summary: Generates a summary for objects fitted by 'bnec'

In bayesnec: A Bayesian No-Effect- Concentration (NEC) Algorithm

Generates a summary for objects fitted by bnec

Description

Generates a summary for objects fitted by bnec. object should be of class bayesnecfit or bayesmanecfit.

Usage

## S3 method for class 'bayesnecfit'
summary(object, ..., ecx = FALSE, ecx_vals = c(10, 50, 90))

## S3 method for class 'bayesmanecfit'
summary(object, ..., ecx = FALSE, ecx_vals = c(10, 50, 90))

Arguments

object	An object of class bayesnecfit or bayesmanecfit.
...	Unused.
ecx	Should summary ECx values be calculated? Defaults to FALSE.
ecx_vals	ECx targets (between 1 and 99). Only relevant if ecx = TRUE. If no value is specified by the user, returns calculations for EC10, EC50, and EC90.

Details

The summary method for both bayesnecfit and bayesmanecfit also returns a 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).

Value

A summary of the fitted model. In the case of a bayesnecfit object, the summary contains most of the original contents of a brmsfit object with the addition of an R2. In the case of a bayesmanecfit object, summary displays the family distribution information, model weights and averaging method, and Bayesian R2 estimates for each individual model. Warning messages are also printed to screen in case model fits are not satisfactory with regards to their Rhats.

References

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.

Examples

library(bayesnec)
summary(manec_example)
nec4param <- pull_out(manec_example, "nec4param")
summary(nec4param)

bayesnec documentation built on Sept. 26, 2023, 9:06 a.m.