Bchron is an R package that enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); Age-depth modelling as per the algorithm of Haslett and Parnell (2008); Relative sea level rate estimation incorporating time uncertainty in polynomial regression models; and non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM).
The official instruction manual with a detailed walkthrough for Bchron is available here as a vignette. The development version is available on GitHub. There is also a facility on the GitHub page to report bugs or request new features.
SIAR is a package for estimating dietary proportions from stable isotope-type data. If you would like to start using SIAR, then I suggest reading this excellent introduction document written by my collaborator Richard Inger.
Bclim is a package written (with James Sweeney and Thinh Doan) for palaeoclimate reconstruction from pollen data using stochastic volatility models whilst incorporating time uncertainty. Instructions for using the package are available here. This package is under active development so is likely to undergo rapid changes.