Bayesian Modelling of Raman Spectroscopy

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Documentation for package ‘serrsBayes’ version 0.5-0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.