pmwg0.2.7 package

An altered version of the utils:txtProgressBar that shows acceptance r...

Return the acceptance rate for new particles across all subjects

Return a CODA mcmc object with the required samples

Augment existing sampler object to have subject specific epsilon stora...

Check whether the adaptation phase has successfully completed

Check for efficient proposals if necessary

Test the arguments to the run_stage function for correctness

Obtain the efficent mu and sigma from the adaptation phase draws

Create distribution parameters for efficient proposals

Extend the main data store with empty space for new samples

Extract relevant samples from the list for conditional dist calc

Generate proposal particles

Gibbs step of the Particle Metropolis within Gibbs sampler

Error handler for the gibbs_step call

Initialise values for the random effects

Test whether object is a pmwgs

Create a list with the last samples in the pmwgs object

Generate particles and select one to be the new sample

Error handler forany error in new_sample function call(s)

Check and normalise the number of each particle type from the mix_prop...

Generate a cloud of particles from a multivariate normal distribution

Error handler for the particle selection call

pmwg: Particle Metropolis Within Gibbs.

Create a PMwG sampler and return the created object

Relabel requested burn-in samples as adaptation

The Inverse Wishart Distribution

Run a stage of the PMwG sampler

The Wishart Distribution

Create a new list for storage samples in the pmwgs object

Set default values for epsilon

Set default values for mix

Setup the proposal distribution arguments (if in sample stage)

Test that the sampler has successfully adapted

Trim the unneeded NA values from the end of the sampler

Unwinds variance matrix to a vector

Update the subject specific scaling parameters (epsilon)

A function that updates the accept_progress_bar with progress and acce...

Winds a variance vector back to a vector