, 100, e02876. doi:10.1002/ecy.2876