Estimate Bayesian Multilevel Models for Compositional Data

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Documentation for package ‘multilevelcoda’ version 1.3.1

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

Help Pages

as.data.frame.complr	Extract Compositional Data from 'complr' object.
as.matrix.complr	Extract Compositional Data from 'complr' object.
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
bsubmargins	Between-person Average Substitution
build.basesub	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)
create_substitution	Constructor function for 'substitution' class.
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	Helper functions used only internally to estimate substitution model
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
print.summary.complr	Summary for a 'complr' 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
submargins	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
update.complr	Update 'complr'
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
wsubmargins	Within-person Average Substitution