Package {BayesianDEB}

BayesianDEB: Bayesian Dynamic Energy Budget Modelling

Description

Provides a Bayesian framework for Dynamic Energy Budget (DEB) modelling via 'Stan'. Implements the standard DEB model of Kooijman (2010, doi:10.1017/CBO9780511805400) as a state-space model with Hamiltonian Monte Carlo inference (Carpenter et al., 2017, doi:10.18637/jss.v076.i01). Includes individual-level growth models, growth-reproduction models, hierarchical multi-individual models with partial pooling, and toxicokinetic-toxicodynamic (TKTD) models for ecotoxicology following the DEBtox framework (Jager et al., 2006, doi:10.1007/s10646-006-0060-x). Supports prior specification from biological knowledge, convergence diagnostics (Vehtari et al., 2021, doi:10.1214/20-BA1221), posterior predictive checks, derived quantity estimation, and visualisation via 'ggplot2'.

Embeds the standard Dynamic Energy Budget (DEB) model of Kooijman (2010) within a Bayesian state-space framework, using Stan (Carpenter et al., 2017) for Hamiltonian Monte Carlo inference. The DEB ordinary differential equation system describes how organisms allocate assimilated energy to maintenance, growth, and reproduction according to the \kappa-rule. This package wraps pre-compiled Stan programs with a declarative R interface so that users can fit DEB models without writing Stan code.

Models

Four model types are implemented, covering the most common DEB applications in ecology and ecotoxicology:

"individual"

Two-state model (reserve E, structure V) for a single organism. The ODE follows Eqs. 2.4 and 2.6 of Kooijman (2010, Ch. 2).

"growth_repro"

Three-state model (E, V, reproduction buffer E_R) with negative-binomial observation model for offspring counts.

"hierarchical"

Two-state model with lognormal random effects on the surface-area-specific assimilation rate \{p_{Am}\}, using the non-centred parameterisation of Betancourt & Girolami (2015) to avoid pathological funnel geometry.

"debtox"

Four-state TKTD model (E, V, E_R, scaled damage D_w) following the DEBtox framework of Jager et al. (2006). Stress on assimilation is currently implemented; the damage dynamics follow dD_w/dt = k_d(\max(C_w - z_w, 0) - D_w).

Workflow

The recommended workflow follows the iterative Bayesian modelling cycle described in Gelman et al. (2013, Ch. 6):

1. Prepare data with bdeb_data().

2. Specify model and priors with bdeb_model().

3. Fit via MCMC with bdeb_fit().

4. Check convergence with bdeb_diagnose() (\hat{R}, ESS, divergences; Vehtari et al., 2021).

5. Perform posterior predictive checks with bdeb_ppc() (Gelman et al., 2013, Ch. 6).

6. Compute derived quantities with bdeb_derived().

7. Compare models via bdeb_loo() (individual and growth_repro models only).

8. Iterate: revise priors or model structure as needed.

Key DEB equations

\dot{p}_A = f \{p_{Am}\} L^2

\dot{p}_C = \frac{E \cdot v \cdot L}{E + [E_G] V}

dE/dt = \dot{p}_A - \dot{p}_C

dV/dt = (\kappa \dot{p}_C - [p_M] V) / [E_G]

where L = V^{1/3} is structural length, f is the scaled functional response, and all symbols follow the DEB notation of Kooijman (2010, Table 1.1).

Numerical layers

The package uses two distinct numerical engines:

Stan inference (exact)

bdeb_fit(), bdeb_diagnose(), summary() on a bdeb_fit, bdeb_ec50(), bdeb_loo(), bdeb_ppc() for individual/growth_repro. These use Stan's BDF stiff ODE solver with adaptive step size and tolerances 10^{-6}. Posteriors, derived quantities, and log-likelihoods from this layer are publication-grade.

R-side simulation

bdeb_prior_predictive(), bdeb_predict(newdata=...), plot(fit, type="trajectory") for hierarchical/debtox, plot_dose_response(). These use the LSODA solver from deSolve (adaptive step size, tolerances 10^{-6}), matching Stan's BDF solver. They are visualisation and exploration tools, not exact inference. For quantitative results, use the Stan-based functions.

Lifecycle

Stable

bdeb_data(), bdeb_model(), bdeb_fit(), bdeb_diagnose(), bdeb_derived(), bdeb_ppc(), bdeb_predict(), bdeb_loo(), bdeb_ec50(), bdeb_tox(), bdeb_prior_predictive(), plot_dose_response(), summary(), coef(), confint(), fitted(), residuals(), nobs(), vcov(), logLik(), all prior and observation model constructors, arrhenius(), deb_fluxes(), repro_to_intervals(), bdeb_session_info().

Deprecated

bdeb_summary() (use summary() on a bdeb_fit object instead).

Stable models

"individual", "growth_repro", "hierarchical".

Beta models

"debtox" (group-level, 1 ODE per concentration; hierarchical individual-level DEBtox is planned).

Planned

Survival endpoint, per-observation temperature, DEBtox stress on maintenance/growth cost, hierarchical DEBtox (individual-level TKTD), weight endpoint with shape coefficient estimation, wider maturity dynamics, real-data benchmark dataset.

Author(s)

Maintainer: Branimir K. Hackenberger branimir@sciom.hr

Authors:

• Tamara Djerdj

• Domagoj K. Hackenberger

References

Kooijman, S.A.L.M. (2010). Dynamic Energy Budget Theory for Metabolic Organisation. 3rd edition. Cambridge University Press. doi:10.1017/CBO9780511805400

Carpenter, B., Gelman, A., Hoffman, M.D., Lee, D., Goodrich, B., Betancourt, M., Brubaker, M.A., Guo, J., Li, P. and Riddell, A. (2017). Stan: A probabilistic programming language. Journal of Statistical Software, 76(1), 1–32. doi:10.18637/jss.v076.i01

Gelman, A., Carlin, J.B., Stern, H.S., Dunson, D.B., Vehtari, A. and Rubin, D.B. (2013). Bayesian Data Analysis. 3rd edition. Chapman & Hall/CRC.

Jager, T., Heugens, E.H.W. and Kooijman, S.A.L.M. (2006). Making sense of ecotoxicological test results: towards application of process-based models. Ecotoxicology, 15(3), 305–314. doi:10.1007/s10646-006-0060-x

Betancourt, M. and Girolami, M. (2015). Hamiltonian Monte Carlo for hierarchical models. In: Upadhyay, S.K. et al. (eds) Current Trends in Bayesian Methodology with Applications. CRC Press, pp. 79–101.

Vehtari, A., Gelman, A., Simpson, D., Carpenter, B. and Bürkner, P.-C. (2021). Rank-normalization, folding, and localization: an improved \hat{R} for assessing convergence of MCMC. Bayesian Analysis, 16(2), 667–718. doi:10.1214/20-BA1221

See Also

Useful links:

• https://github.com/sciom/BayesianDEB

• Report bugs at https://github.com/sciom/BayesianDEB/issues

Arrhenius Temperature Correction

Description

Computes the temperature correction factor for DEB rate parameters based on the Arrhenius relationship (Kooijman, 2010, Eq. 1.2). In DEB theory all rate parameters (e.g., \{p_{Am}\}, [p_M], v) scale with temperature by the same factor:

Usage

arrhenius(temp, T_ref = 293.15, T_A = 8000)

Arguments

Details

c_T = \exp\!\left(\frac{T_A}{T_{\mathrm{ref}}} - \frac{T_A}{T}\right)

where T and T_{\mathrm{ref}} are in Kelvin and T_A is the Arrhenius temperature (a species-specific constant, typically 6000–12000 K for ectotherms; Kooijman, 2010, Table 8.1). At T = T_{\mathrm{ref}}, the factor is exactly 1.

Value

Numeric correction factor (dimensionless, > 0).

