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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.