Tools for Bayesian Analyses

---

Documentation for package ‘BayesTools’ version 0.2.17

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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

BayesTools-package

BayesTools

-- A --

add_column

Adds column to BayesTools table

-- 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.independent	Independent contrast matrix
contr.meandif	Mean difference contrast matrix
contr.orthonormal	Orthornomal contrast matrix

-- 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

-- 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
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.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

-- 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_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
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
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_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_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_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
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

-- V --

var	Creates generic for var function
var.prior	Prior var

-- W --

weightfunctions	Weight functions
weightfunctions_mapping	Create coefficient mapping between multiple weightfunctions

-- misc --

_PACKAGE

BayesTools