BayesianDEB 0.1.4

CRAN-review compliance release. Addresses reviewer feedback on the use of T as an identifier, which can shadow R’s built-in T symbol (= TRUE).

Breaking changes

• arrhenius(): first argument renamed from T to temp. Positional calls are unaffected (arrhenius(298.15)). Code that passed the argument by name (arrhenius(T = 298.15)) must be updated to arrhenius(temp = 298.15).
• bdeb_model(temperature = ...): the list field T was renamed to T_obs to match the Stan data naming and to remove the T shadow. Replace list(T = 298.15, T_ref = ..., T_A = ...) with list(T_obs = 298.15, T_ref = ..., T_A = ...).

CRAN compliance

• bdeb_diagnose() and bdeb_ec50() now expose a verbose = TRUE argument. All user-facing output (diagnostic alerts and summary tables) is routed through cli / [message()] rather than direct print() calls, so it can be silenced with [suppressMessages()] or by passing verbose = FALSE. Return values are unchanged.

Documentation

• Updated R/utils.R, R/data_prep.R, R/model_spec.R and man/arrhenius.Rd, man/bdeb_model.Rd, man/temperature_to_stan_data.Rd, man/build_stan_data_individual.Rd to reflect the renaming.
• Case-study vignette updated to use arrhenius(temp = ...).
• Tests updated for the new temperature$T_obs field.
• \dontrun{} replaced with runnable examples for prior_species(), bdeb_tox() and bdeb_prior_predictive() (all execute in < 0.2 s against bundled datasets). bdeb_fit() retains \dontrun{} because it requires the external CmdStan toolchain and a single Stan compilation + MCMC run takes > 30 seconds; the Rd comment explains the reason.

Citation

• Switched README badge and CITATION.cff from the version-specific DOI (10.5281/zenodo.19500753, v0.1.3) to the concept DOI (10.5281/zenodo.19443804), which always resolves to the latest archived version. The v0.1.4 version DOI is 10.5281/zenodo.19642839 for anyone needing to cite this specific release.

BayesianDEB 0.1.3

New features and data release.

New features

• prior_species(): species-specific priors from the AmP collection for E. fetida, E. andrei, F. candida, D. magna, and L. rubellus.
• plot(fit, type = "prior_posterior"): prior vs. posterior density comparison plot.

New datasets

• eisenia_neuhauser: real E. fetida growth data from Neuhauser, Hartenstein & Kaplan (1980), 37 group-mean measurements over 250 days.
• eisenia_cd: real Eisenia andrei cadmium toxicity data from Van Gestel et al. (1991), 5 concentration groups over 85 days.

Documentation

• Updated DOI to Zenodo 10.5281/zenodo.19500753.

BayesianDEB 0.1.2

ODE solver upgrade and bug fix release.

Breaking changes

• R-side ODE integration now uses deSolve::lsoda() (adaptive BDF/Adams) instead of fixed-step Euler. This matches the BDF solver used in Stan, ensuring numerical consistency between R-side simulation and Stan-side inference. The dt parameter now controls output resolution, not integration accuracy.
• deSolve (>= 1.40) added to Imports.

Bug fixes

• Fixed bdeb_ec50()$NEC returning a data frame instead of numeric draws — median(ec50$NEC) now works correctly.
• Fixed build_stan_data_hierarchical() crashing when growth data starts at time = 0 (same fix as individual model in 0.1.1).
• Fixed build_stan_data_debtox() crashing when growth or reproduction data starts at time = 0.
• Fixed build_stan_data_growth_repro() t=0 handling producing NA index matches — replaced convoluted fix with consistent epsilon shift across growth and reproduction times.

Internal

• Renamed internal helpers sim_deb_euler() / sim_debtox_euler() to sim_deb_lsoda() / sim_debtox_lsoda() to reflect solver.
• Updated package documentation to describe LSODA solver instead of Euler.

BayesianDEB 0.1.1

Bug fix and hardening release.

Bug fixes

• Fixed ode_bdf_tol crash when growth data starts at time = 0: replaced with 1e-3 epsilon since Stan requires t_obs > t0.
• Fixed %||% operator not imported: replaced with explicit if (is.null(...)) in bdeb_predict().
• Fixed silent rnorm() fallback for unknown prior families in bdeb_prior_predictive(): now throws informative error.
• Fixed bdeb_predict(newdata = NULL) using t_obs instead of t_L for "growth_repro" models.
• Fixed bdeb_predict() silently returning raw draws when L_hat is missing: now throws informative error.
• Fixed DEBtox reproduction using cumulative R instead of interval delta_R = k_R * (R(t_end) - R(t_start)): now consistent with growth_repro model.
• Fixed phi_R prior hardcoded in DEBtox Stan model: now uses prior_phi_R_mu/sd from R prior system.
• Fixed deb_fluxes() computing p_G with redundant / E_G * E_G.
• Fixed growth_rate formula: was v/3 * p_M/(kappa*E_G), now correct Kooijman Eq. 3.23: k_M * g / (3*(f+g)).

