Allow addSpecies() to proceed with warning when growth stops after maturity

[Copilot]

Currently addSpecies() aborts if newly-added species have zero growth rates anywhere before reaching maximum size, preventing interactive parameter tuning. This should only error if species cannot reach maturity.

Changes

• R/steadySingleSpecies.R: Modified growth check to distinguish between pre-maturity (error) and post-maturity (warning) zero growth

  • Find first index where growth becomes zero
  • Error only if first_zero_idx < w_mat_idx
  • Warning if first_zero_idx >= w_mat_idx

• tests/testthat/test-steadySingleSpecies.R: Added test coverage for both error and warning cases

Example

# Previously would error - now issues warning and succeeds
params <- newTraitParams()
species_params <- data.frame(
    species = "species_with_high_metabolism",
    w_max = 100,
    w_mat = 50,
    ks = 10  # High metabolic rate causes zero growth after maturity
)
params <- addSpecies(params, species_params)
# Warning: species_with_high_metabolism has zero growth rate after maturity size

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• cloud.r-project.org
  • Triggering command: /usr/local/lib/R/bin/exec/R --no-save --no-restore --no-echo --no-restore -e install.packages("remotes",~+~repos="REDACTED") (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

---

This section details on the original issue you should resolve

<issue_title>In addSpecies() only issue warning if feeding level drops below critical level</issue_title>
<issue_description>Currently, if one of the newly-added species has predation parameters that lead to a feeding level that drops below the critical feeding level, the function aborts with an error message: "Can not compute steady state due to zero growth rates for ...". This should be changed so that an error is issued only if the growth rate becomes zero already before the species reaches maturity size. If the species does make it to maturity before growth stops then only a warning should be issued. That will make it easier for the user to make adjustments to the new species interactively with tuneParams().</issue_description>

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

• Fixes In addSpecies() only issue warning if feeding level drops below critical level #280

---

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.