References

Kooijman, S.A.L.M. (2010). Dynamic Energy Budget Theory for Metabolic Organisation. 3rd edition. Cambridge University Press, Eq. 1.2. doi:10.1017/CBO9780511805400

Examples

# Correction at 25 C relative to 20 C reference
arrhenius(298.15, T_ref = 293.15, T_A = 8000)  # ~ 1.74

# No correction at reference temperature
arrhenius(293.15)  # exactly 1

Validate finite numeric scalar

Description

Validate finite numeric scalar

Usage

assert_finite_scalar(x, name)

Validate positive numeric scalar

Description

Validate positive numeric scalar

Usage

assert_positive(x, name)

Prepare Data for BDEB Models

Description

Converts long-format data frames into the structured list required by the BayesianDEB Stan programs. Growth observations are matched to the DEB state variable L = V^{1/3} (structural length); reproduction records are interval counts of offspring over [t_{\mathrm{start}}, t_{\mathrm{end}}). The function validates column names, rejects negative times/lengths, sorts by individual and time, and (for hierarchical models) pads ragged observation vectors into matrices with NaN fill, as required by Stan's fixed-size array declarations.

Usage

bdeb_data(growth = NULL, reproduction = NULL, concentration = NULL, f_food = 1)

Arguments

Value

A bdeb_data object (S3 list) ready for bdeb_model().

References

Kooijman, S.A.L.M. (2010). Dynamic Energy Budget Theory for Metabolic Organisation. 3rd edition. Cambridge University Press. doi:10.1017/CBO9780511805400

Examples

# Simple growth data
df <- data.frame(
  id = rep(1, 10),
  time = seq(0, 45, by = 5),
  length = c(0.1, 0.15, 0.22, 0.30, 0.38, 0.44, 0.49, 0.52, 0.54, 0.55)
)
dat <- bdeb_data(growth = df)

Compute Derived Biological Quantities from the Posterior

Description

Transforms the raw DEB parameter draws into biologically interpretable quantities, automatically propagating parameter uncertainty. All formulas follow Kooijman (2010, Ch. 3, Table 3.1) strictly.

Usage

bdeb_derived(object, ...)

## Default S3 method:
bdeb_derived(object, ...)

## S3 method for class 'bdeb_fit'
bdeb_derived(object, quantities = c("L_inf", "k_M", "growth_rate"), f = 1, ...)

Arguments

Value

A posterior::draws_df with one column per requested quantity and one row per posterior draw.

DEB length terminology

DEB theory distinguishes several length measures. This function returns structural length L = V^{1/3}, which is the cube root of structural volume. Structural length is not the same as physical (observed) length L_w, which relates to L via the shape coefficient: L_w = L / \delta_M. The shape coefficient \delta_M is species-specific (typically 0.1–0.5) and is not estimated by this package. If your data are physical lengths, you should either (a) convert to structural length before fitting, or (b) divide L_inf by your species' \delta_M to obtain the physical asymptotic length.

Available quantities

"L_m"

Maximum structural length at f = 1 (Kooijman, 2010, Table 3.1):

L_m = \kappa \, \{p_{Am}\} / [p_M]

This is a species-level constant independent of food. Units: cm.

"L_inf"

Ultimate structural length at food level f (Kooijman, 2010, Eq. 3.4):

L_i = f \cdot L_m = f \, \kappa \, \{p_{Am}\} / [p_M]

The asymptotic length when dV/dt = 0 at constant food. Depends on f. Units: cm. Dimensional check: (-)(-)(\text{J d}^{-1}\text{cm}^{-2}) / (\text{J d}^{-1}\text{cm}^{-3}) = \text{cm}.

"k_M"

Somatic maintenance rate constant:

k_M = [p_M] / [E_G]

Units: d^{-1}.

"growth_rate"

Von Bertalanffy growth rate (Kooijman, 2010, Eq. 3.23):

\dot{r}_B = \frac{k_M \, g}{3\,(f + g)}

where g = [E_G] \, v / (\kappa \, \{p_{Am}\}) is the energy investment ratio. Depends on f. Units: d^{-1}.

"g"

Energy investment ratio (Kooijman, 2010, Table 3.1):

g = [E_G] \, v / (\kappa \, \{p_{Am}\})

Dimensionless. Large g means growth is expensive relative to reserve turnover.

Reference example

For Eisenia fetida with AmP parameters \{p_{Am}\} = 5.0, [p_M] = 0.5, \kappa = 0.75: L_m = 0.75 \times 5.0 / 0.5 = 7.5 cm (structural). With \delta_M \approx 0.24, the physical maximum length would be L_m / \delta_M \approx 31 mm, consistent with observations.

References

Kooijman, S.A.L.M. (2010). Dynamic Energy Budget Theory for Metabolic Organisation. 3rd edition. Cambridge University Press. doi:10.1017/CBO9780511805400

Marques, G.M., Augustine, S., Lika, K., Pecquerie, L., Domingos, T. and Kooijman, S.A.L.M. (2018). The AmP project: comparing species on the basis of dynamic energy budget parameters. PLOS Computational Biology, 14(5), e1006100. doi:10.1371/journal.pcbi.1006100

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  bdeb_derived(fit, quantities = c("L_inf", "k_M"))
}

MCMC Convergence Diagnostics

Description

Reports a comprehensive set of NUTS/HMC diagnostics following the recommendations of Vehtari et al. (2021):

Divergent transitions

Indicate that the numerical leapfrog integrator encountered regions of high curvature. Even a single divergence can bias the posterior. Remedy: increase adapt_delta.

Treedepth saturation

The NUTS trajectory hit the maximum allowed tree depth, meaning it could not find a U-turn. Remedy: increase max_treedepth.

E-BFMI

Energy Bayesian Fraction of Missing Information. Values below 0.3 indicate that the momentum resampling is inefficient (Betancourt, 2016).

\hat{R}

Split-\hat{R} convergence diagnostic. Values > 1.01 indicate incomplete mixing across chains.

Bulk and tail ESS

Effective sample size for the bulk and tails of the posterior. Values below 400 suggest that posterior summaries may be unreliable.

Usage

bdeb_diagnose(fit, pars = NULL)

Arguments

Details

Returns a bdeb_diagnostics S3 object. The object has dedicated print(), summary() and plot() methods. When called interactively the print method is invoked automatically; assign the result (d <- bdeb_diagnose(fit)) to suppress output.

Value

An object of class bdeb_diagnostics with components n_divergent, n_max_treedepth, ebfmi, summary (a posterior::summarise_draws() tibble), pars, and model_type.

References

Vehtari, A., Gelman, A., Simpson, D., Carpenter, B. and Bürkner, P.-C. (2021). Rank-normalization, folding, and localization: an improved \hat{R} for assessing convergence of MCMC. Bayesian Analysis, 16(2), 667–718. doi:10.1214/20-BA1221

Betancourt, M. (2016). Diagnosing biased inference with divergences. Stan case study. https://mc-stan.org/users/documentation/case-studies/divergences_and_bias.html

See Also

print.bdeb_diagnostics(), summary.bdeb_diagnostics(), plot.bdeb_diagnostics()

Examples

# Requires the CmdStan toolchain (Suggests: cmdstanr); gated on its
# availability and wrapped in \donttest{} so example("bdeb_diagnose")
# runs it when a toolchain is present, mirroring bdeb_fit().

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(),
                    error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  d <- bdeb_diagnose(fit)
  print(d)
  summary(d)
  plot(d, type = "rhat")
}

Extract EC50 and NEC from a DEBtox Fit

Description

Extracts the full posterior distribution of the \mathrm{EC}_{50} and the NEC (no-effect concentration, z_w) from a fitted DEBtox model. Both quantities are computed analytically in the Stan ⁠generated quantities⁠ block, avoiding the need for post-hoc root finding. At toxicokinetic steady state the stress factor equals s = b_w(C_w - z_w) for C_w > z_w, so setting s = 0.5 yields

Usage

bdeb_ec50(fit, prob = 0.9, verbose = TRUE)

Arguments

Details

\mathrm{EC}_{50} = z_w + \frac{0.5}{b_w}.

The NEC is the threshold concentration below which no effect occurs; it corresponds directly to the parameter z_w in the damage model of Kooijman & Bedaux (1996).

