Package: multilevelcoda 1.3.1

multilevelcoda: Estimate Bayesian Multilevel Models for Compositional Data

Implement Bayesian Multilevel Modelling for compositional data in a multilevel framework. Compute multilevel compositional data and Isometric log ratio (ILR) at between and within-person levels, fit Bayesian multilevel models for compositional predictors and outcomes, and run post-hoc analyses such as isotemporal substitution models. References: Le, Stanford, Dumuid, and Wiley (2024) <doi:10.48550/arXiv.2405.03985>, Le, Dumuid, Stanford, and Wiley (2024) <doi:10.48550/arXiv.2411.12407>.

Authors:Flora Le [aut, cre], Joshua F. Wiley [aut]

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multilevelcoda.pdf |multilevelcoda.html✨
multilevelcoda/json (API)
NEWS

# Install 'multilevelcoda' in R:

install.packages('multilevelcoda', repos = c('https://florale.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/florale/multilevelcoda/issues

Datasets:

mcompd - Multilevel Compositional Data
psub - Possible Pairwise Substitutions
sbp - Sequential Binary Partition
sim - Multilevelcoda Simulation Study results

On CRAN:

bayesian-inference compositional-data-analysis multilevel-models multilevelcoda

8.31 score 13 stars 120 scripts 336 downloads 23 exports 151 dependencies

Last updated 5 hours agofrom:518aeb117a. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 23 2024
R-4.5-win	OK	Nov 23 2024
R-4.5-linux	OK	Nov 23 2024
R-4.4-win	OK	Nov 23 2024
R-4.4-mac	OK	Nov 23 2024
R-4.3-win	OK	Nov 23 2024
R-4.3-mac	OK	Nov 23 2024

Exports:brmcoda bsub bsubmargins build.basesub build.rg build.sbp compilr complr fixef is.brmcoda is.complr is.substitution multilevelcoda_sim pivot_coord pivot_coord_refit pivot_coord_rotate ranef sub submargins substitution VarCorr wsub wsubmargins

Dependencies:abind askpass backports base64enc bayesm bayesplot bayestestR BH bridgesampling brms Brobdingnag bslib cachem callr checkmate cli coda codetools colorspace colourpicker commonmark compositions cpp11 crayon crosstalk curl data.table datawizard DEoptimR desc digest distributional doFuture dplyr DT dygraphs emmeans estimability evaluate extrafont extrafontdb extraoperators fansi farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver foreach fs future future.apply gdtools generics ggplot2 ggridges globals glue gridExtra gtable gtools highr hrbrthemes htmltools htmlwidgets httpuv httr igraph inline insight isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle listenv loo magrittr markdown MASS Matrix matrixStats memoise mgcv mime miniUI munsell mvtnorm nleqslv nlme numDeriv openssl parallelly pillar pkgbuild pkgconfig plotly plyr posterior processx promises ps purrr QuickJSR R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel reshape2 rlang rmarkdown robustbase rstan rstantools Rttf2pt1 sass scales shiny shinyjs shinystan shinythemes sourcetools StanHeaders stringi stringr sys systemfonts tensorA threejs tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun xtable xts yaml zoo

Compositional Substitution Multilevel Analysis

Rendered fromD-substitution.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-06-09
Started: 2024-05-26

Improving MCMC Sampling for Bayesian Compositional Multilevel Models

Flora Le

Rendered fromE-simmodel-diag.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-11-18
Started: 2023-08-08

Introduction to Bayesian Compositional Multilevel Modelling

Rendered fromA-introduction.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-05-26
Started: 2023-07-27

Multilevel Model with Compositional Outcomes

Rendered fromC-composition-MMLM.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-05-26
Started: 2023-08-04

Multilevel Models with Compositional Predictors

Rendered fromB-composition-MLM.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-06-09
Started: 2023-08-04

Citation

Development and contributors

Readme and manuals

Help Manual

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