Build a pairwise host-sharing data set from an interaction table

Expands an interaction table into all (focal host, target host) pairs per parasite. For every parasite, each of its known hosts is used as a focal host, and every other host in phydist is a target host whose response is 1 if it is also a known host of that parasite and 0 otherwise.

Usage

prepare_pair_data(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 phylogenetic (or taxonomic) distance matrix among hosts, with matching row and column names. Hosts in interactions absent from phydist are dropped with a warning.
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 (e.g. function(x) sub(" .*", "", x) for the genus).

Value

A data.frame of class "phylopred_pairs" with columns:

parasite: Parasite species (cluster identifier).
focal: Focal (known) host.
target: Target host.
phydist: Distance between focal and target host.
suscept: 1 if the target host is a known host of the parasite.
group: Grouping factor (only if group is supplied).

Details

Unlike the legacy workflow (which samples a single focal host per parasite), this uses every known host as a focal host, so no information is discarded and results are deterministic. Rows belonging to the same parasite are not independent; account for this with cluster_bootstrap_phylopred when computing uncertainty.

Examples

pairs <- prepare_pair_data(beetleTreeInteractions, phy_dist)
#> Warning: 22 interaction record(s) dropped: host not in 'phydist'.
head(pairs)
#>                parasite    focal        target  phydist suscept
#> 1 Ambrosiodmus obliquus Lysiloma     Ailanthus 443.1818       0
#> 2 Ambrosiodmus obliquus Lysiloma Phellodendron 443.1818       0
#> 3 Ambrosiodmus obliquus Lysiloma        Citrus 443.1818       0
#> 4 Ambrosiodmus obliquus Lysiloma   Zanthoxylum 443.1818       0
#> 5 Ambrosiodmus obliquus Lysiloma       Murraya 443.1818       0
#> 6 Ambrosiodmus obliquus Lysiloma   Chloroxylon 443.1818       0