Bayesian methods including penalized B-splines for fitting bomb radiocarbon reference series and assessing aging bias
About
The BayesianBombCarbon R package provides Bayesian models in stan to estimate ∆14C reference series, estimate aging bias of samples with unvalidated formation/birth years given a reference series, and assess if the aging of samples are valid via hypothesis testing. Currently, reference series are fit using a Bayesian penalized B-spline with a random walk prior to control the degree of smoothing, first presented in Chamberlin et al. 2023.
Installing the package
The development version of BayesianBombCarbon can be installed from GitHub as shown below. Please note that the package is still in early development and may be subject to breaking changes.
remotes::install_github("zsiders/BayesianBombCarbon", dependencies = TRUE)BayesianBombCarbon also requires CmdStan to be installed on your system. This can be done using the install_cmdstan() function from cmdstanr. If you experience any problems installing CmdStan, see the cmdstanr vignette for help.
cmdstanr::check_cmdstan_toolchain()
cmdstanr::install_cmdstan(cores = 2) # use more cores to speed upThe stan models used by BayesianBombCarbon need to be compiled for your device. This is only necessary once - after installing or updating the package - and can be done using the bombcarbon_compile() function.
BayesianBombCarbon::bombcarbon_compile()If the models are not successfully compiled, please ensure that cmdstan is properly set up and try updating it to a newer version using cmdstanr::install_cmdstan(). If the problem persists, please run BayesianBombCarbon::bombcarbon_compile(verbose = TRUE) and post the output in a new issue on GitHub, along with your cmdstanr::cmdstan_version().
