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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).
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 = ...).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.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.arrhenius(temp = ...).temperature$T_obs field.\dontrun{} replaced with runnable examples for
prior_species(), bdeb_tox() and
bdeb_prior_predictive() (all execute in < 0.2 s against
bundled datasets). bdeb_fit() retains
\dontrun{} because it requires the external CmdStan
toolchain and a single Stan compilation + MCMC run takes > 30
seconds; the Rd comment explains the reason.CITATION.cff from the
version-specific DOI (10.5281/zenodo.19500753, v0.1.3) to
the concept DOI (10.5281/zenodo.19443804),
which always resolves to the latest archived version. The v0.1.4 version
DOI is 10.5281/zenodo.19642839 for anyone needing to cite
this specific release.New features and data release.
prior_species(): species-specific priors from the AmP
collection for E. fetida, E. andrei, F.
candida, D. magna, and L. rubellus.plot(fit, type = "prior_posterior"): prior
vs. posterior density comparison plot.eisenia_neuhauser: real E. fetida growth data
from Neuhauser, Hartenstein & Kaplan (1980), 37 group-mean
measurements over 250 days.eisenia_cd: real Eisenia andrei cadmium
toxicity data from Van Gestel et al. (1991), 5 concentration groups over
85 days.ODE solver upgrade and bug fix release.
deSolve::lsoda()
(adaptive BDF/Adams) instead of fixed-step Euler. This matches the BDF
solver used in Stan, ensuring numerical consistency between R-side
simulation and Stan-side inference. The dt parameter now
controls output resolution, not integration accuracy.deSolve (>= 1.40) added to Imports.bdeb_ec50()$NEC returning a data frame instead of
numeric draws — median(ec50$NEC) now works correctly.build_stan_data_hierarchical() crashing when
growth data starts at time = 0 (same fix as individual
model in 0.1.1).build_stan_data_debtox() crashing when growth or
reproduction data starts at time = 0.build_stan_data_growth_repro() t=0 handling
producing NA index matches — replaced convoluted fix with consistent
epsilon shift across growth and reproduction times.sim_deb_euler() /
sim_debtox_euler() to sim_deb_lsoda() /
sim_debtox_lsoda() to reflect solver.Bug fix and hardening release.
ode_bdf_tol crash when growth data starts at
time = 0: replaced with 1e-3 epsilon since
Stan requires t_obs > t0.%||% operator not imported: replaced with
explicit if (is.null(...)) in
bdeb_predict().rnorm() fallback for unknown prior
families in bdeb_prior_predictive(): now throws informative
error.bdeb_predict(newdata = NULL) using
t_obs instead of t_L for
"growth_repro" models.bdeb_predict() silently returning raw draws when
L_hat is missing: now throws informative error.R instead of
interval delta_R = k_R * (R(t_end) - R(t_start)): now
consistent with growth_repro model.phi_R prior hardcoded in DEBtox Stan model: now
uses prior_phi_R_mu/sd from R prior system.deb_fluxes() computing p_G with
redundant / E_G * E_G.growth_rate formula: was
v/3 * p_M/(kappa*E_G), now correct Kooijman Eq. 3.23:
k_M * g / (3*(f+g))."individual" and "growth_repro" models now
hard-error (not warn) when data contains multiple individuals.survival argument from bdeb_data()
(was accepted but not implemented — “feature mirage”).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).match() instead of nearest-neighbour
which.min().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.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().bdeb_fit object.inst/CITATION with package and Kooijman (2010)
entries.CITATION.cff with Zenodo DOI.Initial release.
bdeb_model().prior_lognormal(), prior_beta(),
prior_halfnormal(), and others.prior_default(), calibrated against the AmP collection
(Marques et al., 2018).obs_normal(),
obs_lognormal(), obs_student_t(),
obs_poisson(), obs_negbinom().cmdstanr with
bdeb_fit().bdeb_diagnose() reports R-hat,
ESS, divergences, and E-BFMI (Vehtari et al., 2021).bdeb_ppc().bdeb_derived() for
ultimate length, von Bertalanffy growth rate, and somatic maintenance
rate constant.bdeb_tox(), bdeb_ec50(),
plot_dose_response().arrhenius() temperature correction,
deb_fluxes() energy flux calculator,
repro_to_intervals() data converter.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).getting_started: overview of the package workflow.case_study_eisenia_folsomia: full workflow with Eisenia
growth (individual + hierarchical) and Folsomia DEBtox analysis.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.