Plot functional trait space — plot_trait

Places species in a two-dimensional functional trait space, the first two axes of a principal coordinates analysis (PCoA) of their trait dissimilarities, as is usual for multidimensional functional diversity indices (Villeger et al. 2008). With data, each group of sites gets the convex hull of the species it holds, whose area is the two-dimensional functional richness, and its community-weighted mean position (CWM).

Usage

plot_trait_space(
  traits,
  data = NULL,
  species = species,
  group = NULL,
  abundance = NULL,
  distance = NULL,
  labels = FALSE,
  palette = "okabe_ito",
  theme = theme_tidydiversity(grid = "none")
)

Arguments

traits: A data frame with a species column and trait columns.
data: Optional data frame of species records by group.
species: The species column of traits and data.
group: Column of data defining the groups to compare, such as habitats.
abundance: Optional abundance column of data, used for the CWM.
distance: Optional species dissimilarities (a dist with species labels). By default Gower distances from trait_dist().
labels: Label the species.
palette: Colours for the groups: "okabe_ito", "grey" or a vector of colours.
theme: A ggplot2 theme, by default theme_tidydiversity().

Value

A ggplot object.

References

Villeger, S., Mason, N. W. H. and Mouillot, D. (2008). New multidimensional functional diversity indices for a multifaceted framework in functional ecology. Ecology, 89, 2290-2301. doi:10.1890/07-1206.1

Examples

aravo <- data_aravo()
plot_trait_space(aravo$traits, aravo$community, group = ZoogD, abundance = cover)