Default metrics for community_sharing_pq()

Returns the 4 default metrics: shared species count, Bray-Curtis similarity, Jaccard binary similarity, and proportion of shared genera.

bray_sim, jac_sim, and genus_prop use bounds = c(0, 1) for globally consistent linewidth scaling. shared_sp uses bounds = NULL (count metric without a fixed upper bound; rescaled within the observed range).

Usage

default_sharing_metrics()

Value

A named list of metric definitions.

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Default set of 4 metrics
mets <- default_sharing_metrics()
community_sharing_pq(data_fungi, fact = "Height", metrics = mets)

# Extend defaults with a robust Aitchison similarity metric
mets_plus <- c(
  default_sharing_metrics(),
  list(
    rob_aitch = make_sharing_metric(
      label = "Robust Aitchison similarity",
      color = "#FF7F00",
      prep  = function(physeq, fact, modalities) {
        otu_sp <- .agg_by_mod(physeq, fact, modalities)
        as.matrix(vegan::vegdist(t(otu_sp), method = "robust.aitchison"))
      },
      fn    = \(a, b, otu_sp, cache) 1 - cache[a, b]
    )
  )
)
community_sharing_pq(data_fungi, fact = "Height", metrics = mets_plus)

# Keep only a subset of the defaults
community_sharing_pq(
  data_fungi,
  fact    = "Height",
  metrics = default_sharing_metrics()[c("shared_sp", "bray_sim")]
)
} # }