Joint Bayesian 4PL Models for Thermal Load Sensitivity

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Documentation for package ‘bayesTLS’ version 1.0.0

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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