Safety improvements

• "individual" and "growth_repro" models now hard-error (not warn) when data contains multiple individuals.
• DEBtox auto-aggregates multi-individual concentration groups to means with explicit warning.
• Removed survival argument from bdeb_data() (was accepted but not implemented — “feature mirage”).
• All prior constructors validate hyperparameters (sigma > 0, a > 0, rate > 0, nu > 1).
• bdeb_data() validates f_food in [0, 1].
• bdeb_fit() validates all sampling parameters (chains, iterations, adapt_delta, max_treedepth, threads).
• arrhenius() validates T > 0, T_ref > 0, T_A >= 0.
• bdeb_model() validates prior objects, observation objects, and temperature fields (must be positive finite scalars).
• bdeb_fit() wraps Stan compilation and sampling in tryCatch with contextualised error messages.
• repro_to_intervals() warns when dropping individuals with < 2 observations.
• validate_growth() warns when max length > 10 cm (possibly physical rather than structural length).
• DEBtox reproduction time matching now uses strict match() instead of nearest-neighbour which.min().

New features

• bdeb_loo(): LOO cross-validation via loo::loo() with endpoint argument for "growth_repro" models.
• bdeb_prior_predictive(): R-side prior predictive simulation with print() and plot() methods.
• bdeb_session_info(): reproducibility report (R, Stan, package versions, fit configuration, Stan model hash).
• coef.bdeb_fit(): S3 method returning posterior medians or means.
• deb_simulate(), debtox_simulate(): standalone DEB/DEBtox simulators, independent of Stan.
• L_m added to bdeb_derived(): maximum structural length at f=1.
• plot.bdeb_prediction(): S3 plot method for prediction objects.
• Observation model switching now fully implemented in all 4 Stan models via integer flags (no recompilation needed).
• Arrhenius temperature correction implemented in all 4 Stan models.
• Within-chain parallelism via reduce_sum for hierarchical and DEBtox models.
• threads_per_chain argument in bdeb_fit().
• seed argument in bdeb_predict(), plot_dose_response(), and plot(fit, type = "trajectory").
• dt and t_end arguments in plot_dose_response().
• Reproducibility metadata (seed, versions, timestamp) stored in bdeb_fit object.
• inst/CITATION with package and Kooijman (2010) entries.
• CITATION.cff with Zenodo DOI.

Documentation

• Structural vs physical length documented throughout (delta_M).
• All derived quantity formulas reference Kooijman (2010) equations.
• Prior calibration rationale documented with AmP ranges.
• Feature status table in README with stable/beta/planned.
• “Current limitations” section in README.
• “Numerical layers” section in package docs (Stan exact vs R-side approximate).
• Lifecycle annotations on all functions and models.

Tests

• 901 tests across 16 files (up from 58).
• New test categories: API contracts, scientific consistency, snapshot/regression, deep validation, end-to-end integration.

BayesianDEB 0.1.0

Initial release.

Models

• Individual-level growth model (2-state DEB: reserve, structure).
• Growth + reproduction model (3-state DEB: reserve, structure, reproduction buffer) with negative binomial observation model.
• Hierarchical multi-individual growth model with non-centred parameterisation and partial pooling of assimilation rates.
• DEBtox (TKTD) model for ecotoxicology with scaled internal damage, stress on assimilation, and analytical EC50/NEC computation.

Features

• Declarative model specification via bdeb_model().
• Prior specification functions for all standard DEB parameters: prior_lognormal(), prior_beta(), prior_halfnormal(), and others.
• Sensible weakly informative default priors via prior_default(), calibrated against the AmP collection (Marques et al., 2018).
• Observation model selection: obs_normal(), obs_lognormal(), obs_student_t(), obs_poisson(), obs_negbinom().
• MCMC fitting via cmdstanr with bdeb_fit().
• Convergence diagnostics: bdeb_diagnose() reports R-hat, ESS, divergences, and E-BFMI (Vehtari et al., 2021).
• Posterior predictive checks with bdeb_ppc().
• Derived quantity computation: bdeb_derived() for ultimate length, von Bertalanffy growth rate, and somatic maintenance rate constant.
• Publication-quality plots: trace, posterior density, pairs, trajectory, and PPC overlays.
• DEBtox helpers: bdeb_tox(), bdeb_ec50(), plot_dose_response().
• Utility functions: arrhenius() temperature correction, deb_fluxes() energy flux calculator, repro_to_intervals() data converter.

Data

• eisenia_growth: simulated Eisenia fetida growth (21 individuals, 12 weeks).
• folsomia_repro: simulated Folsomia candida reproduction test (5 Cd concentrations, 6 replicates).
• debtox_growth: simulated growth under toxicant exposure (4 concentrations, 10 individuals each, 6 weeks).

Vignettes

• getting_started: overview of the package workflow.
• case_study_eisenia_folsomia: full workflow with Eisenia growth (individual + hierarchical) and Folsomia DEBtox analysis.