# Tools for Bayesian Analyses

## Documentation for package ‘BayesTools’ version 0.3.0

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

## Help Pages

A B C D E F G I J K L M P Q R S T U V W

BayesTools-package | BayesTools

## -- A --

add_column | Adds column to BayesTools table
as_marginal_inference | Model-average marginal posterior distributions and marginal Bayes factors based on BayesTools JAGS model via 'marginal_inference'
as_mixed_posteriors | Export BayesTools JAGS model posterior distribution as model-average posterior distributions via 'mix_posteriors'

## -- B --

BayesTools | BayesTools
BayesTools_ensemble_tables | Create BayesTools ensemble summary tables
BayesTools_model_tables | Create BayesTools model tables
bridgesampling_object | Create a 'bridgesampling' object

## -- C --

ccdf | Creates generics for common statistical functions
ccdf.prior | Elementary prior related functions
cdf | Creates generics for common statistical functions
cdf.prior | Elementary prior related functions
check_bool | Check input
check_char | Check input
check_input | Check input
check_int | Check input
check_list | Check input
check_real | Check input
compute_inference | Compute posterior probabilities and inclusion Bayes factors
contr.BayesTools | BayesTools Contrast Matrices
contr.independent | BayesTools Contrast Matrices
contr.meandif | BayesTools Contrast Matrices
contr.orthonormal | BayesTools Contrast Matrices

## -- D --

density.prior | Prior density
dmpoint | Multivariate point mass distribution
dpoint | Point mass distribution

## -- E --

ensemble_diagnostics_empty_table | Create BayesTools ensemble summary tables
ensemble_diagnostics_table | Create BayesTools ensemble summary tables
ensemble_estimates_empty_table | Create BayesTools ensemble summary tables
ensemble_estimates_table | Create BayesTools ensemble summary tables
ensemble_inference | Compute posterior probabilities and inclusion Bayes factors
ensemble_inference_empty_table | Create BayesTools ensemble summary tables
ensemble_inference_table | Create BayesTools ensemble summary tables
ensemble_summary_empty_table | Create BayesTools ensemble summary tables
ensemble_summary_table | Create BayesTools ensemble summary tables

## -- F --

format_BF | Format Bayes factor
format_parameter_names | Clean parameter names from JAGS
formula_add_intercept | Add an Intercept to a Formula

## -- G --

geom_prior | Add prior object to a ggplot
geom_prior_list | Add list of prior objects to a plot

## -- I --

inclusion_BF | Compute inclusion Bayes factors
interpret | Interpret ensemble inference and estimates
interpret2 | Interpret ensemble inference and estimates
interpret_records | Normalize structured interpretation sources
interpret_tables | Normalize structured interpretation sources
is.prior | Reports whether x is a a prior object
is.prior.discrete | Reports whether x is a a prior object
is.prior.factor | Reports whether x is a a prior object
is.prior.independent | Reports whether x is a a prior object
is.prior.meandif | Reports whether x is a a prior object
is.prior.mixture | Reports whether x is a a prior object
is.prior.none | Reports whether x is a a prior object
is.prior.orthonormal | Reports whether x is a a prior object
is.prior.PEESE | Reports whether x is a a prior object
is.prior.PET | Reports whether x is a a prior object
is.prior.point | Reports whether x is a a prior object
is.prior.simple | Reports whether x is a a prior object
is.prior.spike_and_slab | Reports whether x is a a prior object
is.prior.treatment | Reports whether x is a a prior object
is.prior.vector | Reports whether x is a a prior object
is.prior.weightfunction | Reports whether x is a a prior object
is_prior_bias | Reports whether x is a composed publication-bias prior
is_prior_phacking | Reports whether x is a p-hacking prior

## -- J --

JAGS_add_priors | Add 'JAGS' prior
JAGS_bridgesampling | Compute marginal likelihood of a 'JAGS' model
JAGS_bridgesampling_posterior | Prepare 'JAGS' posterior for 'bridgesampling'
JAGS_check_and_list | Check and list 'JAGS' fitting settings
JAGS_check_and_list_autofit_settings | Check and list 'JAGS' fitting settings
JAGS_check_and_list_fit_settings | Check and list 'JAGS' fitting settings
JAGS_check_convergence | Assess convergence of a runjags model
JAGS_diagnostics | Plot diagnostics of a 'JAGS' model
JAGS_diagnostics_autocorrelation | Plot diagnostics of a 'JAGS' model
JAGS_diagnostics_density | Plot diagnostics of a 'JAGS' model
JAGS_diagnostics_trace | Plot diagnostics of a 'JAGS' model
JAGS_estimates_empty_table | Create BayesTools model tables
JAGS_estimates_table | Create BayesTools model tables
JAGS_evaluate_formula | Evaluate JAGS formula using posterior samples
JAGS_extend | Fits a 'JAGS' model
JAGS_fit | Fits a 'JAGS' model
JAGS_formula | Create JAGS formula syntax and data object
JAGS_formula_design | Extract Fitted JAGS Formula Design Metadata
JAGS_get_inits | Create initial values for 'JAGS' model
JAGS_inference_empty_table | Create BayesTools model tables
JAGS_inference_table | Create BayesTools model tables
JAGS_marglik_parameters | Extract parameters for 'JAGS' priors
JAGS_marglik_parameters_formula | Extract parameters for 'JAGS' priors
JAGS_marglik_priors | Compute marginal likelihood for 'JAGS' priors
JAGS_marglik_priors_formula | Compute marginal likelihood for 'JAGS' priors
JAGS_parameter_names | Clean parameter names from JAGS
JAGS_summary_table | Create BayesTools model tables
JAGS_to_monitor | Create list of monitored parameters for 'JAGS' model

## -- K --

kitchen_rolls | Kitchen Rolls data from Wagenmakers et al. (2015) replication study.

