Restrict plotDiet() to size ranges with meaningful abundance

[Copilot]

plotDiet() was plotting diet information all the way to w_max regardless of whether fish were present at those sizes, showing misleading diet data for extremely rare large individuals.

Changes

• R/plots.R: Added abundance-based filtering to plotDiet()

  • Extract abundance from MizerSim (last time step) or MizerParams (initial values)
  • Calculate per-species threshold: abundance > 1e-5 * max_abundance
  • Filter plot data to exclude sizes beyond the meaningful range
  • Applied per-species to handle faceted plots correctly

• tests/testthat/test-plots.R: Added test verifying size limiting behavior

Example

For a species with w_max = 1000g where abundance becomes negligible beyond 100g, plots now automatically truncate at ~187g instead of extending to 1000g.

Implementation:

# For each predator species
abundance <- n[pred_idx, ]
max_abundance <- max(abundance)
meaningful_idx <- which(abundance > 1e-5 * max_abundance)
w_max_meaningful <- params@w[max(meaningful_idx)]
plot_dat <- plot_dat[!(plot_dat$Predator == pred & plot_dat$w > w_max_meaningful), ]

Fully backward compatible—no changes to function signature or existing parameters.

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Original prompt

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This section details on the original issue you should resolve

<issue_title>Adjust plotDiet() to Restrict Plots to Relevant Size Ranges</issue_title>
<issue_description>When using the plotDiet() function, the diet plots currently extend all the way to w_max, regardless of whether there are any fish left at those sizes. This can make the plots misleading or less helpful for species with little or no biomass in the largest size classes, as they may show diet information for size ranges where the species is no longer present, extending to rare situations where diets would require negative intake rates for very large fish.

It might be helpful to adjust plotDiet() so that it only plots up to the largest size class where fish are present (i.e., where the abundance is greater than zero). This would ensure the plot better represents the relevant size ranges and provides more useful information to the user.

</issue_description>

Comments on the Issue (you are @copilot in this section)

@gustavdelius Thanks @JamesRimmerEco . That would be a good idea. In practice, the abundance of fish actually stays non-zero all the way up to `w_repro_max` but the abundance can become totally negligibly small long before that. So the relevant size range should not be the entire range where the abundance is greater than 0 but only the range where it is greater than some threshold. The trick will be to automatically find a good value for this threshold. @gustavdelius Let's put the upper limit on the size axis to the size beyond which the abundance density is less than 1e-5 of the maximum density.

• Fixes Adjust plotDiet() to Restrict Plots to Relevant Size Ranges #304

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