Tools for Bayesian Analyses

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Documentation for package ‘BayesTools’ version 0.2.13

• 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

-- 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.orthonormal	Orthornomal contrast matrix

-- D --

density.prior	Prior density
dpoint	Point mass distribution

-- E --

ensemble_diagnostics_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_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.dummy	Reports whether x is a a prior object
is.prior.factor	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.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_table	Create BayesTools model tables
JAGS_evaluate_formula	Evaluate JAGS formula using posterior samples
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_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 --

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_table	Create BayesTools model tables
mpdf	Creates generics for common statistical functions
mpdf.prior	Elementary prior related functions
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_models	Plot estimates from models
plot_posterior	Plot samples from the mixed posterior distributions
plot_prior_list	Plot a list of prior distributions
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 --

qpoint	Point mass distribution
quant	Creates generics for common statistical functions
quant.prior	Elementary prior related functions

-- R --

range.prior	Prior range
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 --

sd	Creates generic for sd function
sd.prior	Prior sd
stan_estimates_table	Create BayesTools model tables

-- T --

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