Class bayesmanecfit of models fitted with the brms package

Source: R/bayesmanecfit-class.R

Multiple models fitted with the bayesnec package are represented as a bayesmanecfit object, which contains the original brmsfit fitted objects, names of non-linear models that were fitted, model averaging WAIC stats, sample size, mean posterior no-effect toxicity values (NEC, NSEC or N(S)EC), mean model averaged predictions on the data scale, model averaged residuals, full posterior distribution of predicated values, and summary statistics of no-effect toxicity.

Details

See methods(class = "bayesmanecfit") for an overview of available methods.

Slots

mod_fits

A list of fitted model outputs of class prebayesnecfit for each of the fitted models.

success_models

A character vector indicating the name of the successfully fitted models.

mod_stats

A data.frame of model fit statistics.

sample_size

The size of the posterior sample. Information on the priors used in the model.

w_ne_posterior

The model-weighted posterior estimate of the no-effect toxicity estimate.

w_predicted_y

The model-weighted predicted values for the observed data.

w_residuals

Model-weighted residual values (i.e. observed - w_predicted_y).

w_pred_vals

A list containing model-weighted posterior predicted values based on the supplied resolution and x_range.

w_ne

The summary stats (median and 95% credibility intervals) of w_ne_posterior.

ne_type

A character vector indicating the type of no-effect toxicity estimate. Where the fitted model(s) are NEC models (threshold models, containing a step function) the no-effect estimate is a true no-effect-concentration (NEC, see Fox 2010). Where the fitted model(s) are smooth ECx models with no step function, the no-effect estimate is a no-significant-effect-concentration (NSEC, see Fisher and Fox 2023). In the case of a bayesmanecfit that contains a mixture of both NEC and ECx models, the no-effect estimate is a model averaged combination of the NEC and NSEC estimates, and is reported as the N(S)EC (see Fisher et al. 2023).

References

Fisher R, Barneche DR, Ricardo GF, Fox, DR (2024) An R Package for Concentration-Response Modeling and Estimation of Toxicity Metrics doi:10.18637/jss.v110.i05.

Fisher R, Fox DR (2023). Introducing the no significant effect concentration (NSEC).Environmental Toxicology and Chemistry, 42(9), 2019–2028. doi: 10.1002/etc.5610.

Fisher R, Fox DR, Negri AP, van Dam J, Flores F, Koppel D (2023). Methods for estimating no-effect toxicity concentrations in ecotoxicology. Integrated Environmental Assessment and Management. doi:10.1002/ieam.4809.

Fox DR (2010). A Bayesian Approach for Determining the No Effect Concentration and Hazardous Concentration in Ecotoxicology. Ecotoxicology and Environmental Safety, 73(2), 123–131. doi: 10.1016/j.ecoenv.2009.09.012.