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Calculate All Eight pTO Components (Convenience Wrapper)

Source: R/ozkan_pto.R
pto_components.Rd

Returns a named numeric vector with all eight Ozkan (2018) components: four using all taxonomic levels and four using only the informative levels (max version), matching the Excel macro's Run 1+2+3 output.

Usage

pto_components(community, tax_tree)

Arguments

community

A named numeric vector of species abundances. Names must match the first column of tax_tree.

tax_tree

A data frame with taxonomic hierarchy. First column is species names, subsequent columns are taxonomic ranks from lowest to highest (e.g., Species, Genus, Family, Order, Class, Phylum, Kingdom).

Value

A named numeric vector with eight elements: uTO, TO, uTO_plus, TO_plus, uTO_max, TO_max, uTO_plus_max, TO_plus_max.

See also

ozkan_pto() for the full result including per-level entropy.

Examples

comm <- c(sp1 = 4, sp2 = 2, sp3 = 3, sp4 = 1, sp5 = 2)
tax <- data.frame(
  Species = paste0("sp", 1:5),
  Genus   = c("G1", "G1", "G1", "G2", "G2"),
  Family  = c("F1", "F1", "F1", "F1", "F1"),
  stringsAsFactors = FALSE
)
pto_components(comm, tax)
#>          uTO           TO     uTO_plus      TO_plus      uTO_max       TO_max 
#>     2.632978     3.300651     3.060705     3.753852     2.632978     3.300651 
#> uTO_plus_max  TO_plus_max 
#>     3.060705     3.753852