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Build a taxonomic step-distance matrix (Poulin & Mouillot scale)

Source: R/poulin_std.R
taxonomic_step_matrix.Rd

Constructs a symmetric taxonomic distance matrix among species from a taxonomic hierarchy table, following the step scale of Poulin and Mouillot (2003): 1 if two species share a genus, 2 if they share a family but not a genus, 3 if they share an order but not a family, 4 if they share a class but not an order, and 5 if they share none of the above (different class / phylum). Any subset of genus, family, order, class may be supplied; missing ranks are skipped and the maximum step for that pair falls back to length(ranks) + 1.

Usage

taxonomic_step_matrix(tax_table)

Arguments

tax_table

A data.frame with one row per species and columns species plus at least two of genus, family, order, class. No NA values are allowed in the rank columns (see host_specificity_index for handling hosts with incomplete taxonomy).

Value

A square numeric matrix with row/column names equal to tax_table$species, diagonal 0, suitable as the phydist argument of poulin_std or host_specificity_index.

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

See also

poulin_std, host_specificity_index

Examples

tax <- data.frame(
  species = c("Caligus elongatus", "Caligus curtus",
              "Lepeophtheirus salmonis", "Ergasilus sieboldi"),
  genus  = c("Caligus", "Caligus", "Lepeophtheirus", "Ergasilus"),
  family = c("Caligidae", "Caligidae", "Caligidae", "Ergasilidae"),
  order  = c("Siphonostomatoida", "Siphonostomatoida",
              "Siphonostomatoida", "Cyclopoida")
)
taxonomic_step_matrix(tax)
#>                         Caligus elongatus Caligus curtus
#> Caligus elongatus                       0              1
#> Caligus curtus                          1              0
#> Lepeophtheirus salmonis                 2              2
#> Ergasilus sieboldi                      4              4
#>                         Lepeophtheirus salmonis Ergasilus sieboldi
#> Caligus elongatus                             2                  4
#> Caligus curtus                                2                  4
#> Lepeophtheirus salmonis                       0                  4
#> Ergasilus sieboldi                            4                  0