# Bayesian analysis of longitudinal metabolomics data

## Documentation for package ‘MetaboDynamics’ version 2.0.2

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

## Help Pages

cluster_dynamics | cluster dynamics profiles of metabolites
compare_dynamics | Comparison of metabolite dynamics clusters under different experimental conditions
compare_metabolites | Comparison of metabolite sets between dynamics clusters of different experimental conditions
diagnostics_dynamics | Extracts diagnostic criteria from numeric fit of Bayesian model of dynamics
estimates_dynamics | Extracts parameter estimates from numeric fit of Bayesian model of dynamics
fit_dynamics_model | Fits dynamics model
get_ORA_annotations | Retrieve background and annotation information for over-representation analysis (ORA)
heatmap_dynamics | plot bubble heatmap from the numerical fit of compare_dynamics()
heatmap_metabolites | plot heatmap from comparison of metabolite composition compare_metabolites()
IDs | KEGG ID mapping of metabolites in data set longitudinalMetabolomics
longitudinalMetabolomics | A simulated data set of longitudinal concentration tables of metabolites.
longitudinalMetabolomics_df | A simulated data set of longitudinal concentration tables of metabolites. In contrast to "longitudinalMetabolomics" this dataset is in data frame format. It was simulated with a different seed compared to longitudinalMetabolomics so the results can deviate.
metabolite_modules | KEGG Query Results of experimental metabolites
modules_compounds | Background KEGG Query Results Of Functional Modules
ORA_hypergeometric | OverRepresentationAnalysis with a hypergeometric model
plot_cluster | visualize clustering solution of cluster_dynamics()
plot_diagnostics | Plot diagnostic criteria of numerical fit of Bayesian model of dynamics
plot_estimates | Visualization of parameter estimates from numeric fit of Bayesian model of dynamics
plot_ORA | Plot results of over-representation analysis with ORA_hypergeometric()
plot_PPC | Plots posterior predictive check of numerical fit of Bayesian dynamics model