Bayesian Dynamic Energy Budget Modelling

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Documentation for package ‘BayesianDEB’ version 0.2.1

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

arrhenius	Arrhenius Temperature Correction
bdeb_data	Prepare Data for BDEB Models
bdeb_derived	Compute Derived Biological Quantities from the Posterior
bdeb_derived.bdeb_fit	Compute Derived Biological Quantities from the Posterior
bdeb_derived.default	Compute Derived Biological Quantities from the Posterior
bdeb_diagnose	MCMC Convergence Diagnostics
bdeb_ec50	Extract EC50 and NEC from a DEBtox Fit
bdeb_fit	Fit a BDEB Model via Hamiltonian Monte Carlo
bdeb_loo	LOO Cross-Validation for Model Comparison
bdeb_model	Specify a BDEB Model
bdeb_plots	Plot Methods for BDEB Objects
bdeb_ppc	Posterior Predictive Checks for BDEB Models
bdeb_predict	Predict from a BDEB Fit
bdeb_prior-methods	Methods for 'bdeb_prior' Objects
bdeb_prior_predictive	Prior Predictive Check
bdeb_session_info	Reproducibility Report
bdeb_tox	DEBtox Model Specification
coef.bdeb_fit	Extract Point Estimates from a BDEB Fit
confint.bdeb_fit	Posterior Credible Intervals for BDEB Model Parameters
debtox_growth	Simulated DEBtox Growth Data
debtox_simulate	Simulate DEBtox Growth Under Toxicant Exposure
deb_fluxes	Compute DEB Energy Fluxes
deb_simulate	Simulate DEB Growth Trajectory
eisenia_cd	Eisenia andrei Cadmium Toxicity Data (Van Gestel 1991)
eisenia_growth	Simulated Eisenia fetida Growth Data
eisenia_neuhauser	Eisenia fetida Growth Data (Neuhauser 1980)
fitted.bdeb_fit	Fitted Values from a BDEB Fit
folsomia_repro	Simulated Folsomia candida Reproduction Data
logLik.bdeb_fit	Log-Likelihood of a BDEB Fit
nobs.bdeb_fit	Number of Observations Used in a BDEB Fit
observation_models	Observation Model Specifications
obs_lognormal	Observation Model Specifications
obs_negbinom	Observation Model Specifications
obs_normal	Observation Model Specifications
obs_poisson	Observation Model Specifications
obs_student_t	Observation Model Specifications
plot.bdeb_data	Plot a BDEB Data Object
plot.bdeb_diagnostics	Plot Convergence Diagnostics
plot.bdeb_fit	Plot a BDEB Fit
plot.bdeb_model	Plot a BDEB Model Specification
plot.bdeb_ppc	Plot Posterior Predictive Checks
plot.bdeb_prediction	Plot Posterior Predictive Trajectories
plot.bdeb_prior	Methods for 'bdeb_prior' Objects
plot_dose_response	Plot DEBtox Dose-Response
predict.bdeb_fit	Predict from a BDEB Fit
print.bdeb_data	Print a BDEB Data Object
print.bdeb_diagnostics	Print a BDEB Diagnostics Report
print.bdeb_fit	Print a BDEB Fit
print.bdeb_model	Print a BDEB Model Specification
print.bdeb_ppc	Print a BDEB Posterior Predictive Check
print.bdeb_prediction	Print a BDEB Prediction
print.bdeb_prior	Methods for 'bdeb_prior' Objects
print.summary.bdeb_data	Summary of a BDEB Data Object
print.summary.bdeb_model	Summary of a BDEB Model Specification
print.summary.bdeb_prior	Methods for 'bdeb_prior' Objects
priors	Prior Distribution Specifications for BDEB Models
prior_beta	Prior Distribution Specifications for BDEB Models
prior_default	Default Priors for DEB Parameters
prior_exponential	Prior Distribution Specifications for BDEB Models
prior_halfcauchy	Prior Distribution Specifications for BDEB Models
prior_halfnormal	Prior Distribution Specifications for BDEB Models
prior_lognormal	Prior Distribution Specifications for BDEB Models
prior_normal	Prior Distribution Specifications for BDEB Models
prior_species	Species-Specific Priors from the AmP Collection
repro_to_intervals	Convert Cumulative Reproduction to Intervals
residuals.bdeb_fit	Residuals from a BDEB Fit
summary.bdeb_data	Summary of a BDEB Data Object
summary.bdeb_diagnostics	Compact Summary of a BDEB Diagnostics Report
summary.bdeb_fit	Posterior Summary for a BDEB Fit
summary.bdeb_model	Summary of a BDEB Model Specification
summary.bdeb_prediction	Tabulate Posterior Predictive Quantiles
summary.bdeb_prior	Methods for 'bdeb_prior' Objects
vcov.bdeb_fit	Posterior Covariance Matrix of BDEB Model Parameters