synchronization.default: Default variables in synchronization

In eirikmn/bremla: Bayesian Regression Modeling of Layer-Counted Archives

Default variables in synchronization

Description

Sets the default variables in the list synchronization used to specify the tie-points used for synchronization. The list contains the following arguments:

• locations Numeric describing the locations of the tie-points. Default value is here NULL meaning that this has to be given by the user.

• locations_unit Character giving which axis the locations are given. Can be "depth" (default), "age" or "index".

• samples data.frame giving pre-computed samples. This should be used if you want to provide the sampled tie-points yourself. nrow must correspond to the number of samples and ncol to the number of tie-points. Default value is NULL.

• method Character giving which method should be used to generate tie-points. Currently supported: "adolphi" (default) uses tie-point distributions given by Adolphi et al. (2018) and Muscheler et al. (2020), "normal" uses a normal distribution with mean and standard deviations supplied by user (TODO). If "adolphi" is used, then locations, locations_unit is filled out accordingly.

• x.ref Numeric giving a reference for the x-axis (given by locations_unit) that will be included in future plot.

• params List object containing parameters for parametric tie-point distributions. for method="gauss" the list has two numeric objects called mean and sd representing the mean and standard deviation for each tie point, respectively.

• agedisc List containing arguments relating to the age-discrepancy model. If NULL, no age-discrepancy model is assigned and the tie-points are treated as realizations of the posterior predictive of the layer model.

  model

  Age-discrepancy model. Currently, only 2nd order random walk model (rw2) is supported.

  method

  How the age-discrepancy model should be fitted. Currently, only INLA is supported.

  options

  A set of options passed into the fitting procedure. For method=INLA, this sets the additional arguments for the inla function.

  hyperprior

  List corresponding to the hyper object in INLA's f function which specifies the priors of the hyperparameters. Default is NULL which sets INLA's default priors.

  stepsizes

  If INLA struggles to converge, attempt again with different stepsizes according to stepsizes. default value is 0.005.

Usage

synchronization.default()

Value

Returns a list including default values for all variables in synchronization.

Author(s)

Eirik Myrvoll-Nilsen, [e-mail]

See Also

bremla, tiepointsimmer, bremla_synchronized_simulation,set.options

eirikmn/bremla documentation built on Jan. 25, 2025, 4:41 a.m.