Value

A named list with:

• draws: posterior draws of EC50

• summary: mean, median, sd, lower, upper

• NEC: posterior summary of the no-effect concentration

References

Kooijman, S.A.L.M. and Bedaux, J.J.M. (1996). The Analysis of Aquatic Toxicity Data. VU University Press, Amsterdam.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(debtox_growth)
  dat <- bdeb_data(growth = debtox_growth,
                   concentration = c("1" = 0, "11" = 20,
                                    "21" = 80, "31" = 200))
  fit <- bdeb_fit(bdeb_tox(dat, stress = "assimilation"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  init = 0.5, refresh = 0)
  bdeb_ec50(fit, prob = 0.95)
}

Fit a BDEB Model via Hamiltonian Monte Carlo

Description

Compiles the bundled Stan program via cmdstanr (which handles caching internally based on the Stan source hash) and runs the No-U-Turn Sampler (NUTS; Hoffman & Gelman, 2014). The Stan ODE system is solved at each leapfrog step using the BDF stiff solver (ode_bdf) with absolute and relative tolerances of 10^{-6}.

Usage

bdeb_fit(
  model,
  chains = 4,
  iter_warmup = 1000,
  iter_sampling = 1000,
  adapt_delta = 0.8,
  max_treedepth = 10,
  seed = NULL,
  parallel_chains = NULL,
  threads_per_chain = NULL,
  refresh = 200,
  algorithm = c("sampling", "variational"),
  ...
)

Arguments

Details

Tuning guidance. If bdeb_diagnose() reports divergent transitions, increase adapt_delta toward 1.0 (e.g., 0.95 or 0.99). This reduces the step size, trading speed for geometric fidelity of the sampler. If the maximum treedepth is frequently saturated, increase max_treedepth (e.g., 12 or 15). For hierarchical models, starting values can matter; the non-centred parameterisation used in bdeb_hierarchical_growth.stan should suffice in most cases.

Value

A bdeb_fit object containing the CmdStanMCMC (or CmdStanVB) result, the model specification, and sampling metadata. The list element algorithm records which inference engine was used.

Notes on Stan informational messages

During warmup it is normal for Stan to emit informational messages such as "Informational Message: The current Metropolis proposal is about to be rejected because of the following issue(s)" or occasional ODE solver warnings. These are emitted whenever the leapfrog integrator probes a region of parameter space where the DEB ODE is stiff or numerically extreme; the proposal is then rejected and the chain continues. As of version 0.2.0 the bundled Stan models call ode_bdf_tol with max_num_steps = 1e5 (raised from 1e4 in 0.1.x) which substantially reduces these messages but does not eliminate them in pathological priors or with very few warmup iterations. These messages are benign as long as bdeb_diagnose() reports no divergent transitions, no max treedepth saturation, and adequate \hat{R}/ESS for all parameters.

References

Hoffman, M.D. and Gelman, A. (2014). The No-U-Turn Sampler: adaptively setting path lengths in Hamiltonian Monte Carlo. Journal of Machine Learning Research, 15(47), 1593–1623.

Vehtari, A., Gelman, A., Simpson, D., Carpenter, B. and Bürkner, P.-C. (2021). Rank-normalization, folding, and localization: an improved \hat{R} for assessing convergence of MCMC. Bayesian Analysis, 16(2), 667–718. doi:10.1214/20-BA1221

Examples

# bdeb_fit() requires the external CmdStan toolchain (Suggests:
# cmdstanr) and a fresh fit takes > 30 seconds (Stan compilation
# plus MCMC).  The example is wrapped in \donttest{} and gated on
# cmdstanr availability so that R CMD check skips it on CRAN's
# toolchain-free workers but power users can run it after
# cmdstanr::install_cmdstan().

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(),
                    error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  mod <- bdeb_model(dat, type = "individual")
  fit <- bdeb_fit(mod, chains = 1, iter_warmup = 200,
                  iter_sampling = 200, refresh = 0)
  print(fit)
}

LOO Cross-Validation for Model Comparison

Description

Computes approximate leave-one-out cross-validation (LOO-CV) using Pareto-smoothed importance sampling (PSIS; Vehtari et al., 2017). Requires that the Stan model includes a log_lik array in the ⁠generated quantities⁠ block.

Usage

bdeb_loo(fit, endpoint = c("all", "growth", "reproduction"), ...)

Arguments

Details

Currently supported for "individual" and "growth_repro" models only. The "hierarchical" and "debtox" models do not store per-observation log_lik in ⁠generated quantities⁠: "hierarchical" computes the likelihood inside reduce_sum (no access to individual contributions outside the function); "debtox" uses the same reduce_sum approach and its ⁠generated quantities⁠ block only computes EC50/NEC. Adding per-group log_lik to DEBtox is planned for a future version. An informative error is raised for unsupported types.

Value

A loo object (see loo::loo()).

Conditional independence assumption

For "growth_repro" models with endpoint = "all", growth and reproduction observations are concatenated and each treated as an independent data point. This is valid because the two endpoints are conditionally independent given the latent DEB process (growth observations depend only on V(t), reproduction counts depend only on \Delta E_R; given the ODE solution, they share no additional error). Use endpoint = "growth" or endpoint = "reproduction" to compute LOO for a single endpoint.

References

Vehtari, A., Gelman, A. and Gabry, J. (2017). Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC. Statistics and Computing, 27(5), 1413–1432. doi:10.1007/s11222-016-9696-4

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  bdeb_loo(fit)
}

Specify a BDEB Model

Description

Creates a model specification that binds together the prepared data, the DEB process model (encoded as a pre-written Stan program), the prior distributions, and the observation model. Internally it calls the appropriate ⁠build_stan_data_*()⁠ function to assemble the list of named values that Stan expects. The Stan program is not compiled at this stage — compilation and sampling happen in bdeb_fit().

Usage

bdeb_model(
  data,
  type = c("individual", "growth_repro", "hierarchical", "debtox"),
  priors = list(),
  observation = list(),
  temperature = NULL
)

Arguments

Details

The four model types correspond to increasingly complex DEB formulations:

"individual"

Standard 2-state DEB (reserve E, structure V), Kooijman (2010, Ch. 2). The ODE is solved with Stan's ode_bdf (stiff BDF solver) at tolerances 10^{-6}.

"growth_repro"

3-state model adding the reproduction buffer E_R. Offspring counts are modelled as R_i \sim \mathrm{NegBin}(k_R \Delta E_R, \phi), where \Delta E_R = E_R(t_{\mathrm{end}}) - E_R(t_{\mathrm{start}}).

"hierarchical"

2-state model with a lognormal random effect on \{p_{Am}\}: \log p_{Am,j} = \mu + \sigma z_j, z_j \sim N(0,1) (non-centred). Shared parameters [p_M], \kappa, v, [E_G] are estimated from all individuals jointly (partial pooling; Gelman & Hill, 2006). Initial structural length L_{0,j} varies per individual; initial reserve density E_0 is shared (assumes organisms start with the same reserve state, which is typical for lab-reared cohorts).

"debtox"

4-state TKTD model following Jager et al. (2006). Adds scaled damage D_w with dD_w/dt = k_d(\max(C_w - z_w, 0) - D_w). The \mathrm{EC}_{50} is computed analytically as z_w + 0.5/b_w.

Value

A bdeb_model object (S3 list).

References

Kooijman, S.A.L.M. (2010). Dynamic Energy Budget Theory for Metabolic Organisation. 3rd edition. Cambridge University Press. doi:10.1017/CBO9780511805400

Gelman, A. and Hill, J. (2006). Data Analysis Using Regression and Multilevel/Hierarchical Models. Cambridge University Press.

Jager, T., Heugens, E.H.W. and Kooijman, S.A.L.M. (2006). Making sense of ecotoxicological test results: towards application of process-based models. Ecotoxicology, 15(3), 305–314. doi:10.1007/s10646-006-0060-x

Examples

df <- data.frame(id = 1, time = 0:5, length = seq(0.1, 0.6, by = 0.1))
dat <- bdeb_data(growth = df)
mod <- bdeb_model(dat, type = "individual")
print(mod)
summary(mod)

Plot Methods for BDEB Objects

Description

Visualisation methods for BDEB fits, posterior predictive checks, and derived quantities using ggplot2. All plots return ggplot2 objects that can be further customised.

