Bayesian inversion of a model

Performs an inversion of an arbitrary model using a modified Metropolis Hastings algorithm with block sampling. This may be slightly slower than the implementation in Fortran, but is much more customizable, as the model can be any R function.

invert.custom(observed, invert.options, quiet = FALSE,
  return.resume = FALSE, runID = NULL)

Arguments

observed

Vector, matrix, or data frame (coerced to matrix) of observed values. For spectral data, wavelengths are rows and spectra are columns. Dimensions must align with the output of model.
invert.options

R list object containing inversion settings. See details.
quiet

Suppress progress bar and status messages. Default=FALSE
return.resume

If TRUE, return results as list that includes current Jump distribution (useful for continuing an ongoing run) and acceptance rate. Default = FALSE.
runID

Run-unique ID. Useful for parallel runs. Default=NULL

Details

inversion.options contains the following:

  • inits -- Vector of initial values of model parameters to be inverted.

  • ngibbs -- Number of MCMC iterations

  • prior.function -- Function for use as prior. Should take a vector of parameters as input and return a single value -- the sum of their log-densities -- as output.

  • param.mins -- Vector of minimum values for inversion parameters

  • param.maxs -- Vector of minimum values for inversion parameters

  • model -- The model to be inverted. This should be an R function that takes params and runID as input and returns one column of observed (nrows should be the same). Constants should be implicitly included here.

  • adapt -- Number of steps for adapting covariance matrix (i.e. adapt every 'n' steps). Default=100

  • adj_min -- Minimum threshold for rescaling Jump standard deviation. Default = 0.1.

  • target -- Target acceptance rate. Default=0.234, based on recommendation for multivariate block sampling in Haario et al. 2001

  • do.lsq -- Perform least squares optimization first (see invert.lsq), and use outputs to initialize Metropolis Hastings. This may improve mixing time, but risks getting caught in a local minimum. Default=FALSE

  • catch_error -- If TRUE (default), wrap model in tryCatch to prevent sampling termination on model execution error.

References

  • Haario, Heikki; Saksman, Eero; Tamminen, Johanna. An adaptive Metropolis algorithm. Bernoulli 7 (2001), no. 2, 223--242. http://projecteuclid.org/euclid.bj/1080222083.