A Bayesian No-Effect- Concentration (NEC) Algorithm
Class bayesmanecfit
of models fitted with the brms
package
Extract and object of class brmsfit
from bayesnecfit
or `bayesmane...
Amends an existing bayesmanecfit
object
bayesnec standard ggplot2 plotting method
average_estimates
The 'bayesnec' package.
Class bayesnecfit
of models fitted with the brms
package
Set up a model formula for use in bayesnec
bnec_newdata
bnec
Class bnecfit
of models fitted with function bnec
Concatenate multiple bnecfit
objects into one single bayesmanecfit
...
Checking chain convergence
Check if input model formula is appropriate to use with bayesnec
Plots the prior and posterior parameter probability densities from an ...
compare_estimates
compare_fitted
compare_posterior
Posterior dispersion
Extracts the predicted ECx value
Extracts a range of statistics from a list of prebayesnecfit
objects.
Extracts a range of statistics from a prebayesnecfit
object.
Generates mean posterior linear predictions for objects fitted by `bne...
Retrieve formulas from models fitted by bnec
Creates the data.frame for plotting with autoplot
.
Checks if argument is a manecsummary
object
Checks if argument is a necsummary
object
Expose the final brmsformula
Class manecsummary
of models fitted with the brms
package
Model.frame methods in bayesnec.
models
Extracts the predicted NEC value as desired from an object of class `b...
Class necsummary
of models fitted with the brms
package
Extracts the predicted NSEC value as desired from an object of class `...
Generates a plot for objects fitted by bnec
"Add" multiple bnecfit
objects into one single bayesmanecfit
objec...
Generates posterior linear predictions for objects fitted by bnec
Generates posterior predictions for objects fitted by bnec
Class prebayesnecfit
of models fitted with the brms
package
Generates mean posterior predictions for objects fitted by bnec
Prints a summary for objects fitted by bnec
pull_out
pull_prior
Custom beta-binomial family
Extract Diagnostic Quantities of 'brms' Models
sample_priors
show_params
step
Generates a summary for objects fitted by bnec
Update an object of class bnecfit
as fitted by function bnec
.
Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).