nestedSampling: nestedSampling

In babar: Bayesian Bacterial Growth Curve Analysis in R

Description

Perform nested sampling for the given model (expressed through the log likelihood function).

Usage

nestedSampling(llFun, numberOfParameters, prior.size, transformParams, 
    exploreFn = ballExplore, tolerance = 0.1)

Arguments

llFun	The loglikelihood function, which should be of the form: llFun(params) where params is a vector containing a single instance of parameters, and should return the log likelihood for those parameters.
numberOfParameters	The number of parameters to be inferred. Should always equal the number of parameters in the likelihood function.
prior.size	The number of initial prior objects to sample. This is the size of the active set of samples maintained throughout the procedure.
transformParams	Function to transform parameters from the unit hypercube into the correct distribution
exploreFn	Preferred exploration routine. Defaults to a dodgy implementation currently but ballExplore likely to be more robust.
tolerance	The tolerance at which the routine should stop. Changing this will affect how long it takes to run nested sampling. Larger values will terminate sooner but may give inaccurate evidence scores. This is the expected maximum remaining contribution to logZ from the points in the active set. delta Z_i = L_max*X_i < tolerance.

Value

logevidence: The logarithm of the evidence, a scalar.

posterior.samples: The samples from the posterior, together with their log weights and log likelihoods as a m x n matrix, where m is the number of posterior samples and n is the number of parameters + 2. The log weights are the first column and the log likelihood values are the second column of this matrix. The sum of the log-weights = logZ.

logZerror: An estimate of the numerical uncertainty of the log evidence.

parameterMeans: A vector of the mean of each parameter, length = no. of parameters.

parameterVariances: A vector of the variance of each parameter, length = no. of parameters.

entropy: The information — the natural logarithmic measure of the prior-to-posterior shrinkage.

Author(s)

Lydia Rickett, Matthew Hartley, Richard Morris and Nick Pullen

Examples

mu <- 1
sigma <- 1
data <- rnorm(100, mu, sigma)

transform <- function(params) {
  tParams = numeric(length=length(params))
  tParams[1] = GaussianPrior(params[1], mu, sigma)
  tParams[2] = UniformPrior(params[2], 0, 2 * sigma)
  return(tParams)
}

llf <- function(params) {
  tParams = transform(params)
  mean = tParams[1]
  sigma = tParams[2]
  n <- length(data)
  ll <- -(n/2) * log(2*pi) - (n/2) * log(sigma**2) - (1/(2*sigma**2)) * sum((data-mean)**2)
  return(ll)
}

prior.size <- 25
tol <- 0.5

ns.results <- nestedSampling(llf, 2, prior.size, transform, tolerance=tol)

babar documentation built on May 1, 2019, 10:18 p.m.