Plot pTO Iteration Results from Run 2 or Run 3

Visualizes the iteration-by-iteration pTO values from stochastic resampling (Run 2) or sensitivity analysis (Run 3). Each iteration's value is shown as a point, with the deterministic (Run 1) value displayed as a horizontal reference line.

Usage

plot_iteration(resample_result, component = "TO", title = NULL)

Arguments

resample_result: The list returned by ozkan_pto_resample (Run 2) or ozkan_pto_sensitivity (Run 3).
component: Character string specifying which pTO component to plot. One of "uTO", "TO", "uTO_plus", "TO_plus". Default is "TO".
title: Optional character string for the plot title.

Value

A ggplot object showing iteration values as points, the deterministic value as a dashed red line, and the maximum value as a dashed blue line.

Details

The plot includes three visual elements:

Grey points: Individual iteration values
Red dashed line: Deterministic (Run 1) value
Blue dashed line: Maximum value across all iterations

This helps assess how stochastic species removal affects the pTO index and whether the maximum exceeds the deterministic value.

Examples

# \donttest{
comm <- c(sp1 = 10, sp2 = 20, sp3 = 15, sp4 = 5)
tax <- build_tax_tree(
  species = paste0("sp", 1:4),
  Genus = c("G1", "G1", "G2", "G2"),
  Family = c("F1", "F1", "F1", "F2")
)
res <- ozkan_pto_resample(comm, tax, n_iter = 101, seed = 42)
plot_iteration(res, component = "TO")

# }