tmb-likelihood-review

name	tmb-likelihood-review
description	Review the freqTLS TMB 4PL likelihood and parameterisation before merging.

TMB Likelihood Review

Use this skill for any change to src/profile_tls.cpp, the numeric header, the density code, or the parameter transforms. Gauss leads; Noether checks the math-to-code match.

Review Checklist

• Are all constrained parameters represented internally on unconstrained scales: k, phi, z on log; low on logit; the asymptote gap on the nested-gap transform up = low + (1 - low) * invlogit(beta_gap) so up > low is guaranteed?
• Is the midpoint map exactly mid = log10(tref) - (temp - CTmax) / z, and the fitted survival p = low + (up - low) * invlogit(-k * (log10(duration) - mid)) (descending: high survival at short durations)?
• Is the probability clamp branch-free (CppAD::CondExpLt / CondExpGt to [eps, 1 - eps]), not an if on a Type?
• Are y and n DATA_VECTOR (Type), not IVECTOR, so the beta-binomial lgamma(y + a) works with a a Type? Is there a shape floor on a, b?
• Is the beta-binomial phi convention the sum of the Beta shapes (a = p * phi, b = (1 - p) * phi), matching simulate_tls() (R-PHI)?
• Are gradients finite for simulated data, and does sdreport() report interpretable transformed parameters (low, up, k, phi, beta_CT, z_group)?
• Does simulation recover truth under ordinary sample sizes for both families?
• Are boundary and weak-identification cases tested (asymptote on the boundary, phi toward the binomial limit, threshold never crossed)?
• Is the equivalence to the bayesTLS constant-shape parameterisation preserved (z = -1 / beta1, CTmax = Tbar + (log10(tref) - beta0) / beta1)?

Provenance

Any pattern adapted from drmTMB (the Boolean.h pre-include guard, the beta-binomial lgamma form, the CondExp clamp, the stable log1p_exp switch) must be recorded in inst/COPYRIGHTS before the change is treated as complete.