climate_histories: Create Bclim climate_histories

Description Usage Arguments Details Value References See Also

Description

Runs a number of algorithms to create climate histories for a given set of slice clouds (from slice_clouds and a set of chronologies. For examples why not see the wonderful Bclim vignette (available at https://cran.r-project.org/web/packages/Bclim/index.html) and the author's personal webpage (https://maths.ucd.ie/parnell)?

Usage

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climate_histories(slice_clouds, chronology, time_grid, n_mix = 10,
  mix_warnings = FALSE, n_chron = 2000, keep_parameters = TRUE,
  control_mcmc = list(iterations = 1e+05, burnin = 20000, thinby = 40, report
  = 100), control_chains = list(v_mh_sd = 2, phi1_mh_sd = 1, phi2_mh_sd = 10,
  v_start = statmod::rinvgauss(slice_clouds$n_slices - 1, 2, 1), Z_start =
  sample(1:n_mix, slice_clouds$n_slices, replace = TRUE), phi1_start = rep(3,
  slice_clouds$n_dimensions), phi2_start = rep(20, slice_clouds$n_dimensions)),
  control_priors = list(phi1_dl_mean = rep(1.275, slice_clouds$n_dimensions),
  phi1_dl_sd = rep(0.076, slice_clouds$n_dimensions), phi2_dl_mean = rep(4.231,
  slice_clouds$n_dimensions), phi2dl_sd = rep(0.271,
  slice_clouds$n_dimensions)))

Arguments

slice_clouds

An object of class slice_clouds obtained from slice_clouds

chronology

A set of chronologies given as a matrix. These should be provided in thousands of years before present. See details below

time_grid

The time grid on which to create the climate histories

n_mix

The number of mixture components for the Mclust mixture algorithm

mix_warnings

Whether to display warnings related to the mixture algorithm

n_chron

The number of chronologies to use

keep_parameters

Whether to keep latent parameters or not. Useful for convergence checking so default is TRUE

control_mcmc

A list containing elements that control the MCMC, including the number of iterations, the size of the burn-in period, the amount to thinby, and how often for the algorithm to report its progress

control_chains

A list containing elements that control the starting values of the parameters (v_start, Z_start, phi1_start and phi2_start) and the Metropolis-Hastings proposal standard deviation for v, phi1 and phi2

control_priors

A list containing the prior parameters for the volatilities, given by phi1 and phi2, both of which should be the log-mean and log-sd of the log-normal distribution. The values provided here are for the GISP2 ice core for the period 0 to 10k years BP

Details

This function takes the slice_clouds produced by slice_clouds uses a set of algorithms to produce climate histories on the provided time grid. The full details are in the paper referenced below. The options listed above allow quite a detailed level of control over the behaviour of the algorithm, and convergence should be checked using suitable means (see e.g. the R package boa or coda).

One of the key inputs to this function is a chronology. This should be a matrix of n_chron by n_slices containing sample chronologies as produced by, e.g. the R package Bchron. These are used by the climate_histories function to take account of chronological uncertainty. In the (unlikely) event that there is no chronological uncertainty, the rows of the chronologies can be identical.

Value

A list object with the following elements

References

Parnell, A. C., et al. (2015), Bayesian inference for palaeoclimate with time uncertainty and stochastic volatility. Journal of the Royal Statistical Society: Series C (Applied Statistics), 64: 115–138.

See Also

slice_clouds for producing the input for this function. See plot.climate_histories and summary.climate_histories for plotting and summary details


Bclim documentation built on May 2, 2019, 12:38 a.m.