adjustSizeGrid(): warn on per-species diet loss instead of resource biomass#453
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The high-end resource truncation check previously warned when
non-negligible resource *biomass* was discarded above the new maximum
size. Biomass loss is not the relevant quantity: what matters is whether
truncation changes the food a fish actually gets. This replaces that
check with a per-species diet-loss check, mirroring the existing low-end
check, evaluated at the largest size each species occupies (where the
largest resource matters most). It reports the fraction of the fish's
total encounter that is lost.
The low-end and high-end resource checks now use consistent wording
("diet of smallest/largest fish ... lost due to resource truncation"),
and the tol documentation makes clear that all three checks (biomass,
smallest-fish diet, largest-fish diet) are applied separately to each
species.
Lost fractions are now reported with 3 significant figures rather than
two decimal places, so a loss just above the default tol = 1e-6 shows as
0.0001% instead of 0.00%.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Reworks the resource-truncation warnings in
adjustSizeGrid()so they report what actually matters for the model dynamics — how much of each species' food (encounter) is discarded — rather than resource biomass.Changes
High-end resource truncation now warns on diet loss, not resource biomass. The previous check warned when a non-negligible fraction of resource biomass was discarded above the new maximum size. Biomass loss is not the relevant quantity: encounter feeds growth and reproduction only through the fish's total food intake. The new check mirrors the existing low-end (smallest-fish) check but is evaluated at the largest size each species occupies, where the largest resource particles matter most. It reports the lost resource encounter as a fraction of that fish's total encounter.
Consistent wording. The low-end and high-end messages now read symmetrically — "Non-negligible diet of smallest/largest fish was lost due to resource truncation: ...". Both are the same kind of ratio (lost resource encounter ÷ total encounter), sampled at the most-exposed fish size for the part of the resource being removed.
Per-species clarity in the docs. The
tolparameter documentation now states explicitly that all three checks — species biomass, smallest-fish diet, largest-fish diet — are applied separately to each species, and the warning lists the affected species.More useful precision. Lost fractions are reported with 3 significant figures (
%gofsignif(x, 3)) instead of two decimal places. With the defaulttol = 1e-6, a loss just above threshold now shows as0.0001%rather than the uninformative0.00%.Testing
testthat::test_file("tests/testthat/test-manipulate_species.R")— all 137 tests pass. The existing high-end-truncation test was updated to expect the new largest-fish diet message.🤖 Generated with Claude Code