set.initvals: Set initial values for the Bacon MCMC run.

In rbacon: Age-Depth Modelling using Bayesian Statistics

Set initial values for the Bacon MCMC run.

Description

Select initial values th0 and th1 for a Bacon MCMC run and write them into a file that can be read by Bacon.

Usage

set.initvals(set = get("info"), core = set$core, values = c(), click = 1)

Arguments

set	Detailed information of the current run, stored within this session's memory as variable info.
core	The name of the core for which a bacon.init file needs to be made
values	use this if you wish to provide the values (2 rows with starting age, accumulation rates for each model section, and memory parameter w).
click	use this if you wish to use the cursor to manually select age-depth points from the current graphic device. This is the default option. Right click once you have selected all datapoints, or provide the number of expected datapoints as a value (e.g., click=5).

Details

By default, the initial MCMC values th0 and th1 of the Bacon age-depth model (upper ages and accumulation rate for each model section) are estimated randomly. Since version 3.1.0, these starting values can also be provided in a file with extension _bacon.init, placed within the core's folder. This file will need to have two rows, each for one of the two initial sets of parameters required (the t-walk requires two starting estimates for all MCMC parameters). If such a file is found (and correctly formatted), Bacon will use the values within this file as starting points for the MCMC run.

Value

A .bacon.init file

Author(s)

Maarten Blaauw, J. Andres Christen

rbacon documentation built on Sept. 30, 2024, 9:40 a.m.