Posterior Predictive Checks for BDEB Models

Description

Extracts replicated data y^{\mathrm{rep}} generated in the Stan ⁠generated quantities⁠ block and pairs them with the observed data y. Following Gelman et al. (2013, Ch. 6), posterior predictive checks (PPCs) answer: "could the observed data plausibly have been generated by the fitted model?" If the replicated data envelopes consistently miss systematic features of y, the model is mis-specified.

Usage

bdeb_ppc(fit, type = c("growth", "reproduction", "all"))

Arguments

Details

For growth endpoints, the replicated lengths L^{\mathrm{rep}}_i are drawn as L^{\mathrm{rep}}_i \sim N(\hat{L}_i, \sigma_L) in the Stan program. For reproduction, R^{\mathrm{rep}}_i \sim \mathrm{NegBin}(k_R \Delta E_R, \phi).

Value

A bdeb_ppc object containing observed data (L_obs or R_obs), a matrix of replicated data (L_rep or R_rep), and metadata for plot.bdeb_ppc().

Supported models

"individual"

Full PPC with L_rep and L_obs.

"growth_repro"

Growth PPC via L_rep; reproduction PPC via R_rep.

"hierarchical"

Not available. The Stan model uses reduce_sum and does not generate L_rep. Use bdeb_diagnose() and trace plots for model checking.

"debtox"

Not available for the same reason. Use plot_dose_response() for visual model checking.

References

Gelman, A., Carlin, J.B., Stern, H.S., Dunson, D.B., Vehtari, A. and Rubin, D.B. (2013). Bayesian Data Analysis. 3rd edition. Chapman & Hall/CRC. (Chapter 6: Model checking.)

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  ppc <- bdeb_ppc(fit, type = "growth")
  plot(ppc)
}

Methods for bdeb_prior Objects

Description

Display, summarise, and plot a bdeb_prior object returned by prior_lognormal(), prior_normal(), prior_beta(), prior_halfnormal(), prior_halfcauchy(), or prior_exponential().

Usage

## S3 method for class 'bdeb_prior'
print(x, ...)

## S3 method for class 'bdeb_prior'
summary(object, ...)

## S3 method for class 'summary.bdeb_prior'
print(x, ...)

## S3 method for class 'bdeb_prior'
plot(x, n = 200, ...)

Arguments

Value

print() returns the object invisibly. summary() returns a list with theoretical mean, sd, and the 5th, 50th, and 95th quantiles where defined for the family. plot() returns a ggplot2::ggplot object showing the prior density between the 0.001 and 0.999 quantiles.

Examples

p <- prior_lognormal(mu = 1.5, sigma = 0.5)
print(p)
summary(p)
plot(p)

Prior Predictive Check

Description

Simulates growth trajectories by sampling parameters from the prior distributions and forward-integrating the DEB ODE in R (Euler method). This is the prior analogue of bdeb_ppc() and answers: "what range of data does the model predict before seeing any data?" Following Gabry et al. (2019), if the prior predictive distribution covers biologically implausible values, the priors should be tightened.

Usage

bdeb_prior_predictive(model, n_draws = 500, dt = 0.5, seed = NULL)

Arguments

Details

Does not require CmdStan — all sampling and simulation is done in R using Euler integration (step size dt). This is an approximate visualisation tool, not exact Stan inference. The ODE trajectories may differ slightly from the BDF solver used during fitting.

Value

A list with class "bdeb_prior_predictive" containing:

t

Time vector.

L

Matrix of simulated trajectories (draws x time points).

L_inf

Vector of prior-predictive ultimate lengths.

priors

Named list of prior objects used.

References

Gabry, J., Simpson, D., Vehtari, A., Betancourt, M. and Gelman, A. (2019). Visualization in Bayesian workflow. Journal of the Royal Statistical Society: Series A, 182(2), 389–402. doi:10.1111/rssa.12378

Examples

dat <- bdeb_data(growth = data.frame(id = 1, time = 0:10,
  length = seq(0.1, 0.5, length.out = 11)))
mod <- bdeb_model(dat, type = "individual")
pp <- bdeb_prior_predictive(mod, n_draws = 100, seed = 1)
plot(pp, n_draws = 30)

Reproducibility Report

Description

Prints a concise summary of the software environment used for a BayesianDEB analysis. Useful for supplementary materials in publications or for diagnosing cross-machine discrepancies.

Usage

bdeb_session_info(fit = NULL)

Arguments

Value

Invisibly returns a named list with all reported information.

Examples

bdeb_session_info()

Posterior Summary for BDEB Parameters (deprecated)

Description

bdeb_summary() is deprecated as of BayesianDEB 0.2.0. Call cmdstanr::summary() on a bdeb_fit() object instead; the two are equivalent. This wrapper will be removed in a future release.

Usage

bdeb_summary(fit, pars = NULL, prob = 0.9, ...)

Arguments

Value

A posterior::draws_summary data frame.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  bdeb_summary(fit)  # equivalent to summary(fit); deprecated
}

DEBtox Model Specification

Description

Convenience wrapper for bdeb_model() that sets type = "debtox" and provides a stress argument to select the physiological mode of action (PMoA) of the toxicant. The underlying TKTD framework follows Jager et al. (2006) and the GUTS-RED-SD simplification of Jager & Zimmer (2012):

Usage

bdeb_tox(
  data,
  stress = c("assimilation", "maintenance", "growth_cost"),
  priors = list(),
  ...
)

Arguments

Details

Toxicokinetics. Scaled internal damage D_w tracks the external concentration with first-order kinetics:

\frac{dD_w}{dt} = k_d\bigl(\max(C_w - z_w,\, 0) - D_w\bigr)

where k_d is the dominant rate constant, z_w is the NEC (no-effect concentration), and C_w is the external concentration.

Stress on assimilation. The assimilation flux is reduced by a factor \max(1 - b_w D_w, 0), where b_w is the effect intensity. At steady state (D_w = C_w - z_w), the \mathrm{EC}_{50} for 50\ z_w + 0.5/b_w.

Value

A bdeb_model object of type "debtox".

Note

Lifecycle: beta. Stress on assimilation is implemented and tested; "maintenance" and "growth_cost" modes are planned.

Important limitation: the DEBtox model fits one ODE per concentration group, not per individual. If your data contain multiple individuals per concentration, they are automatically aggregated to group means per time point (with a warning). This is appropriate for group-level summary data but does not capture within-group individual variation. A hierarchical DEBtox extension is planned for a future version.

References

Jager, T., Heugens, E.H.W. and Kooijman, S.A.L.M. (2006). Making sense of ecotoxicological test results: towards application of process-based models. Ecotoxicology, 15(3), 305–314. doi:10.1007/s10646-006-0060-x

Jager, T. and Zimmer, E.I. (2012). Simplified Dynamic Energy Budget model for analysing ecotoxicity data. Ecological Modelling, 225, 74–81. doi:10.1016/j.ecolmodel.2011.11.012

Examples

# R-side specification only (no Stan sampling)
data(debtox_growth)
# one replicate per concentration avoids aggregation warning
dt <- debtox_growth[debtox_growth$id %in% c(1, 11, 21, 31), ]
dat <- bdeb_data(growth = dt, concentration = c(0, 20, 80, 200))
mod <- bdeb_tox(dat, stress = "assimilation")

Build Stan Data List for DEBtox

Description

Build Stan Data List for DEBtox

Usage

build_stan_data_debtox(data, priors, temperature = NULL, observation = NULL)

Arguments

Value

Named list suitable for Stan.

Build Stan Data List for Growth + Reproduction

Description

Build Stan Data List for Growth + Reproduction

Usage

build_stan_data_growth_repro(
  data,
  priors,
  temperature = NULL,
  observation = NULL
)

Arguments

Value

Named list suitable for Stan.

Build Stan Data List for Hierarchical Growth

Description

Build Stan Data List for Hierarchical Growth

Usage

build_stan_data_hierarchical(
  data,
  priors,
  temperature = NULL,
  observation = NULL
)

Arguments

Value

Named list suitable for Stan.

