hamstr_control: Return a List of hamstr Control Arguments
In andrewdolman/baconr: Hierarchical Accumulation Modelling with Stan and R

hamstr_control

R Documentation

Return a List of hamstr Control Arguments

Description

Returns a list arguments to pass to hamstr_control which may be useful for debugging or development

Usage

hamstr_control(
  scale_R = TRUE,
  nu = 6,
  scale_shape = TRUE,
  smooth_s = FALSE,
  inflate_errors = FALSE,
  infl_sigma_sd = NULL,
  infl_shape_shape = 1,
  infl_shape_mean = 1
)

Arguments

`scale_R`	logical: Scale AR1 coefficient by delta_c (as in Bacon) or not. Defaults to TRUE.
`nu`	degrees of freedom for the Student-t distributed error model. Defaults to 6, which is equivalent to the default parametrisation of t.a=3, t.b=4 in Bacon 2.2. Set to a high number to approximate a Gaussian error model, (nu = 100 should do it).
`scale_shape`	scale the shape parameter according to the number of hierarchical levels, to control the total variance of the alpha innovations. This defaults to TRUE as of hamstr verion 0.5.
`smooth_s`	smooth the sedimentation rate used to calculate additional error from bioturbation by taking a mean across nearby sections
`inflate_errors`	logical: If set to TRUE, observation errors are inflated so that data are consistent with a gamma AR1 age-depth model. This is an experimental feature under active development. Defaults to FALSE.
`infl_sigma_sd`	hyperparameter: sets the standard deviation of the half-normal prior on the mean of the additional error terms. Defaults to 10 times the mean observation error in obs_err.
`infl_shape_shape`, `infl_shape_mean`	hyperparameters: parametrises the gamma prior on the shape of the distribution of the additional error terms. Default to 1, 1.