Bayesian Transition Analysis with Markov Chain Monte Carlo

Provides Bayesian age estimation for bioarchaeological skeletal data using ordinal probit regression models implemented in 'JAGS' and 'NIMBLE'. The package is designed to handle multiple ordinal traits of adult individuals and incorporates a Gompertz prior on age to reflect population-level mortality. It accounts for estimation uncertainties and supports full customization of model parameters and Markov Chain Monte Carlo settings. For more details see Müller-Scheeßel et al. (2026) .

baytaAAR

baytaAAR provides Bayesian age estimation for bioarchaeological skeletal data of human adults using ordinal probit regression models implemented in JAGS and NIMBLE. The package is designed to handle multiple ordinal traits and incorporates a Gompertz prior on age to reflect population-level mortality trends. It accounts for estimation uncertainties and supports full customization of model parameters and MCMC settings.

For further information, please have a look at the documentation with several vignettes.

How to cite this package

You can cite this package like this "we estimated age-at-death of human adults with the baytaAAR R-package (Müller-Scheeßel & Rinne 2026)". Here is the full bibliographic reference to include in your reference list (don't forget to update the 'last accessed' date):

N. Müller-Scheeßel & C. Rinne (2026). baytaAAR: Bayesian Transition Analysis with Markov Chain Monte Carlo (vers. 1.0.0). https://github.com/ISAAKiel/baytaAAR.

Installation

baytaAAR is not yet available on CRAN but you can install the development version with:

if(!require('remotes')) install.packages('remotes')
remotes::install_github('ISAAKiel/baytaAAR', build_vignettes = TRUE)

Licence

baytaAAR is released under the GNU General Public Licence, version 3. Comments and feedback are welcome, as are code contributions.