Build Stan Data List for Individual Growth

Description

Build Stan Data List for Individual Growth

Usage

build_stan_data_individual(
  data,
  priors,
  temperature = NULL,
  observation = NULL
)

Arguments

Value

Named list suitable for Stan.

Check that cmdstanr is available

Description

Since cmdstanr is listed under Suggests (it is not on CRAN), every function that needs it must call this guard first.

Usage

check_cmdstanr()

Value

TRUE invisibly if cmdstanr is available; otherwise throws an informative error.

Extract Point Estimates from a BDEB Fit

Description

Returns posterior medians of all model parameters as a named numeric vector, consistent with the S3 coef() convention.

Usage

## S3 method for class 'bdeb_fit'
coef(object, type = c("median", "mean"), ...)

Arguments

Value

Named numeric vector of point estimates.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  coef(fit)
}

Posterior Credible Intervals for BDEB Model Parameters

Description

Bayesian counterpart to stats::confint(): returns the posterior central credible interval for each model parameter.

Usage

## S3 method for class 'bdeb_fit'
confint(object, parm = NULL, level = 0.95, ...)

Arguments

Value

A matrix with one row per parameter and two columns named by their percentile (e.g. "2.5%", "97.5%" for level = 0.95).

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  confint(fit, level = 0.90)
}

Compute DEB Energy Fluxes

Description

Given current state (E, V) and the core DEB parameters, computes all standard energy fluxes defined by the \kappa-rule (Kooijman, 2010, Eqs. 2.3–2.12):

Usage

deb_fluxes(E, V, f, p_Am, p_M, kappa, v, E_G, k_J = 0, E_Hp = 0)

Arguments

Details

\dot{p}_A

Assimilation: f \{p_{Am}\} L^2.

\dot{p}_C

Mobilisation: E v L / (E + [E_G] V).

\dot{p}_M

Somatic maintenance: [p_M] V.

\dot{p}_G

Growth: \max(\kappa \dot{p}_C - \dot{p}_M, 0).

\dot{p}_J

Maturity maintenance: k_J E_H^p.

\dot{p}_R

Reproduction: \max((1-\kappa)\dot{p}_C - \dot{p}_J, 0).

Value

Named list with fluxes p_A, p_C, p_M, p_G, p_J, p_R, structural length L (V^{1/3}), and scaled reserve density e (E / ([E_m] V + 10^{-12})). The 10^{-12} stabilisation prevents division by zero when V = 0; in that edge case e returns a small finite number rather than Inf or NA.

References

Kooijman, S.A.L.M. (2010). Dynamic Energy Budget Theory for Metabolic Organisation. 3rd edition. Cambridge University Press, Ch. 2. doi:10.1017/CBO9780511805400

Examples

# Energy fluxes for a 1 cm^3 organism with typical Eisenia parameters
deb_fluxes(E = 1, V = 1, f = 1, p_Am = 5, p_M = 0.5,
  kappa = 0.75, v = 0.2, E_G = 4400)

Simulate DEB Growth Trajectory

Description

Forward-integrates the standard 2-state DEB ODE (reserve E, structure V) using Euler's method. This is a standalone simulator independent of Stan — useful for exploring parameter space, generating synthetic data, teaching, and prior predictive checks.

Usage

deb_simulate(t_max, p_Am, p_M, kappa, v, E_G, E0, L0, f = 1, dt = 0.5)

Arguments

Value

Data frame with columns time, E (reserve), V (volume), L (structural length).

Numerical note

This uses the LSODA solver from deSolve, which automatically switches between stiff (BDF) and non-stiff (Adams) methods. This matches the BDF solver used in the Stan models, ensuring numerical consistency between R-side simulation and Stan-side inference. The dt parameter controls output resolution, not integration accuracy (governed by rtol/atol = 1e-6).

Examples

# Simulate E. fetida growth for 84 days
traj <- deb_simulate(t_max = 84, p_Am = 5, p_M = 0.5,
  kappa = 0.75, v = 0.2, E_G = 400, E0 = 1, L0 = 0.1)
plot(traj$time, traj$L, type = "l", xlab = "Days", ylab = "L (cm)")

Simulated DEBtox Growth Data

Description

Simulated growth data under toxicant exposure for 4 concentration groups (0, 20, 80, 200 arbitrary units) with 10 individuals per group measured weekly over 6 weeks. Designed for fitting the DEBtox (TKTD) model in bdeb_tox(). The toxicant acts through stress on assimilation: the effective assimilation rate is reduced by a factor \max(1 - b_w \max(C_w - z_w, 0), \, 0) following the DEBtox framework of Jager et al. (2006).

Usage

debtox_growth

Format

A data frame with 280 rows and 4 columns:

id

Individual identifier (integer, 1–40)

concentration

External toxicant concentration (arbitrary units)

time

Observation time in days (0, 7, 14, ..., 42)

length

Structural length in cm (with measurement error)

Source

Simulated with NEC z_w = 15, effect intensity b_w = 0.003, and base DEB parameters identical to eisenia_growth.

References

Jager, T., Heugens, E.H.W. and Kooijman, S.A.L.M. (2006). Making sense of ecotoxicological test results: towards application of process-based models. Ecotoxicology, 15(3), 305–314. doi:10.1007/s10646-006-0060-x

Examples

data(debtox_growth)
head(debtox_growth)

Simulate DEBtox Growth Under Toxicant Exposure

Description

Forward-integrates the 4-state DEBtox ODE (E, V, E_R, D_w) with stress on assimilation. Standalone simulator independent of Stan.

Usage

debtox_simulate(
  t_max,
  p_Am,
  p_M,
  kappa,
  v,
  E_G,
  E0,
  L0,
  k_d,
  z_w,
  b_w,
  C_w,
  f = 1,
  dt = 0.5
)

Arguments

Value

Data frame with columns time, E, V, L, R (reproduction buffer), Dw (scaled damage).

Examples

traj <- debtox_simulate(t_max = 42, p_Am = 5, p_M = 0.5,
  kappa = 0.75, v = 0.2, E_G = 400, E0 = 1, L0 = 0.1,
  k_d = 0.3, z_w = 15, b_w = 0.003, C_w = 80)
plot(traj$time, traj$L, type = "l")

Eisenia andrei Cadmium Toxicity Data (Van Gestel 1991)

Description

Real experimental growth data for Eisenia andrei exposed to cadmium in natural soil at 23 °C from Van Gestel et al. (1991), obtained via the EGrowth database (Mathieu, 2018). Five concentration groups (0, 10, 32, 100, 320 mg Cd/kg) with 7 time points each over 85 days. Group-mean body mass was converted to structural length via L = (W / d_V)^{1/3} with d_V = 1.05 g cm^{-3}.

Usage

eisenia_cd

Format

A data frame with 35 rows and 4 columns:

id

Concentration group identifier (1–5)

time

Time in days (0–85)

length

Structural length in cm

concentration

Cadmium concentration (mg Cd/kg soil)

Source

EGrowth database, curve IDs gr0119–gr0123. https://github.com/JeromeMathieuEcology/EGrowth

References

Van Gestel, C.A.M., Van Dis, W.A., Dirven-Van Breemen, E.M., Sparenburg, P.M. and Baerselman, R. (1991). Influence of cadmium, copper, and pentachlorophenol on growth and sexual development of Eisenia andrei (Oligochaeta; Annelida). Biology and Fertility of Soils, 12, 117–121. doi:10.1007/BF00341486

Examples

data(eisenia_cd)
plot(eisenia_cd$time, eisenia_cd$length,
     col = as.factor(eisenia_cd$concentration),
     xlab = "Days", ylab = "Structural length (cm)")

Simulated Eisenia fetida Growth Data

Description

Simulated growth dataset for 21 individuals of the earthworm Eisenia fetida measured weekly over 12 weeks under controlled laboratory conditions (20 °C, ad libitum feeding), following a standard OECD 222 test protocol design. DEB parameters are based on the E. fetida entry in the Add-my-Pet collection (AmP; Marques et al., 2018). Individual variation in \{p_{Am}\} was drawn from a lognormal distribution with CV \approx 10\ Gaussian measurement error \sigma_L = 0.015 cm was added to the structural length.

