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Changelog

hamstr 0.8.1

  • Default prior value for acc_shape changed to 4 in light of calibration tests
  • Default values for prior on bioturbation ‘L’ changed following analyis of Solan et al. 2019 data. L_prior_mean = 7.5, L_prior_shape = 2.5
  • Update stan code to reflect new array syntax
  • Allow flat structure by setting K_factor > K_fine
  • Allow t-dist degrees of freedom to be passed as argument to BchronCalibrate from calibrate_14C_age and compare_14C_PDF
  • Change prior on ‘D’ from half-normal to Gamma with shape = 1.5, mean = 2
  • Displacement / depth uncertainty is now hierarchically modelled
  • Add ability to put a maximum length on a hiatus (in age units) - increases stability
  • Changes to plotting colours

hamstr 0.8.0

  • Hierarchical structure of sections changed so that child sections are offset from parents. This will eventually break backwards compatibility, for now if the old argument “K” is used, “K_fine” is calculated from “K”. The change improves the age models by reducing the influence of the positions of the breaks in the low resolution layers.

hamstr 0.7.2

  • 1 sigma quantiles now included in summaries
  • calibration function can handle offset uncertainties (e.g. reservoir age uncertainty)
  • Hamstr logo added to Readme

hamstr 0.7.1

  • patchwork used instead of ggpubr to reduce dependencies

hamstr 0.7.0

  • some little used arguments moved to hamstr_control and stan_sampler_args to simplify main function
  • default K structure changed to powers of 2

hamstr 0.6.2

  • ability to model hiatuses reimplemented

hamstr 0.6.1

  • Smoothing of accumulation rates in plots and output

hamstr 0.6.0

  • Ability added to model age-heterogeneity from bioturbation and its effect on age models.
  • Default plot changed to put diagnostic plots at the bottom.

hamstr 0.5.2

  • Minor change to the way acc_shape is adjusted to account for the number of hierarchical levels. acc_shape is now adjusted to control the shape of the gamma distributed alpha parameters, not the total variance. The difference is minor.

  • New methods to extract and plot accumulation rates

hamstr 0.5.1

New default hierarchical structure K based on default resolution of 1 cm (up to 1000 cm) and number of levels approximately equal to number of new child sections per parent per level.

hamstr 0.5.0

  • Significant update to behaviour when using hierarchical structure. The acc_shape parameter is now adjusted to control the total variance in the alpha parameters when there are multiple levels
  • Default mem_mean and mem_strength values updated to 0.5 and 10 to match updated defaults from bacon 2.5.1 onwards

hamstr 0.4.1

  • Methods written for generic functions plot and summary

hamstr 0.4

  • Package and main function renamed to hamstr (hierarchical accumulation models with Stan and R)
  • dev branch with hierarchical sections merged to master