freqTLS 0.1.0 (release candidate)

• Corrected grouped contrast direction so dCTmax:A-B, dlog_z:A-B, and dz:A-B now follow their written meaning: group A minus group B.

freqTLS is the frequentist counterpart to the Bayesian bayesTLS package: it fits the four-parameter logistic thermal-load-sensitivity (thermal death-time) model by maximum likelihood via TMB, parameterised directly in CTmax and thermal sensitivity (z). Under the matched relative-threshold, constant-shape configuration, it targets the same fitted curve as bayesTLS; uncertainty is reported through a frequentist trio — Wald (delta), profile-likelihood, and bootstrap — instead of a posterior. Forked from profileTLS (commit 6f963a9, v0.3.3), which it supersedes.

bayesTLS-twin API

• standardize_data() — the shared raw-data entry point for count or continuous-proportion responses (adopted from bayesTLS).
• fit_4pl() + make_4pl_formula() — the direct CTmax/z formula interface (ctmax/z/up/low/k/by, plus threshold, t_ref, bounds, family), fitted by maximum likelihood through the TMB engine; returns a freq_tls workflow object.
• tls() / tls_z() / tls_ctmax() / tls_tcrit() — z, CTmax, and T_crit with confidence intervals at the relative midpoint, the absolute (LT50) threshold, or any LTx.
• extract_tdt() with get_z_* / get_ctmax_* / get_tcrit_* accessors — the nested z / CTmax / T_crit structure, with parametric-bootstrap replicates as the frequentist analogue of posterior draws.
• predict_survival_curves() — the fitted survival surface with bootstrap bands.
• diagnose_tdt_fit() and tdt_parameter_table() — convergence diagnostics (optimiser/Hessian/gradient) and the 4PL parameter table.
• two_stage (ts_stage1() / ts_stage2() / ts_ci() / ts_curve()) — the classical two-stage comparator, reporting both normal and small-sample t intervals.
• The plots (plot_confidence_eye(), plot_survival_curves(), plot_tdt_curve(), plot_heat_injury()) and extractors accept the freq_tls workflow object.
• Six shared case-study datasets, including aphid_tdt (Li et al. 2023) and zebrafish_o2 (Saruhashi et al. 2026).

Inference and calibration

• Small-sample Bates–Watts profile-t / Wald-t calibration: confidence intervals reference a t distribution with residual df = n − p, restoring nominal coverage at small n and reducing to the asymptotic interval as n grows. The evidence is a coverage + width simulation (repository-only data-raw/calibration-study.R, not installed): at df ≈ 10 the asymptotic 95% interval covers ~0.93 and the t-correction restores ~0.96.
• A three-way benchmark (repository-only data-raw/benchmark-vs-bayes.R, not installed): freqTLS reproduces bayesTLS’s CTmax to ~0.07 °C on the brown-shrimp data, beside the classical two-stage estimator.

Twin S3 surface

• confint(), summary(), ranef(), and coef()/logLik()/vcov()/nobs(), the heat-injury functions (predict_heat_injury() / plot_heat_injury() / heat_injury_envelope()), and check_tls() all accept the freq_tls workflow object — this listed post-fit surface works on the fit_4pl() result.
• fit_4pl(by = "g") now labels groups by the bare factor levels (CTmax:young_embryos), identical to the column interface, end to end.

Case studies and vignettes (render without Stan)

• The frequentist-and-bayesian centerpiece carries the coverage panel and the three-way benchmark; comparing-to-bayesTLS carries the live + cached comparison.
• Worked case studies mirroring the shared manuscript: brown shrimp; zebrafish under hypoxia / normoxia / hyperoxia (OCLTT); cereal aphids (Li 2023); D. suzukii by sex; and a cross-taxon summary.

Simulation

• The build-excluded repository directory scripts/simulations/ contains a freqTLS (ML/TMB) twin of the bayesTLS two-stage-bias simulation (shared data-generating process + scoring), with a comparison to the bayesTLS results. These maintainer scripts and their DRAC launcher are not installed with the package.

Engine

• Asymptotes use bayesTLS’s disjoint-bounds reparameterisation (compute_4pl_bounds); up is now a direct coordinate.
• Convergence / positive-definite-Hessian status is surfaced at fit time.

Superseding profileTLS

• freqTLS is the intended successor to profileTLS, its engine donor.

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