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