Host specificity index (S_TD) for every parasite in an interaction table

Applies poulin_std to every parasite in an interaction table, following the same expansion logic as prepare_pair_data. Useful for contrasting the Poulin and Mouillot (2003) specificity index against phylopred's model-based host-range metric b* (host_threshold_metric) across many parasites.

Usage

host_specificity_index(interactions, phydist, group = NULL)

Arguments

interactions: A data.frame with at least two columns: the first the parasite (or symbiont) species, the second the host species. Extra columns are ignored. Duplicated rows are removed.
phydist: A square, numeric distance matrix among hosts (taxonomic steps or phylogenetic distances), with matching row and column names.
group: Optional. Either the name of a column in interactions giving a grouping factor for each parasite (e.g. genus or clade), or a function applied to the parasite name to derive the group.

Value

A data.frame of class "phylopred_specificity" with columns parasite, n_hosts (known hosts present in phydist), std (\(S_{TD}\)), var_std (\(Var(S_{TD})\)), and group (only if group is supplied).

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

Examples

std_by_parasite <- host_specificity_index(beetleTreeInteractions, phy_dist)
head(std_by_parasite)
#>                    parasite n_hosts      std  var_std
#> 1     Ambrosiodmus obliquus       6 477.4053 11989.14
#> 2  Ambrosiodmus rubricollis       7 477.6867 22962.69
#> 3 Ambrosiodmus tachygraphus       4 467.0644 24030.53
#> 4   Coptoborus pseudotenuis      10 394.9607  5115.38
#> 5     Euwallacea fornicatus      31 457.2600 13711.36
#> 6        Euwallacea validus      22 511.3490 22369.51