Package: bayesTLS 1.0.0

bayesTLS: Joint Bayesian 4PL Models for Thermal Load Sensitivity

Fits joint Bayesian four-parameter logistic (4PL) models to thermal-tolerance proportion data, extracts the classical thermal load sensitivity quantities (z, CTmax at 1 hour, T_crit) with full posterior uncertainty, and predicts heat-injury accumulation and survival under fluctuating temperature regimes with optional Sharpe-Schoolfield repair. Models are fitted with 'Stan' via the 'brms' package. Implements the framework described in Noble, Arnold, Nakagawa and Pottier (2026; bioRxiv). \doi{10.64898/2026.07.16.738378}.

Authors:Daniel W. A. Noble [aut, cre], Pieter A. Arnold [aut], Shinichi Nakagawa [aut], Patrice Pottier [aut]

bayesTLS_1.0.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bayesTLS/json (API)

# Install 'bayesTLS' in R:
install.packages('bayesTLS', repos = c('https://daniel1noble.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/daniel1noble/bayestls/issues

Datasets:
  • aphid_tdt - Cereal-aphid lethal-TDT data, three species across three ages
  • dsuzukii - Drosophila suzukii multi-trait thermal-tolerance data
  • snowgum_psii - Snow gum leaf PSII functional-impairment thermal-tolerance data
  • zebrafish_o2 - Zebrafish lethal-TDT data across an oxygen gradient

On CRAN:

Conda:

4.62 score 2 stars 43 exports 77 dependencies

Last updated from:a9d5832356. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK318
source / vignettesOK456
linux-release-x86_64OK300
macos-release-arm64OK95
macos-oldrel-arm64OK130
windows-devel-x86_64OK121
windows-release-x86_64OK119
windows-oldrel-x86_64OK130
wasm-releaseOK310

Exports:bayes_R2_tlsclock_to_minutesderive_tdt_curvederive_tdt_landscapederive_temperature_for_durationderive_zdiagnose_tdt_fitextract_4pl_parsfit_4plformat_intervalget_4pl_estget_brmsfitget_hi_drawsget_surv_drawsget_tls_esthas_fitmake_4pl_formulamake_4pl_priorsmake_temperature_scenariosplanted_dose_from_traceplot_heat_injuryplot_repair_rateplot_survival_curvesplot_tdt_curveplot_tdt_landscapeplot_temperature_densityplot_temperature_scenariospredict_heat_injurypredict_survival_curvesrepair_rate_schoolfieldstandardize_datasummarise_observed_survivaltdt_parameter_tabletdt_quantiletheme_tdttlstls_ctmaxtls_tcrittls_zts_cits_curvets_stage1ts_stage2

Dependencies:abindbackportsbayesplotBHbridgesamplingbrmsBrobdingnagcallrcheckmateclicodacodetoolscpp11descdigestdistributionaldplyrfarverfuturefuture.applygenericsggplot2ggridgesglobalsgluegridExtragtableinlineisobandlabelinglatticelifecyclelistenvloomagrittrMASSMatrixmatrixStatsmgcvmvtnormnleqslvnlmenumDerivotelparallellypatchworkpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsS7scalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Cereal-aphid lethal-TDT data, three species across three agesaphid_tdt
Bayesian R^2 for a fitted TDT workflowbayes_R2_tls
Convert various clock formats to minutesclock_to_minutes
Posterior LT_x curve: time to reach a survival target at each temperaturederive_tdt_curve
Posterior survival landscape across the temperature × duration planederive_tdt_landscape
Temperature at which survival equals a target after a fixed exposurederive_temperature_for_duration
Per-draw thermal sensitivity z directly from the joint posteriorderive_z
Sampling diagnostics for a fitted TDT workflowdiagnose_tdt_fit
Drosophila suzukii multi-trait thermal-tolerance datadsuzukii
Per-draw natural-scale 4PL parameters from a fitted workflowextract_4pl_pars
Fit the joint Bayesian 4PL to standardised TDT datafit_4pl
Format a posterior median plus credible interval as a single stringformat_interval
Posterior estimates of the natural-scale 4PL parameters (draws or summary)get_4pl_est
Extract the fitted brms model from a workflowget_brmsfit
Posterior draws of heat-injury trajectoryget_hi_draws
Posterior draws of survivalget_surv_draws
Extract TLS estimates (draws or summary) from a 'tls' objectget_tls_est
Whether a workflow has been fittedhas_fit
Build the brms formula for the joint Bayesian 4PLmake_4pl_formula
Default weakly informative priors for the joint Bayesian 4PLmake_4pl_priors
Build reference temperature traces for heat-injury validationmake_temperature_scenarios
Analytical heat-injury accumulation along a temperature traceplanted_dose_from_trace
Plot HI and survival trajectories from 'predict_heat_injury()'plot_heat_injury
Plot a Sharpe-Schoolfield repair TPCplot_repair_rate
Plot posterior survival curvesplot_survival_curves
Plot a posterior LT_x curveplot_tdt_curve
Plot the TDT survival landscape as a heatmapplot_tdt_landscape
Plot a posterior temperature density (e.g. CTmax or T_crit)plot_temperature_density
Plot the three reference temperature scenariosplot_temperature_scenarios
MCMC mixing plot for a fitted 'bayes_tls' workflowplot.bayes_tls
Predict heat injury and survival under a fluctuating temperature tracepredict_heat_injury
Posterior survival curves on a temperature × duration gridpredict_survival_curves
Compact print method for a 'bayes_tls' workflowprint.bayes_tls
Sharpe-Schoolfield thermal performance curve for repair raterepair_rate_schoolfield
Snow gum leaf PSII functional-impairment thermal-tolerance datasnowgum_psii
Standardise a raw survival / proportion dataset for the TDT function librarystandardize_data
Summarise observed survival counts to mean ± SE per (temp, duration) cellsummarise_observed_survival
Summarise a fitted 'bayes_tls' workflowsummary.bayes_tls
Posterior parameter table on the natural scaletdt_parameter_table
Quantile wrapper with TDT-friendly defaultstdt_quantile
Project ggplot themetheme_tdt
Thermal load sensitivity summaries from any fitted 4PL modeltls tls_ctmax tls_tcrit tls_z
Uncertainty for the classical two-stage TDT quantitiests_ci
Median LT-vs-temperature line from a two-stage fitts_curve
Stage 1 of the classical two-stage TDT pipelinets_stage1
Stage 2 of the classical two-stage TDT pipelinets_stage2
Zebrafish lethal-TDT data across an oxygen gradientzebrafish_o2