Nested Adaptive Metropolis-Hastings Sampler — monty_sampler_nested

Create a nested adaptive Metropolis-Hastings sampler, which extends the adaptive sampler monty_sampler_adaptive, tuning the variance covariance matrices for proposal for the separable sections of a nested model (vs the simple nested random walk sampler monty_sampler_random_walk). This sampler requires that models support the has_parameter_groups property.

Usage

monty_sampler_nested_adaptive(
  initial_vcv,
  initial_vcv_weight = 1000,
  initial_scaling = 1,
  initial_scaling_weight = NULL,
  min_scaling = 0,
  scaling_increment = NULL,
  log_scaling_update = TRUE,
  acceptance_target = 0.234,
  forget_rate = 0.2,
  forget_end = Inf,
  adapt_end = Inf,
  pre_diminish = 0,
  boundaries = "reflect"
)

Arguments

initial_vcv

An initial variance covariance matrix; we'll start using this in the proposal, which will gradually become more weighted towards the empirical covariance matrix calculated from the chain.

initial_vcv_weight

Weight of the initial variance-covariance matrix used to build the proposal of the random-walk. Higher values translate into higher confidence of the initial variance-covariance matrix and means that update from additional samples will be slower.

initial_scaling

The initial scaling of the variance covariance matrix to be used to generate the multivariate normal proposal for the random-walk Metropolis-Hastings algorithm. To generate the proposal matrix, the weighted variance covariance matrix is multiplied by the scaling parameter squared times 2.38^2 / n_pars (where n_pars is the number of fitted parameters). Thus, in a Gaussian target parameter space, the optimal scaling will be around 1.

initial_scaling_weight

The initial weight used in the scaling update. The scaling weight will increase after the first pre_diminish iterations, and as the scaling weight increases the adaptation of the scaling diminishes. If NULL (the default) the value is 5 / (acceptance_target * (1 - acceptance_target)).

min_scaling

The minimum scaling of the variance covariance matrix to be used to generate the multivariate normal proposal for the random-walk Metropolis-Hastings algorithm.

scaling_increment

The scaling increment which is added or subtracted to the scaling factor of the variance-covariance after each adaptive step. If NULL (the default) then an optimal value will be calculated.

log_scaling_update

Logical, whether or not changes to the scaling parameter are made on the log-scale.

acceptance_target

The target for the fraction of proposals that should be accepted (optimally) for the adaptive part of the chain.

forget_rate

The rate of forgetting early parameter sets from the empirical variance-covariance matrix in the MCMC chains. For example, forget_rate = 0.2 (the default) means that once in every 5th iterations we remove the earliest parameter set included, so would remove the 1st parameter set on the 5th update, the 2nd on the 10th update, and so on. Setting forget_rate = 0 means early parameter sets are never forgotten.

forget_end

The final iteration at which early parameter sets can be forgotten. Setting forget_rate = Inf (the default) means that the forgetting mechanism continues throughout the chains. Forgetting early parameter sets becomes less useful once the chains have settled into the posterior mode, so this parameter might be set as an estimate of how long that would take.

adapt_end

The final iteration at which we can adapt the multivariate normal proposal. Thereafter the empirical variance-covariance matrix, its scaling and its weight remain fixed. This allows the adaptation to be switched off at a certain point to help ensure convergence of the chain.

pre_diminish

The number of updates before adaptation of the scaling parameter starts to diminish. Setting pre_diminish = 0 means there is diminishing adaptation of the scaling parameter from the offset, while pre_diminish = Inf would mean there is never diminishing adaptation. Diminishing adaptation should help the scaling parameter to converge better, but while the chains find the location and scale of the posterior mode it might be useful to explore with it switched off.

boundaries

Control the behaviour of proposals that are outside the model domain. The supported options are:

"reflect" (the default): we reflect proposed parameters that lie outside the domain back into the domain (as many times as needed)
"reject": we do not evaluate the density function, and return -Inf for its density instead.
"ignore": evaluate the point anyway, even if it lies outside the domain.

The initial point selected will lie within the domain, as this is enforced by monty_sample.

Value

A monty_sampler object, which can be used with monty_sample

Details

Much like the simple nested random walk sampler monty_sampler_random_walk, the strategy is to propose all the shared parameters as a deviation from the current point in parameter space as a single move and accept or reject as a block. Then we generate points for all the region-specific parameters, compute the density and then accept or reject these updates independently. This is possible because the change in likelihood in region A is independent from region B.

The adaptive proposal algorithm of the non-nested adaptive sampler monty_sampler_adaptive is extended here to adaptively tune the variance covariance matrix of each of these parameter chunks.