add-simulation-test

name	add-simulation-test
description	Add simulation-based parameter-recovery tests for freqTLS models.

Add a Simulation Test

Use this skill when testing the 4PL likelihood, the links, the profile machinery, and the fitting workflow. Curie leads.

Procedure

1. Simulate data from known parameters with simulate_tls() (factorial temperature x duration grid; locked data-generating process; fixed seed).
2. Fit the intended model with fit_tls().
3. Check convergence diagnostics (convergence$code == 0, pdHess).
4. Check estimates on the natural scale: CTmax, z, low, up, k, and (for beta-binomial) phi.
5. Check profile behaviour where relevant: |D(MLE)| near zero, a finite closed CI for an interior MLE, and equivariance ci_z == exp(ci_log_z) to about 1e-6.
6. Test edge cases that are scientifically likely and numerically risky.

CRAN-Safe Tests

Keep CRAN tests small and deterministic. Use fixed seeds and moderate tolerances. Put long simulation studies in data-raw/ or an optional workflow, not in routine package checks.

Required Edge Cases

• Too few temperatures (< 3) or durations (< 3, overall and per temperature).
• No mortality and all mortality.
• A threshold never crossed; an asymptote not approached.
• phi near the binomial limit; near-binomial data fit by beta-binomial.
• A sparse design where the profile does not close (expect a warning and an NA endpoint, not a crash).
• Grouped designs with shared shape: CTmax:grp and z:grp finite profiles.

phi Convention (R-PHI)

phi is the sum of the Beta shape parameters: counts are beta-binomial with a = p * phi, b = (1 - p) * phi. Larger phi means less overdispersion. Tests and docs must use this single definition.