Usage

eisenia_growth

Format

A data frame with 273 rows and 3 columns:

id

Individual identifier (integer, 1–21)

time

Observation time in days (0, 7, 14, ..., 84)

length

Structural length in cm (= V^{1/3}), with measurement error

Source

Simulated from the standard DEB model (Kooijman, 2010, Eqs. 2.4–2.6) with parameters: \{p_{Am}\} = 5.0 J/d/cm^2, [p_M] = 0.5 J/d/cm^3, \kappa = 0.75, v = 0.2 cm/d, [E_G] = 400 J/cm^3. Individual variation: \{p_{Am}\}_j \sim \mathrm{LogNormal}(\log 5.0,\, 0.1), L_{0,j} \sim \mathrm{LogNormal}(\log 0.1,\, 0.05). Observation error: \sigma_L = 0.015 cm.

References

Kooijman, S.A.L.M. (2010). Dynamic Energy Budget Theory for Metabolic Organisation. 3rd edition. Cambridge University Press. doi:10.1017/CBO9780511805400

Marques, G.M., Augustine, S., Lika, K., Pecquerie, L., Domingos, T. and Kooijman, S.A.L.M. (2018). The AmP project: comparing species on the basis of dynamic energy budget parameters. PLOS Computational Biology, 14(5), e1006100. doi:10.1371/journal.pcbi.1006100

OECD (2016). Test No. 222: Earthworm Reproduction Test (Eisenia fetida / Eisenia andrei). OECD Guidelines for the Testing of Chemicals.

Examples

data(eisenia_growth)
head(eisenia_growth)

Eisenia fetida Growth Data (Neuhauser 1980)

Description

Real experimental growth data for Eisenia fetida on activated sludge at 25 °C from Neuhauser, Hartenstein & Kaplan (1980), obtained via the EGrowth database (Mathieu, 2018). The dataset comprises 37 group-mean body mass measurements (20 worms per replicate) over 250 days, from hatchling (~8 mg) to adult (~2350 mg). Wet mass was converted to structural length via L = (W / d_V)^{1/3} with tissue density d_V = 1.05 g cm^{-3}.

Usage

eisenia_neuhauser

Format

A data frame with 37 rows and 3 columns:

id

Individual/group identifier (always 1)

time

Time in days since start (1–250)

length

Structural length in cm (0.20–1.31)

Source

EGrowth database, curve ID gr0226. https://github.com/JeromeMathieuEcology/EGrowth

References

Neuhauser, E.F., Hartenstein, R. and Kaplan, D.L. (1980). Growth of the earthworm Eisenia foetida in relation to population density and food rationing. Oikos, 35, 93–98. doi:10.2307/3544730

Mathieu, J. (2018). EGrowth: a global database on intraspecific body growth variability in earthworm. Soil Biology and Biochemistry, 122, 71–80. doi:10.1016/j.soilbio.2018.04.004

Examples

data(eisenia_neuhauser)
plot(eisenia_neuhauser$time, eisenia_neuhauser$length,
     xlab = "Days", ylab = "Structural length (cm)")

Fitted Values from a BDEB Fit

Description

Posterior point estimate (median or mean) of the latent length \hat{L}_i at each observation. Bayesian counterpart of stats::fitted().

Usage

## S3 method for class 'bdeb_fit'
fitted(object, type = c("median", "mean"), ...)

Arguments

Details

Currently supported for "individual" and "growth_repro" models. For "hierarchical" and "debtox" use bdeb_predict() instead.

Value

Named numeric vector of fitted values, one per observation.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  fitted(fit)
}

Simulated Folsomia candida Reproduction Data

Description

Simulated 28-day reproduction dataset for the springtail Folsomia candida exposed to 5 cadmium concentrations (0, 10, 50, 100, 500 mg Cd/kg dry soil) with 6 replicates per concentration. The experimental design follows ISO 11267 (springtail reproduction test). Toxicant effects were simulated using a simple NEC-based model: expected offspring = 120 \times \max(1 - b_w \max(C - z_w, 0), \, 0), with Poisson sampling around the expected value.

Usage

folsomia_repro

Format

A data frame with 30 rows and 5 columns:

id

Replicate identifier (integer, 1–30)

concentration

Cadmium concentration in mg/kg dry soil

t_start

Start of observation interval (day 0)

t_end

End of observation interval (day 28)

count

Number of juveniles produced in the interval

Source

Simulated with NEC z_w = 30 mg/kg, effect intensity b_w = 0.005 (mg/kg)^{-1}, and control offspring count \approx 120.

References

ISO 11267 (2014). Soil quality — Inhibition of reproduction of Collembola (Folsomia candida) by soil contaminants.

Examples

data(folsomia_repro)
head(folsomia_repro)

Log-Likelihood of a BDEB Fit

Description

Computes the log-pointwise predictive density (lppd):

\mathrm{lppd} = \sum_{i=1}^{N} \log\!\left( \frac{1}{S} \sum_{s=1}^{S} \exp(\log p(y_i \mid \theta^{(s)})) \right),

the Bayesian analogue of stats::logLik(). This is the natural point summary of model fit reported by bdeb_loo() (which adds Pareto-smoothed importance sampling for cross-validation).

Usage

## S3 method for class 'bdeb_fit'
logLik(object, ...)

Arguments

Details

Requires the Stan model to store per-observation log_lik in ⁠generated quantities⁠. Currently available for "individual" and "growth_repro" models; "hierarchical" and "debtox" compute the likelihood inside reduce_sum and do not expose individual terms.

Value

A logLik object with attributes df (number of model parameters) and nobs (number of observations).

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  logLik(fit)
}

Number of Observations Used in a BDEB Fit

Description

Returns the total count of growth (and, where relevant, reproduction) observations that contributed to the likelihood. Matches stats::nobs() in spirit.

Usage

## S3 method for class 'bdeb_fit'
nobs(object, ...)

Arguments

Value

Integer scalar: total number of observations.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  nobs(fit)
}

Observation Model Specifications

Description

Observation Model Specifications

Usage

obs_normal()

obs_lognormal()

obs_student_t(nu = 5)

obs_poisson()

obs_negbinom()

Arguments

Value

A bdeb_obs object (list with class "bdeb_obs").

Functions

• obs_normal(): Gaussian observation error (default for growth)

• obs_lognormal(): Log-normal observation error (multiplicative)

• obs_student_t(): Student-t observation error (robust to outliers)

• obs_poisson(): Poisson observations (for count data)

• obs_negbinom(): Negative binomial observations (overdispersed counts)

Examples

obs_normal()
obs_lognormal()
obs_negbinom()

Encode observation model flags for Stan

Description

Encode observation model flags for Stan

Usage

observation_to_stan_data(observation)

Arguments

Value

Named list with obs_growth, obs_nu, obs_repro.

Plot a BDEB Data Object

Description

Visualises the contents of a bdeb_data() object. Growth data are shown as observed length versus time, with one trace per individual. Reproduction data are shown as interval counts versus interval midpoint. When concentration information is available (DEBtox setups) individuals are coloured by group.

Usage

## S3 method for class 'bdeb_data'
plot(x, endpoint = NULL, ...)

Arguments

Value

A ggplot2::ggplot object.

Examples

df <- data.frame(id = 1, time = 0:5, length = seq(0.1, 0.6, by = 0.1))
dat <- bdeb_data(growth = df)
plot(dat)

Plot Convergence Diagnostics

Description

Visualises the per-parameter R-hat or ESS-bulk values from a bdeb_diagnose() object. A dashed red reference line is drawn at the Vehtari et al. (2021) threshold (R-hat = 1.01, ESS-bulk = 400).

Usage

## S3 method for class 'bdeb_diagnostics'
plot(x, type = c("rhat", "ess"), full = FALSE, ...)

Arguments

Details

To keep the plot short and readable, the per-time-point latent states (x_sol[i,j], L_hat[i], ...) are hidden by default and only the scalar model parameters are shown, mirroring print.bdeb_diagnostics(); set full = TRUE to plot every monitored quantity.

