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Poulin and Mouillot taxonomic/phylogenetic distinctness index (S_TD)

Source: R/poulin_std.R
poulin_std.Rd

Computes the average taxonomic (or phylogenetic) distinctness \(S_{TD}\) of Poulin and Mouillot (2003) for a single parasite's known host set: $$S_{TD} = \frac{2 \sum_{i<j} \omega_{ij}}{s(s-1)}$$ where \(\omega_{ij}\) is the distance between hosts \(i\) and \(j\) taken from phydist, and \(s\) is the number of known hosts. When phydist is a taxonomic step matrix (see taxonomic_step_matrix), \(S_{TD}\) is the original 1-5 taxonomic index; when phydist is a matrix of phylogenetic (patristic) distances, this is the continuous phylogenetic generalization noted as possible by Poulin and Mouillot (2003, after Clarke and Warwick, 2001), expressed directly in branch-length units. The corresponding sampling variance \(Var(S_{TD}) = \sum_{i \ne j} (\omega_{ij} - S_{TD})^2 / [s(s-1)]\) is also returned.

Usage

poulin_std(phydist, hosts)

Arguments

phydist

A square, numeric distance matrix among hosts with matching row and column names (taxonomic steps from taxonomic_step_matrix, or phylogenetic/patristic distances such as phy_dist).

hosts

Character vector of known host names for one parasite. Hosts not present in phydist are dropped with a warning.

Value

An object of class "phylopred_std": a list with elements n_hosts, std (\(S_{TD}\)), and var_std (\(Var(S_{TD})\), NA when n_hosts < 3). \(S_{TD}\) is undefined (NA, with a warning) when n_hosts < 2, as noted by Poulin and Mouillot (2003) for single-host parasites.

References

Poulin, R. and Mouillot, D. (2003) Parasite specialization from a phylogenetic perspective: a new index of host specificity. Parasitology 126, 473-480. doi:10.1017/S0031182003002993

Clarke, K.R. and Warwick, R.M. (2001) A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Marine Ecology Progress Series 216, 265-278.

See also

host_specificity_index, taxonomic_step_matrix, host_threshold_metric

Examples

hosts <- unique(beetleTreeInteractions$genus[
  beetleTreeInteractions$beetle == beetleTreeInteractions$beetle[1]])
poulin_std(phy_dist, hosts)
#> Poulin & Mouillot S_TD
#>   n_hosts: 6
#>   S_TD:    477.4053
#>   Var(S_TD): 11989.1383