R: Joint Bayesian 4PL Models for Thermal Load Sensitivity

# Joint Bayesian 4PL Models for Thermal Load Sensitivity

## Documentation for package ‘bayesTLS’ version 1.0.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

aphid_tdt | Cereal-aphid lethal-TDT data, three species across three ages
bayes_R2_tls | Bayesian R^2 for a fitted TDT workflow
clock_to_minutes | Convert various clock formats to minutes
derive_tdt_curve | Posterior LT_x curve: time to reach a survival target at each temperature
derive_tdt_landscape | Posterior survival landscape across the temperature × duration plane
derive_temperature_for_duration | Temperature at which survival equals a target after a fixed exposure
derive_z | Per-draw thermal sensitivity z directly from the joint posterior
diagnose_tdt_fit | Sampling diagnostics for a fitted TDT workflow
dsuzukii | Drosophila suzukii multi-trait thermal-tolerance data
extract_4pl_pars | Per-draw natural-scale 4PL parameters from a fitted workflow
fit_4pl | Fit the joint Bayesian 4PL to standardised TDT data
format_interval | Format a posterior median plus credible interval as a single string
get_4pl_est | Posterior estimates of the natural-scale 4PL parameters (draws or summary)
get_brmsfit | Extract the fitted brms model from a workflow
get_hi_draws | Posterior draws of heat-injury trajectory
get_surv_draws | Posterior draws of survival
get_tls_est | Extract TLS estimates (draws or summary) from a 'tls' object
has_fit | Whether a workflow has been fitted
make_4pl_formula | Build the brms formula for the joint Bayesian 4PL
make_4pl_priors | Default weakly informative priors for the joint Bayesian 4PL
make_temperature_scenarios | Build reference temperature traces for heat-injury validation
planted_dose_from_trace | Analytical heat-injury accumulation along a temperature trace
plot.bayes_tls | MCMC mixing plot for a fitted 'bayes_tls' workflow
plot_heat_injury | Plot HI and survival trajectories from 'predict_heat_injury()'
plot_repair_rate | Plot a Sharpe-Schoolfield repair TPC
plot_survival_curves | Plot posterior survival curves
plot_tdt_curve | Plot a posterior LT_x curve
plot_tdt_landscape | Plot the TDT survival landscape as a heatmap
plot_temperature_density | Plot a posterior temperature density (e.g. CTmax or T_crit)
plot_temperature_scenarios | Plot the three reference temperature scenarios
predict_heat_injury | Predict heat injury and survival under a fluctuating temperature trace
predict_survival_curves | Posterior survival curves on a temperature × duration grid
print.bayes_tls | Compact print method for a 'bayes_tls' workflow
repair_rate_schoolfield | Sharpe-Schoolfield thermal performance curve for repair rate
snowgum_psii | Snow gum leaf PSII functional-impairment thermal-tolerance data
standardize_data | Standardise a raw survival / proportion dataset for the TDT function library
summarise_observed_survival | Summarise observed survival counts to mean ± SE per (temp, duration) cell
summary.bayes_tls | Summarise a fitted 'bayes_tls' workflow
tdt_parameter_table | Posterior parameter table on the natural scale
tdt_quantile | Quantile wrapper with TDT-friendly defaults
theme_tdt | Project ggplot theme
tls | Thermal load sensitivity summaries from any fitted 4PL model
tls_ctmax | Thermal load sensitivity summaries from any fitted 4PL model
tls_tcrit | Thermal load sensitivity summaries from any fitted 4PL model
tls_z | Thermal load sensitivity summaries from any fitted 4PL model
ts_ci | Uncertainty for the classical two-stage TDT quantities
ts_curve | Median LT-vs-temperature line from a two-stage fit
ts_stage1 | Stage 1 of the classical two-stage TDT pipeline
ts_stage2 | Stage 2 of the classical two-stage TDT pipeline
zebrafish_o2 | Zebrafish lethal-TDT data across an oxygen gradient