bayesnec2.1.3.0 package

A Bayesian No-Effect- Concentration (NEC) Algorithm

bayesmanecfit-class

Class bayesmanecfit of models fitted with the brms package

pull_brmsfit

Extract and object of class brmsfit from bayesnecfit or `bayesmane...

amend

Amends an existing bayesmanecfit object

autoplot

bayesnec standard ggplot2 plotting method

average_estimates

average_estimates

bayesnec-package

The 'bayesnec' package.

bayesnecfit-class

Class bayesnecfit of models fitted with the brms package

bayesnecformula

Set up a model formula for use in bayesnec

bnec_newdata

bnec_newdata

bnec

bnec

bnecfit-class

Class bnecfit of models fitted with function bnec

c.bnecfit

Concatenate multiple bnecfit objects into one single bayesmanecfit...

check_chains

Checking chain convergence

check_formula

Check if input model formula is appropriate to use with bayesnec

check_priors

Plots the prior and posterior parameter probability densities from an ...

compare_estimates

compare_estimates

compare_fitted

compare_fitted

compare_posterior

compare_posterior

dispersion

Posterior dispersion

ecx

Extracts the predicted ECx value

expand_manec

Extracts a range of statistics from a list of prebayesnecfitobjects.

expand_nec

Extracts a range of statistics from a prebayesnecfit object.

fitted

Generates mean posterior linear predictions for objects fitted by `bne...

formula

Retrieve formulas from models fitted by bnec

ggbnec_data

Creates the data.frame for plotting with autoplot.

is_manecsummary

Checks if argument is a manecsummary object

is_necsummary

Checks if argument is a necsummary object

make_brmsformula

Expose the final brmsformula

manecsummary-class

Class manecsummary of models fitted with the brms package

model.frame

Model.frame methods in bayesnec.

models

models

nec

Extracts the predicted NEC value as desired from an object of class `b...

necsummary-class

Class necsummary of models fitted with the brms package

nsec

Extracts the predicted NSEC value as desired from an object of class `...

plot

Generates a plot for objects fitted by bnec

plus-.bnecfit

"Add" multiple bnecfit objects into one single bayesmanecfit objec...

posterior_epred

Generates posterior linear predictions for objects fitted by bnec

posterior_predict

Generates posterior predictions for objects fitted by bnec

prebayesnecfit-class

Class prebayesnecfit of models fitted with the brms package

predict

Generates mean posterior predictions for objects fitted by bnec

print

Prints a summary for objects fitted by bnec

pull_out

pull_out

pull_prior

pull_prior

quote-beta_binomial-quote

Custom beta-binomial family

rhat

Extract Diagnostic Quantities of 'brms' Models

sample_priors

sample_priors

show_params

show_params

step

step

summary

Generates a summary for objects fitted by bnec

update.bnecfit

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>).

  • Maintainer: Rebecca Fisher
  • License: GPL-2
  • Last published: 2024-08-19