# Estimate Bayesian Multilevel Models for Compositional Data

## Documentation for package ‘multilevelcoda’ version 1.3.3

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

## Help Pages

as.data.frame.complr | Extract amounts and compositions in conventional formats as data.frames, matrices, or arrays.
as.matrix.complr | Extract amounts and compositions in conventional formats as data.frames, matrices, or arrays.
bayes_factor.brmcoda | Bayes Factors from Marginal Likelihoods
brmcoda | Fit Bayesian generalised (non-)linear multilevel compositional model via full Bayesian inference
bsub | Between-person Simple Substitution
bsubmargin | Between-person Average Substitution
build.base | Build Base Pairwise Substitution
build.rg | Reference Grid for 'substitution' model.
build.sbp | Build Sequential Binary Partition
coef | Model Coefficients
coef.brmcoda | Model Coefficients
compilr | Indices from a (dataset of) Multilevel Composition(s) (deprecated.)
complr | Indices from a (dataset of) Multilevel Composition(s)
diagnostic-quantities-brmcoda | Extract Diagnostic Quantities from 'brmsfit' Models in 'brmcoda'
draws-index-brmcoda | Index 'brmcoda' objects
fitted | Expected Values of the Posterior Predictive Distribution
fitted.brmcoda | Expected Values of the Posterior Predictive Distribution
fixef | Population-Level Estimates
fixef.brmcoda | Population-Level Estimates
get-substitution | Substitution analysis helper functions
get_sbp | Extract Sequential Binary Partition from a 'complr' object.
get_variables | Extract variable names from an object
get_variables.brmcoda | Extract variable names from an object
get_variables.complr | Extract variable names from an object
is.brmcoda | Checks if argument is a 'brmcoda' object
is.complr | Checks if argument is a 'complr' object
is.substitution | Checks if argument is a 'substitution' object
launch_shinystan | Interface to 'shinystan'
launch_shinystan.brmcoda | Interface to 'shinystan'
log_posterior | Extract Diagnostic Quantities from 'brmsfit' Models in 'brmcoda'
log_posterior.brmcoda | Extract Diagnostic Quantities from 'brmsfit' Models in 'brmcoda'
loo | Efficient approximate leave-one-out cross-validation (LOO)
loo.brmcoda | Efficient approximate leave-one-out cross-validation (LOO)
mcmc_plot.brmcoda | MCMC Plots Implemented in 'bayesplot'
mcompd | Multilevel Compositional Data
mean.complr | Mean amounts and mean compositions presented in a 'complr' object.
model.frame.brmcoda | Extracting the Model Frame from a Formula or Fit from 'brmcoda' object
multilevelcoda_sim | multilevelcoda Simulation Study Results
nchains | Index 'brmcoda' objects
nchains.brmcoda | Index 'brmcoda' objects
ndraws | Index 'brmcoda' objects
ndraws.brmcoda | Index 'brmcoda' objects
neff_ratio | Extract Diagnostic Quantities from 'brmsfit' Models in 'brmcoda'
neff_ratio.brmcoda | Extract Diagnostic Quantities from 'brmsfit' Models in 'brmcoda'
niterations | Index 'brmcoda' objects
niterations.brmcoda | Index 'brmcoda' objects
nobs.brmcoda | Extract Number of Observations from 'brmcoda' object
nuts_params | Extract Diagnostic Quantities from 'brmsfit' Models in 'brmcoda'
nuts_params.brmcoda | Extract Diagnostic Quantities from 'brmsfit' Models in 'brmcoda'
nvariables | Index 'brmcoda' objects
nvariables.brmcoda | Index 'brmcoda' objects
pairs.brmcoda | Create a matrix of output plots from a 'brmcoda"s 'brmsfit' object
pivot_coord | Estimate pivot balance coordinates
pivot_coord_refit | Estimate pivot balance coordinates by refitting model.
pivot_coord_rotate | Estimate pivot balance coordinates by rotating sequential binary partition.
plot.brmcoda | Trace and Density Plots for MCMC Draws plot
plot.substitution | Substitution Plot
pp_check | Posterior Predictive Checks for 'brmcoda' Objects
pp_check.brmcoda | Posterior Predictive Checks for 'brmcoda' Objects
predict | Draws from the Posterior Predictive Distribution
predict.brmcoda | Draws from the Posterior Predictive Distribution
print.brmcoda | Print a Summary for a fitted 'brmsfit' model in a 'brmcoda' object
print.complr | Print a Summary for a 'complr' object
print.substitution | Print a Summary for a 'substitution' object
prior_summary.brmcoda | Extract Priors of a 'brmsfit' from a 'brmcoda' object
psub | Possible Pairwise Substitutions
ranef | Group-Level Estimates
ranef.brmcoda | Group-Level Estimates
residuals.brmcoda | Posterior Draws of Residuals/Predictive Errors
rhat | Extract Diagnostic Quantities from 'brmsfit' Models in 'brmcoda'
rhat.brmcoda | Extract Diagnostic Quantities from 'brmsfit' Models in 'brmcoda'
sbp | Sequential Binary Partition
sim | multilevelcoda Simulation Study results
sub | Simple Substitution
submargin | Average Substitution
substitution | Multilevel Compositional Substitution Analysis
summary.brmcoda | Create a Summary of a fitted 'brmsfit' model in a 'brmcoda' object
summary.complr | Create a Summary of a 'complr' object
summary.pivot_coord | Create a Summary of a fitted 'brmsfit' model from a 'pivot_coord' object
summary.substitution | Create a Summary of a Substitution Model represented by a 'substitution' object
update.brmcoda | Update 'brmcoda' models
var.complr | Variance of compositions presented in a 'complr' object.
VarCorr | Extract Variance and Correlation Components
VarCorr.brmcoda | Extract Variance and Correlation Components
variables | Index 'brmcoda' objects
variables.brmcoda | Index 'brmcoda' objects
vcov.brmcoda | Covariance and Correlation Matrix of Population-Level Effects
wsub | Within-person Simple Substitution
wsubmargin | Within-person Average Substitution