A Bayesian No-Effect- Concentration (NEC) Algorithm


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Documentation for package ‘bayesnec’ version 2.1.1.0

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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
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'.