## -- L --

lines.prior | Add prior object to a plot
lines_prior_list | Add list of prior objects to a plot
lpdf | Creates generics for common statistical functions
lpdf.prior | Elementary prior related functions

## -- M --

marginal_estimates_table | Create BayesTools ensemble summary tables
marginal_inference | Model-average marginal posterior distributions and marginal Bayes factors
marginal_posterior | Model-average marginal posterior distributions
mccdf | Creates generics for common statistical functions
mccdf.prior | Elementary prior related functions
mcdf | Creates generics for common statistical functions
mcdf.prior | Elementary prior related functions
mdone.sided | Weight functions
mdone.sided_fixed | Weight functions
mdtwo.sided | Weight functions
mdtwo.sided_fixed | Weight functions
mean.prior | Prior mean
mix_posteriors | Model-average posterior distributions
mlpdf | Creates generics for common statistical functions
mlpdf.prior | Elementary prior related functions
models_inference | Compute posterior probabilities and inclusion Bayes factors
model_summary_empty_table | Create BayesTools model tables
model_summary_table | Create BayesTools model tables
mpdf | Creates generics for common statistical functions
mpdf.prior | Elementary prior related functions
mpoint | Multivariate point mass distribution
mpone.sided | Weight functions
mpone.sided_fixed | Weight functions
mptwo.sided | Weight functions
mptwo.sided_fixed | Weight functions
mqone.sided | Weight functions
mqone.sided_fixed | Weight functions
mqtwo.sided | Weight functions
mqtwo.sided_fixed | Weight functions
mquant | Creates generics for common statistical functions
mquant.prior | Elementary prior related functions

## -- P --

parameter_names | Clean parameter names from JAGS
pdf | Creates generics for common statistical functions
pdf.prior | Elementary prior related functions
phack_alpha_from_pi_null | P-hacking calibration helpers
phack_backend_constants | P-hacking calibration helpers
phack_pi_null | P-hacking calibration helpers
plot.prior | Plots a prior object
plot_marginal | Plot samples from the marginal posterior distributions
plot_models | Plot estimates from models
plot_posterior | Plot samples from the mixed posterior distributions
plot_prior_list | Plot a list of prior distributions
plot_transformed_prior | Plot Transformed Prior Densities
pmpoint | Multivariate point mass distribution
point | Point mass distribution
ppoint | Point mass distribution
print.BayesTools_table | Print a BayesTools table
print.prior | Prints a prior object
prior | Creates a prior distribution
prior_bias | Creates a composed publication-bias prior
prior_factor | Creates a prior distribution for factors
prior_functions | Elementary prior related functions
prior_functions_methods | Creates generics for common statistical functions
prior_informed | Creates an informed prior distribution based on research
prior_informed_medicine_names | Names of medical subfields from the Cochrane database of systematic reviews
prior_mixture | Creates a mixture of prior distributions
prior_none | Creates a prior distribution
prior_PEESE | Creates a prior distribution for PET or PEESE models
prior_PET | Creates a prior distribution for PET or PEESE models
prior_phacking | Creates a prior distribution for a p-hacking selection kernel
prior_PP | Creates a prior distribution for PET or PEESE models
prior_spike_and_slab | Creates a spike and slab prior distribution
prior_weightfunction | Creates a prior distribution for a weight function

## -- Q --

qmpoint | Multivariate point mass distribution
qpoint | Point mass distribution
quant | Creates generics for common statistical functions
quant.prior | Elementary prior related functions

## -- R --

range.prior | Prior range
remove_column | Removes column to BayesTools table
rmpoint | Multivariate point mass distribution
rng | Creates generics for common statistical functions
rng.prior | Elementary prior related functions
rone.sided | Weight functions
rone.sided_fixed | Weight functions
rpoint | Point mass distribution
rtwo.sided | Weight functions
rtwo.sided_fixed | Weight functions
runjags_estimates_empty_table | Create BayesTools model tables
runjags_estimates_table | Create BayesTools model tables
runjags_inference_empty_table | Create BayesTools model tables
runjags_inference_table | Create BayesTools model tables

## -- S --

Savage_Dickey_BF | Compute Savage-Dickey inclusion Bayes factors
sd | Creates generic for sd function
sd.prior | Prior sd
selection_backend_spec | Compile selection priors for backend consumers
stan_estimates_table | Create BayesTools model tables

## -- T --

transform_factor_samples | Transform factor posterior samples into differences from the mean
transform_meandif_samples | Transform meandif posterior samples into differences from the mean
transform_orthonormal_samples | Transform orthonomal posterior samples into differences from the mean
transform_prior_samples | Transform prior samples to original scale
transform_scale_samples | Transform standardized posterior samples back to original scale

## -- U --

update.BayesTools_table | Updates BayesTools table

## -- V --

var | Creates generic for var function
var.prior | Prior var

## -- W --

weightfunctions | Weight functions
weightfunctions_mapping | Create coefficient mapping between multiple weightfunctions
wf_cumulative | Creates a prior distribution for a weight function
wf_fixed | Creates a prior distribution for a weight function
wf_independent | Creates a prior distribution for a weight function