Bayesian Inference Using 'RTMB'

Documentation for package ‘BayesRTMB’ version 0.1.1

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-- A --

Automatic Differentiation Variational Inference (ADVI)

-- B --

bayes_factor	Calculate Bayes Factor
beverage	Beverage Preference Data
BigFive	Big Five Personality Traits Data

-- C --

Classic_Fit	Classic fit object
conditional_effects	Calculate Conditional Effects
conditional_effects.mcmc_fit	Calculate conditional effects for MCMC fit objects

-- D --

debate	Debate Simulation Data
Dim	Define parameter dimensions and types
distance	Euclidean distance
distributions	Probability Distributions for RTMB Models

-- E --

ess_basic	Basic Effective Sample Size for a single chain or pooled chains
ess_bulk	Calculate Bulk Effective Sample Size
ess_tail95	Calculate Tail Effective Sample Size (at 2.5% and 97.5% quantiles)

-- F --

fabs	Smooth absolute value function

-- G --

gaussian_process_lpdf	Gaussian Process Log-Density (Squared Exponential Kernel)
generate_random_init	Generate Random Initial Values

-- I --

inv_logit	Inverse logit function
item_curve	Calculate Item Response Curve / Category Response Curve
item_curve.RTMB_Fit_Base	Item Response Curve for RTMB_Fit_Base
item_info	Calculate Item Information Function
item_info.RTMB_Fit_Base	Item Information Function for RTMB_Fit_Base

-- L --

log1m	Log of one minus x
log1m_exp	Log of one minus exponential of x
log1p_exp	Log of one plus exponential of x
logit	Logit function
log_det_chol	Log determinant of a Cholesky factor
log_mix	Log mixture of two probabilities
log_softmax	Log-softmax function
log_sum_exp	Log-sum-exp function
log_sum_exp_matrix	Log-sum-exp function for matrices (row-wise)
lsmeans	Least Squares Means (Marginal Means)

-- M --

make_bw_from_ydif	Make Best and Worst Responses from Best-Worst Pair Indices
make_glmer_re_terms	Prepare GLMM Formula Components
make_glmer_Z_matrix	Reconstruct an Observation-Level Random-Effect Design Matrix
make_init_mdu	Create Initial Values for Multidimensional Unfolding
make_ydif_from_bw	Make Best-Worst Pair Indices from Best and Worst Responses
map_est	Maximum A Posteriori (MAP) Estimate
MAP_Fit	MAP fit object
math_functions	Mathematical and Matrix Utility Functions for RTMB Models
MCMC_Fit	MCMC fit object
model_code	Model Code Wrapper for RTMB

-- P --

parameters_code	Code block for parameter definitions
parameter_types	Parameter Types and Constraints in RTMB Models
plot.ce_rtmb	Plot method for ce_rtmb class (Base R)
plot.rtmb_lsmeans	Plot marginal means with error bars
plot_acf	Plot autocorrelation for one variable across chains
plot_conditional_effects	Plot conditional effects
plot_dens	Plot posterior densities for MCMC samples
plot_forest	Plot parameter estimates and credible intervals (Forest Plot)
plot_item_curve	Plot item/category response curves
plot_item_info	Plot item information functions
plot_lsmeans	Plot least-squares marginal means
plot_mdu	Plot Multidimensional Unfolding Configuration
plot_pairs	Plot pairs for posterior samples
plot_test_info	Plot test information function
plot_trace	Plot MCMC trace plots
print.bayes_factor	Print method for bayes_factor objects
print.bayes_factor_rtmb	Print method for bayes_factor_rtmb objects
print.ce_rtmb	Print method for ce_rtmb class (automatically calls plot)
print.ce_simple	Print simple effects
print.summary_BayesRTMB	print for summary_BayesRTMB class
prior_flat	Specify a flat prior
prior_jzs	Specify a JZS (Jeffrey-Zellner-Siow) prior for t-tests
prior_normal	Specify normal/exponential priors for MAP and Bayesian inference
prior_rhs	Specify a Regularized Horseshoe prior for continuous shrinkage
prior_ssp	Specify a Spike-and-Slab prior for variable selection
prior_uniform	Specify a flat prior
prior_weak	Specify a weakly informative prior

-- Q --

quad_form_chol	Quadratic form using a Cholesky factor
quad_form_diag	Quadratic form with a diagonal matrix
quantile95	Calculate 95% Quantiles

-- R --

read_mcmc_csv	Restore MCMC Fit from CSV
restore_bw_from_ydif	Make Best and Worst Responses from Best-Worst Pair Indices
rtmb_code	Define an RTMB Model with Stan-like Syntax
rtmb_corr	Fit a Correlation Model using RTMB
rtmb_fa	RTMB-based Factor Analysis Wrapper
RTMB_Fit_Base	Base class for RTMB Fit objects
rtmb_glm	RTMB-based GLM wrapper function (no random effects)
rtmb_glmer	RTMB-based GLMM wrapper function
rtmb_irt	RTMB-based IRT (Item Response Theory) Wrapper
rtmb_lm	RTMB-based Linear Regression wrapper function
rtmb_lmer	RTMB-based Linear Mixed Model (LMM) wrapper function
rtmb_loglinear	RTMB-based Log-linear analysis (Poisson regression)
rtmb_lrt	Fit a Latent Rank Theory (LRT) Model
rtmb_mdu	RTMB-based Multidimensional Unfolding Wrapper
rtmb_mediation	RTMB-based Mediation Analysis Wrapper
rtmb_mixture	Mixture Model Wrapper for RTMB
RTMB_Model	RTMB model object
rtmb_model	Create an RTMB_Model Object
RTMB_Model-class	RTMB model object
rtmb_syntax	Guidelines for Writing RTMB-Compatible Code
rtmb_table	RTMB-based Contingency Table Analysis (Chi-squared Test)
rtmb_ttest	RTMB-based Bayesian two-sample t-test wrapper function
rtmb_wrappers	Common Features and Arguments of RTMB Wrapper Functions
r_hat	Calculate Rank-normalized Split-R-hat

-- S --

safe_rtmb_model	Safe RTMB model construction (with error message translation)
simple_effects	Calculate Simple Effects
simple_effects.mcmc_fit	Simple effects for MCMC fit objects
softmax	Softmax function
sort_loadings	Sort and display factor loadings neatly
squared_distance	Squared Euclidean distance
stz_basis	stz basis function
summary.ce_rtmb	Summary method for ce_rtmb class
sum_to_zero	Sum-to-zero transformation

-- T --

test_info	Calculate Test Information Function
to_centered_matrix	Vector to centered matrix (RTMB compatible)
to_centered_tri	Vector to centered triangular matrix (RTMB compatible)
to_long	Convert Wide Data to Long Format
to_lower_tri	Vector to lower triangular matrix (RTMB compatible)
to_wide	Convert Long Data to Wide Format
training	Social Skills Training Data
transform_code	Transformed Code Wrapper for RTMB

-- V --

validate_data	Pre-validation of data and parameters
VB_Fit	VB fit object