Value

A ggplot2::ggplot object.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  plot(bdeb_diagnose(fit), type = "ess")
}

Plot a BDEB Fit

Description

Plot a BDEB Fit

Usage

## S3 method for class 'bdeb_fit'
plot(
  x,
  type = c("trace", "posterior", "pairs", "trajectory", "prior_posterior"),
  pars = NULL,
  n_draws = 100,
  seed = NULL,
  ...
)

Arguments

Value

A ggplot2 object.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  plot(fit, type = "trace")
  plot(fit, type = "trajectory", n_draws = 50)
}

Plot a BDEB Model Specification

Description

Displays the prior densities for the model parameters as a faceted panel of curves. Each parameter prior is drawn between the 0.001 and 0.999 quantiles of its prior distribution; for bounded supports (Beta, half-normal, half-Cauchy, exponential) the lower bound is fixed at zero (or a small epsilon for densities that diverge there). Useful for sanity-checking prior choices before calling bdeb_fit().

Usage

## S3 method for class 'bdeb_model'
plot(x, pars = NULL, n = 200, ...)

Arguments

Value

A ggplot2::ggplot object.

Examples

df <- data.frame(id = 1, time = 0:5, length = seq(0.1, 0.6, by = 0.1))
dat <- bdeb_data(growth = df)
mod <- bdeb_model(dat, type = "individual")
plot(mod, pars = c("p_Am", "kappa"))

Plot Posterior Predictive Checks

Description

Plot Posterior Predictive Checks

Usage

## S3 method for class 'bdeb_ppc'
plot(x, n_draws = 50, ...)

Arguments

Value

A ggplot2 object.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  plot(bdeb_ppc(fit, type = "growth"))
}

Plot Posterior Predictive Trajectories

Description

Overlays a sample of the posterior trajectory draws stored in a bdeb_prediction object.

Usage

## S3 method for class 'bdeb_prediction'
plot(x, n_draws = 100, ...)

Arguments

Value

A ggplot2::ggplot object.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  plot(predict(fit), n_draws = 50)
}

Plot DEBtox Dose-Response

Description

Produces a dose-response curve by forward-simulating the full 4-state DEBtox ODE from the posterior in R (Euler integration). For each posterior draw, the ODE is solved at every concentration in a fine grid from 0 to 1.2 \times \max(C_w). The y-axis shows the predicted final structural length relative to the control (C = 0) at the same draw, so that each curve propagates the full parameter uncertainty through the dynamic model.

Usage

plot_dose_response(
  fit,
  endpoint = "growth",
  n_draws = 100,
  n_conc = 50,
  dt = 1,
  t_end = NULL,
  seed = NULL
)

Arguments

Details

This is a visualisation tool, not exact Stan inference. The R-side Euler integrator (step size dt) is an approximation of the BDF solver used during fitting. For quantitative results, use bdeb_ec50() which extracts the analytically computed EC_{50} and NEC directly from the Stan posterior.

Performance note. Each draw requires n_conc ODE integrations, so n_draws * n_conc total. With default settings (100 draws, 50 concentrations) this takes a few seconds. Reduce n_draws for faster interactive use.

Value

A ggplot2 object.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(debtox_growth)
  dat <- bdeb_data(growth = debtox_growth,
                   concentration = c("1" = 0, "11" = 20,
                                    "21" = 80, "31" = 200))
  fit <- bdeb_fit(bdeb_tox(dat, stress = "assimilation"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  init = 0.5, refresh = 0)
  plot_dose_response(fit, n_draws = 50)
}

Predict from a BDEB Fit

Description

When newdata = NULL, extracts the fitted trajectories (L_hat) from the Stan posterior (exact). When newdata is provided, performs R-side forward simulation (Euler integration) from the posterior draws under new environmental conditions or extended time horizons. The Euler integrator is an approximation — for quantitative results at the original data conditions, prefer newdata = NULL.

Usage

## S3 method for class 'bdeb_fit'
predict(object, newdata = NULL, n_draws = 200, dt = 0.5, seed = NULL, ...)

bdeb_predict(fit, newdata = NULL, n_draws = 200, dt = 0.5, seed = NULL)

Arguments

Value

A bdeb_prediction object with components t (time vector), L_hat (matrix: draws x time points), n_draws, model_type.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  pred <- predict(fit, n_draws = 200)
  summary(pred); plot(pred)
}

Print a BDEB Data Object

Description

Print a BDEB Data Object

Usage

## S3 method for class 'bdeb_data'
print(x, ...)

Arguments

Value

The input object, invisibly.

Print a BDEB Diagnostics Report

Description

Default printing for bdeb_diagnose() output. Displays divergence / treedepth / E-BFMI alerts, R-hat and ESS warnings, and a compact parameter summary table. To keep the on-screen output short, the per-time-point latent states (x_sol[i,j], L_hat[i], ...) are hidden by default; the scalar model parameters are always shown. Output uses cli::cli alerts and is therefore silenceable via cli::cli_inform() sinks.

Usage

## S3 method for class 'bdeb_diagnostics'
print(x, full = FALSE, ...)

Arguments

Value

The input object, invisibly.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  print(bdeb_diagnose(fit))
}

Print a BDEB Fit

Description

Print a BDEB Fit

Usage

## S3 method for class 'bdeb_fit'
print(x, ...)

Arguments

Value

The input object, invisibly.

Print a BDEB Model Specification

Description

Print a BDEB Model Specification

Usage

## S3 method for class 'bdeb_model'
print(x, ...)

Arguments

Value

The input object, invisibly.

Print a BDEB Posterior Predictive Check

Description

Print a BDEB Posterior Predictive Check

Usage

## S3 method for class 'bdeb_ppc'
print(x, ...)

Arguments

Value

The input object, invisibly.

Print a BDEB Prediction

Description

One-line metadata printer for predict.bdeb_fit() output.

Usage

## S3 method for class 'bdeb_prediction'
print(x, ...)

Arguments

Value

The input object, invisibly.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  print(predict(fit))
}

Default Priors for DEB Parameters

Description

Returns a named list of weakly informative priors for standard DEB parameters. The defaults are calibrated against the parameter ranges observed in the Add-my-Pet (AmP) collection (Marques et al., 2018) for standard ecotoxicological test species. All positive rate parameters use log-normal priors whose 95 \ roughly one order of magnitude around typical values; \kappa uses \mathrm{Beta}(2,2) which is symmetric on (0,1) with prior mean 0.5.

Usage

prior_default(type = c("individual", "growth_repro", "hierarchical", "debtox"))

Arguments

Value

Named list of bdeb_prior objects.

References

Marques, G.M., Augustine, S., Lika, K., Pecquerie, L., Domingos, T. and Kooijman, S.A.L.M. (2018). The AmP project: comparing species on the basis of dynamic energy budget parameters. PLOS Computational Biology, 14(5), e1006100. doi:10.1371/journal.pcbi.1006100

Examples

prior_default("individual")

Species-Specific Priors from the AmP Collection

Description

Returns priors calibrated to a specific species using parameter estimates from the Add-my-Pet (AmP) collection (Marques et al., 2018). The log-normal priors are centred on the AmP point estimate (log scale) with a moderate spread (\sigma = 0.3) that places 95\ value.

Usage

prior_species(
  species,
  type = c("individual", "growth_repro", "hierarchical", "debtox")
)

Arguments

Details

Currently supported species (more will be added):

Eisenia_fetida

Compost earthworm; AmP entry Eisenia_fetida.

Eisenia_andrei

Sibling species of E. fetida; shares similar DEB parameters.

Folsomia_candida

Springtail; standard ISO reproduction test species.

Daphnia_magna

Water flea; classic aquatic ecotox model.

Lumbricus_rubellus

Field earthworm; common biomonitoring species.

Value

Named list of bdeb_prior objects, suitable for the priors argument of bdeb_model() or bdeb_tox().

