# A Bayesian No-Effect- Concentration (NEC) Algorithm

## Documentation for package ‘bayesnec’ version 2.1.3.1

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

## Help Pages

bayesnec-package | The 'bayesnec' package.
"beta_binomial" | Custom beta-binomial family
+.bnecfit | "Add" multiple 'bnecfit' objects into one single 'bayesmanecfit' object containing Bayesian model averaging statistics.
amend | Amends an existing 'bayesmanecfit' object
autoplot | bayesnec standard ggplot2 plotting method
autoplot.bayesmanecfit | bayesnec standard ggplot2 plotting method
autoplot.bayesnecfit | bayesnec standard ggplot2 plotting method
average_estimates | average_estimates
bayesmanecfit | Class 'bayesmanecfit' of models fitted with the 'brms' package
bayesmanecfit-class | Class 'bayesmanecfit' of models fitted with the 'brms' package
bayesnec | The 'bayesnec' package.
bayesnecfit | Class 'bayesnecfit' of models fitted with the 'brms' package
bayesnecfit-class | Class 'bayesnecfit' of models fitted with the 'brms' package
bayesnecformula | Set up a model formula for use in 'bayesnec'
bnec | bnec
bnecfit | Class 'bnecfit' of models fitted with function 'bnec'
bnecfit-class | Class 'bnecfit' of models fitted with function 'bnec'
bnec_newdata | bnec_newdata
bnf | Set up a model formula for use in 'bayesnec'
c.bnecfit | Concatenate multiple 'bnecfit' objects into one single 'bayesmanecfit' object containing Bayesian model averaging statistics.
check_chains | Checking chain convergence
check_chains.bayesmanecfit | Checking chain convergence
check_chains.bayesnecfit | 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 object of class 'bayesnecfit' or 'bayesmanecfit'.
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 'prebayesnecfit' objects.
expand_nec | Extracts a range of statistics from a 'prebayesnecfit' object.
fitted | Generates mean posterior linear predictions for objects fitted by 'bnec'
fitted.bayesmanecfit | Generates mean posterior linear predictions for objects fitted by 'bnec'
fitted.bayesnecfit | Generates mean posterior linear predictions for objects fitted by 'bnec'
formula | Retrieve formulas from models fitted by 'bnec'
formula.bayesmanecfit | Retrieve formulas from models fitted by 'bnec'
formula.bayesnecfit | Retrieve formulas from models fitted by 'bnec'
ggbnec_data | Creates the data.frame for plotting with 'autoplot'.
herbicide | Herbicide phytotoxicity data
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 'manecsummary' of models fitted with the 'brms' package
manecsummary-class | Class 'manecsummary' of models fitted with the 'brms' package
manec_example | Example bayesmanecfit object
model.frame | Model.frame methods in bayesnec.
model.frame.bayesmanecfit | Model.frame methods in bayesnec.
model.frame.bayesnecfit | Model.frame methods in bayesnec.
model.frame.bayesnecformula | Model.frame methods in bayesnec.
models | models
nec | Extracts the predicted NEC value as desired from an object of class 'bayesnecfit' or 'bayesmanecfit'.
necsummary | Class 'necsummary' of models fitted with the 'brms' package
necsummary-class | Class 'necsummary' of models fitted with the 'brms' package
nec_data | Example data of non-linear decay
nsec | Extracts the predicted NSEC value as desired from an object of class 'bayesnecfit' or 'bayesmanecfit'.
plot | Generates a plot for objects fitted by 'bnec'
plot.bayesmanecfit | Generates a plot for objects fitted by 'bnec'
plot.bayesnecfit | Generates a plot for objects fitted by 'bnec'
posterior_epred | Generates posterior linear predictions for objects fitted by 'bnec'
posterior_epred.bayesmanecfit | Generates posterior linear predictions for objects fitted by 'bnec'
posterior_epred.bayesnecfit | Generates posterior linear predictions for objects fitted by 'bnec'
posterior_predict | Generates posterior predictions for objects fitted by 'bnec'
posterior_predict.bayesmanecfit | Generates posterior predictions for objects fitted by 'bnec'
posterior_predict.bayesnecfit | Generates posterior predictions for objects fitted by 'bnec'
prebayesnecfit | Class 'prebayesnecfit' of models fitted with the 'brms' package
prebayesnecfit-class | Class 'prebayesnecfit' of models fitted with the 'brms' package
predict | Generates mean posterior predictions for objects fitted by 'bnec'
predict.bayesmanecfit | Generates mean posterior predictions for objects fitted by 'bnec'
predict.bayesnecfit | Generates mean posterior predictions for objects fitted by 'bnec'
print | Prints a summary for objects fitted by 'bnec'
print.bayesmanecfit | Prints a summary for objects fitted by 'bnec'
print.bayesnecfit | Prints a summary for objects fitted by 'bnec'
pull_brmsfit | Extract and object of class 'brmsfit' from 'bayesnecfit' or 'bayesmanecfit'.
pull_brmsfit.bayesmanecfit | Extract and object of class 'brmsfit' from 'bayesnecfit' or 'bayesmanecfit'.
pull_brmsfit.bayesnecfit | Extract and object of class 'brmsfit' from 'bayesnecfit' or 'bayesmanecfit'.
pull_out | pull_out
pull_prior | pull_prior
rhat | Extract Diagnostic Quantities of 'brms' Models
rhat.bayesmanecfit | Extract Diagnostic Quantities of 'brms' Models
rhat.bayesnecfit | 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'
summary.bayesmanecfit | Generates a summary for objects fitted by 'bnec'
summary.bayesnecfit | Generates a summary for objects fitted by 'bnec'
update.bnecfit | Update an object of class 'bnecfit' as fitted by function 'bnec'.