Skip to contents

Full Ozkan pTO Pipeline (Islem 1 + 2 + 3)

Source: R/ozkan_pto_resample.R
ozkan_pto_full.Rd

Runs the complete Ozkan taxonomic diversity analysis pipeline: jackknife (Islem 1), stochastic resampling (Islem 2), and sensitivity analysis (Islem 3), returning the maximum values across all three runs. This is equivalent to running all three steps in the Excel macro sequentially.

Usage

ozkan_pto_full(community, tax_tree, n_iter = 101L, seed = NULL)

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.

n_iter

Number of stochastic iterations for Run 2 and Run 3 (default: 101, minimum: 101).

seed

Optional random seed for reproducibility. If provided, Run 2 uses this seed and Run 3 uses seed + 1 to ensure independent randomness.

Value

A named list with components:

uTO_plus

Final maximum uTO+ across all 3 runs

TO_plus

Final maximum TO+ across all 3 runs

uTO

Final maximum uTO across all 3 runs

TO

Final maximum TO across all 3 runs

run1

Deterministic pTO result (from ozkan_pto())

run2

Full Run 2 result (from ozkan_pto_resample())

run3

Full Run 3 result (from ozkan_pto_sensitivity())

jackknife

Jackknife result with species classifications

Details

This function implements the full Excel macro pipeline in a single call:

  1. Islem 1: Leave-one-out jackknife to identify contributing (happy) vs non-contributing (unhappy) species, plus deterministic pTO calculation.

  2. Islem 2: Stochastic resampling – unhappy species are always included, happy species get 50\

  3. Islem 3: Sensitivity analysis – unhappy species get \(P = (S-1)/S\), happy species get a data-driven probability.

  4. Final result: Maximum values across all three runs.

References

Ozkan, K. (2018). A new proposed measure for estimating taxonomic diversity. Turkish Journal of Forestry, 19(4), 336-346. DOI: 10.18182/tjf.441061

See also

ozkan_pto() for deterministic calculation only, ozkan_pto_resample() for Run 2 only, ozkan_pto_sensitivity() for Run 3 only, ozkan_pto_jackknife() for jackknife only.

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
)
set.seed(42)
result <- ozkan_pto_full(comm, tax, n_iter = 101)
result$uTO_plus  # Final maximum uTO+
#> [1] 3.060705
result$TO_plus   # Final maximum TO+
#> [1] 3.753852