References

Marques, G.M., Augustine, S., Lika, K., Pecquerie, L., Domingos, T. and Kooijman, S.A.L.M. (2018). The AmP project: comparing species on the basis of dynamic energy budget parameters. PLOS Computational Biology, 14(5), e1006100. doi:10.1371/journal.pcbi.1006100

Examples

# Use AmP-calibrated priors for E. fetida
prior_species("Eisenia_fetida")

# Combine with model specification (R-side, no Stan sampling)
data(eisenia_growth)
dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
mod <- bdeb_model(dat, type = "individual",
  priors = prior_species("Eisenia_fetida"))

Prior Distribution Specifications for BDEB Models

Description

Constructor functions for prior distribution objects used in bdeb_model(). Each returns a lightweight bdeb_prior S3 object that encodes the distribution family and its hyperparameters. The prior is evaluated inside the Stan model block; hyperparameters are passed as data so that changing priors does not require recompilation.

Usage

prior_lognormal(mu = 0, sigma = 1)

prior_normal(mu = 0, sigma = 1)

prior_beta(a = 2, b = 2)

prior_halfnormal(sigma = 1)

prior_halfcauchy(sigma = 1)

prior_exponential(rate = 1)

Arguments

Details

The choice of prior family follows the recommendations for DEB parameters in Hackenberger (2025, Ch. 6) and general guidelines from Gelman et al. (2013, Sec. 2.9):

• Positive rate parameters (\{p_{Am}\}, [p_M], v, [E_G]) — log-normal, because the log-transform maps the strictly positive domain to the real line.

• Allocation fraction \kappa \in (0,1) — Beta, the natural conjugate for bounded parameters.

• Observation-error standard deviations — half-normal (or half-Cauchy for heavier tails), which place zero mass on negative values (Gelman, 2006).

• Hierarchical standard deviations — exponential, following the advice of Betancourt & Girolami (2015) for non-centred parameterisations.

Value

A bdeb_prior object (list with class "bdeb_prior").

Functions

• prior_lognormal(): Log-normal prior (for positive parameters: p_Am, p_M, v, E_G, etc.)

• prior_normal(): Normal prior (for unconstrained parameters)

• prior_beta(): Beta prior (for (0,1)-constrained parameters: kappa)

• prior_halfnormal(): Half-normal prior (for scale parameters: sigma_L, etc.)

• prior_halfcauchy(): Half-Cauchy prior (for scale parameters, heavier tails)

• prior_exponential(): Exponential prior (for variance components in hierarchical models)

References

Gelman, A. (2006). Prior distributions for variance parameters in hierarchical models. Bayesian Analysis, 1(3), 515–534. doi:10.1214/06-BA117A

Gelman, A., Carlin, J.B., Stern, H.S., Dunson, D.B., Vehtari, A. and Rubin, D.B. (2013). Bayesian Data Analysis. 3rd edition. Chapman & Hall/CRC.

Examples

# Log-normal prior on assimilation rate: median ~ exp(1.5) ~ 4.5
prior_lognormal(mu = 1.5, sigma = 0.5)

# Beta(2,2) prior on kappa — symmetric, favouring 0.5
prior_beta(a = 2, b = 2)

Convert Cumulative Reproduction to Intervals

Description

Many ecotoxicological protocols (e.g., ISO 11267 for Folsomia candida, OECD 222 for Eisenia fetida) report cumulative offspring counts at successive observation times. The DEB reproduction buffer model, however, requires interval counts \Delta R = R(t_{\mathrm{end}}) - R(t_{\mathrm{start}}) so that the negative-binomial likelihood can be applied to each counting period. This function computes the first-difference per individual.

Usage

repro_to_intervals(df)

Arguments

Value

Data frame with columns: id, t_start, t_end, count.

Examples

cumul <- data.frame(
  id = rep(1, 5),
  time = c(0, 7, 14, 21, 28),
  cumulative = c(0, 10, 30, 60, 100)
)
repro_to_intervals(cumul)

Residuals from a BDEB Fit

Description

Observed minus fitted length for each observation, using the posterior point estimate from fitted(). Bayesian counterpart of stats::residuals().

Usage

## S3 method for class 'bdeb_fit'
residuals(object, type = "response", ...)

Arguments

Details

Currently supported for "individual" and "growth_repro" models.

Value

Named numeric vector of residuals.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  residuals(fit)
}

Get path to a bundled Stan model file

Description

Get path to a bundled Stan model file

Usage

stan_file(model_name)

Arguments

Value

Full path to the .stan file.

Summary of a BDEB Data Object

Description

Returns a compact list of summary statistics describing a bdeb_data() object: number of observations, number of unique individuals, time range, presence of growth/reproduction endpoints, the functional response, and (for DEBtox data) the unique concentration levels.

Usage

## S3 method for class 'bdeb_data'
summary(object, ...)

## S3 method for class 'summary.bdeb_data'
print(x, ...)

Arguments

Value

An object of class summary.bdeb_data (a list).

Examples

df <- data.frame(id = 1, time = 0:5, length = seq(0.1, 0.6, by = 0.1))
dat <- bdeb_data(growth = df)
summary(dat)

Compact Summary of a BDEB Diagnostics Report

Description

Returns counts of problematic parameters (divergences, treedepth saturations, low-EBFMI chains, R-hat > 1.01, ESS-bulk < 400) suitable for a one-line health check or programmatic gating.

Usage

## S3 method for class 'bdeb_diagnostics'
summary(object, ...)

Arguments

Value

An object of class summary.bdeb_diagnostics (a list).

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  summary(bdeb_diagnose(fit))
}

Posterior Summary for a BDEB Fit

Description

Returns a tidy summary table of posterior draws for model parameters (and optionally derived quantities), analogous to stats::summary.lm() for frequentist fits.

Usage

## S3 method for class 'bdeb_fit'
summary(object, pars = NULL, prob = 0.9, ...)

Arguments

Value

A posterior::draws_summary data frame with columns variable, mean, sd, median, two quantile columns named by their percentile (e.g. "5%" / "95%" for prob = 0.90), rhat, ess_bulk, and ess_tail.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  summary(fit, pars = c("p_Am", "kappa"), prob = 0.95)
}

Summary of a BDEB Model Specification

Description

Returns a list summarising the structure of a bdeb_model() object: model type, Stan program name, names of model parameters, prior families, observation models, and (when present) the temperature correction settings. Useful for one-glance verification before calling bdeb_fit().

Usage

## S3 method for class 'bdeb_model'
summary(object, ...)

## S3 method for class 'summary.bdeb_model'
print(x, ...)

Arguments

Value

An object of class summary.bdeb_model (a list).

Tabulate Posterior Predictive Quantiles

Description

Reduces the matrix of posterior trajectory draws stored in a bdeb_prediction object to per-time-point credible intervals.

Usage

## S3 method for class 'bdeb_prediction'
summary(object, prob = 0.9, ...)

Arguments

Value

A data frame with columns time, lower, median, upper. Carries class summary.bdeb_prediction and attribute prob.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  summary(predict(fit), prob = 0.95)
}

Encode temperature correction for Stan

Description

Encode temperature correction for Stan

Usage

temperature_to_stan_data(temperature)

Arguments

Value

Named list with has_temperature, T_obs, T_ref, T_A.

Posterior Covariance Matrix of BDEB Model Parameters

Description

Computes the empirical covariance matrix of the posterior draws for all model parameters. Bayesian counterpart of stats::vcov().

Usage

## S3 method for class 'bdeb_fit'
vcov(object, ...)

Arguments

Value

A symmetric numeric matrix with model parameters on rows and columns.

Examples

if (requireNamespace("cmdstanr", quietly = TRUE) &&
    nzchar(tryCatch(cmdstanr::cmdstan_path(), error = function(e) ""))) {
  data(eisenia_growth)
  dat <- bdeb_data(growth = eisenia_growth[eisenia_growth$id == 1, ])
  fit <- bdeb_fit(bdeb_model(dat, type = "individual"),
                  chains = 2, iter_warmup = 200, iter_sampling = 200,
                  refresh = 0)
  vcov(fit)
}