Package index • freqTLS

Fit and extract (shared-name workflow analogues)

The primary frequentist workflow: standardise the same data, fit the 4PL by maximum likelihood, and extract analogous thermal-death-time quantities.

standardize_data(): Standardise a raw survival / proportion dataset for the TDT function library
make_4pl_formula(): Build a freqTLS 4PL formula from the direct CTmax/z interface
fit_4pl(): Fit the 4PL thermal-load-sensitivity model by maximum likelihood (TMB)
tls() tls_z() tls_ctmax() tls_tcrit(): Thermal-load-sensitivity quantities (z, CTmax) with confidence intervals
extract_tdt(): Extract z, CTmax and (optionally) T_crit with bootstrap confidence intervals
get_z_summary() get_z_draws() get_ctmax_summary() get_ctmax_draws() get_tcrit_summary() get_tcrit_draws(): Accessors for an extract_tdt() result
predict_survival_curves(): Predict the fitted survival surface with bootstrap confidence bands
diagnose_tdt_fit(): Diagnose a freqTLS fit (frequentist analogue of diagnose_tdt_fit)
tdt_parameter_table(): 4PL parameter table (frequentist analogue of tdt_parameter_table)

The per-temperature GLM + OLS estimator, for benchmarking.

The TMB engine behind freqTLS; use it directly for full formula control.

fit_tls(): Fit a single-stage 4PL thermal-load-sensitivity model by maximum likelihood
tls_bf(): Build a freqTLS formula object (brms/drmTMB-style)
print(<profile_tls>) summary(<profile_tls>) print(<summary.profile_tls>) coef(<profile_tls>) vcov(<profile_tls>) logLik(<profile_tls>) AIC(<profile_tls>) nobs(<profile_tls>): S3 methods for fitted freqTLS models
tidy_parameters(): Tidy the parameters of a fitted freqTLS model
get_ctmax(): Extract the CTmax estimate(s)
get_z(): Extract the thermal-sensitivity (z) estimate(s)
get_shape(): Extract the shape parameters (low, up, k, and phi)
ranef(): Random-effect BLUPs (conditional modes) for a freqTLS fit
check_tls(): Report identifiability diagnostics for a fitted model
binomial_tls() beta_binomial_tls() beta_tls(): Response families for thermal-load-sensitivity models

Profile-likelihood deviance curves and prior-free confidence intervals.

profile(<profile_tls>) print(<profile_tls_profile>): Profile-likelihood curves for a fitted thermal-load-sensitivity model
confint(<profile_tls>): Confidence intervals for a fitted thermal-load-sensitivity model

Predict survival, derive lethal times, and draw the fitted curves, the survival surface, and the Confidence Eye.

predict(<profile_tls>) predict(<freq_tls>): Predict survival, link, or midpoint from a fitted freqTLS model
predict_survival_surface(): Predict a survival surface over a temperature-by-duration grid
predict_heat_injury(): Predict cumulative heat injury under a temperature trace
heat_injury_envelope(): Parametric-bootstrap confidence envelope for a heat-injury trajectory
plot_heat_injury(): Plot a heat-injury survival trajectory with a bootstrap confidence band
derive_lt(): Derive the lethal / survival-threshold duration at a temperature
derive_ctmax(): Derive the temperature giving a target survival at a fixed exposure
derive_tcrit(): Derive the critical temperature at a damage-rate floor (T_crit)
plot_survival_curves(): Plot fitted survival curves against duration
plot_tdt_curve(): Plot the thermal death-time (TDT) curve: survival-threshold time vs temperature
plot_survival_surface(): Plot the fitted survival surface over temperature and duration
plot_confidence_eye(): Confidence-Eye (or line) display of headline confidence intervals
plot(<profile_tls_profile>): Plot a profile-likelihood deviance curve

Generate data from the locked data-generating process.

simulate_tls(): Simulate survival-count data from the 4PL thermal-load-sensitivity model

Small shared helpers (time conversion, interval formatting, quantiles).

clock_to_minutes(): Convert various clock formats to minutes
format_interval(): Format a point estimate plus confidence interval as a single string
tdt_quantile(): Quantile wrapper with TDT-friendly defaults

Published empirical examples mirrored from the pinned bayesTLS supplement; see each help page for source-specific credit and component licences.

freqTLS freqTLS-package: freqTLS: Frequentist Inference for Thermal Load Sensitivity Models