# Bayesian Modelling of Raman Spectroscopy

## Documentation for package ‘serrsBayes’ version 0.5-0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

computeLogLikelihood | Compute the log-likelihood.
copyLogProposals | Initialise the vector of Metropolis-Hastings proposals.
effectiveSampleSize | Compute the effective sample size (ESS) of the particles.
fitSpectraMCMC | Fit the model using Markov chain Monte Carlo.
fitSpectraSMC | Fit the model using Sequential Monte Carlo (SMC).
fitVoigtIBIS | Fit the model with Voigt peaks using iterated batch importance sampling (IBIS).
fitVoigtPeaksSMC | Fit the model with Voigt peaks using Sequential Monte Carlo (SMC).
getBsplineBasis | Compute cubic B-spline basis functions for the given wavenumbers.
getVoigtParam | Compute the pseudo-Voigt mixing ratio for each peak.
lsTamra | Surface-enhanced Raman spectram of tetramethylrhodamine+DNA (T20)
marginalMetropolisUpdate | Update all of the parameters using a single Metropolis-Hastings step.
methanol | Raman spectrum of methanol (CH3OH)
mhUpdateVoigt | Update the parameters of the Voigt peaks using marginal Metropolis-Hastings.
mixedVoigt | Compute the spectral signature using Voigt peaks.
resampleParticles | Resample in place to avoid expensive copying of data structures, using a permutation of the ancestry vector.
residualResampling | Compute an ancestry vector for residual resampling of the SMC particles.
result | SMC particles for TAMRA+DNA (T20)
result2 | SMC particles for methanol (CH3OH)
reWeightParticles | Update the importance weights of each particle.
serrsBayes | Bayesian modelling and quantification of Raman spectroscopy
sumDexp | Sum log-likelihoods of i.i.d. exponential.
sumDlogNorm | Sum log-likelihoods of i.i.d. lognormal.
sumDnorm | Sum log-likelihoods of Gaussian.
weightedGaussian | Compute the spectral signature using Gaussian peaks.
weightedLorentzian | Compute the spectral signature using Lorentzian peaks.
weightedMean | Compute the weighted arithmetic means of the particles.
weightedVariance | Compute the weighted variance of the particles.