We estimate microbial abundances by combining compositional data and observed absolute abundance data and modeling efficiencies. We use Stan to fit the chosen hierarchical model to the data: this may result in differences in speed and accuracy between the hierarchical models, depending on the dataset and initial values chosen. Please read any warning messages returned by the algorithm carefully, as these can help diagnose convergence issues. We return credible intervals and point estimates for the true concentrations, and point estimates and prediction intervals for the unobserved absolute abundances.
The preprint: https://www.biorxiv.org/content/10.1101/761486v1 Other useful links:
Stan Development Team (2018). RStan: the R interface to Stan. R package version 2.17.4. http://mc-stan.org