NEWS

serrsBayes 0.5-0 (2021-06-28)

Zero MCMC iterations will be performed if the number of unique particles is already >= minPart (adaptive number of MCMC steps)
Replaced the default uniform prior distribution for the peak amplitudes with an exponential prior

Merged pull request from Rcpp team to use constant M_PI instead of PI to support STRICT_R_HEADERS
Fixed issue with plots in Introduction vignette
Fixed broken link to EPSRC grants website (now uses UKRI Gateway to Research)
Added package Hmisc to suggests to fix Undeclared package in Rd xrefs NOTE on CRAN
Try-catch when computing Cholesky decomposition of the Gaussian random walk variance-covariance matrix (fallback to diagonal matrix by default)
Removed Travis CI from README, since builds have ceased on June 15, 2021

MCMC iterations will stop when temp ESS reaches the total number of particles (adaptive number of MCMC steps)
Added DOI from Zenodo to CITATION file.

Fixed issue with digits = 0 in vignettes (CRAN WARN)
Removed obsolete call to Rcpp::LdFlags() from Makevars.win
Added fallback to boost MCMC acceptance rate if it falls below 15% of proposals
Regenerated the datasets result.rda & result2.rda to adjust for the new way of calculating FWHM

Added example of fitSpectraSMC with informative priors to the methanol vignette.

Removed the R package hyperSpec from Suggests because it is no longer available on CRAN.
Fixed dependency on hyperSpec in Introduction vignette due to new CRAN check. This also affects the TAMRA dataset.
Fixed a rare bug in reweighting that could potentially result in an infinite loop.
Peak locations are now constrained to lie within the range of observed wavelengths.
Locations are sorted to preserve identifiability.
Fixed error in equations for FWHM in mixedVoigt & getVoigtParam as well as in both vignettes.

OpenMP implementation of mhUpdateVoigt provides around 3x improvement in elapsed runtime
New vignette illustrates when to use the 3 functions fitSpectraMCMC, fitSpectraSMC, and fitVoigtPeaksSMC
New datasets methanol and TAMRA for use in the vignettes
Debug output prints the means of the amplitudes of the peaks at each SMC iteration

Fixed bug in fitVoigtPeaksSMC where it was using the upper-triangular instead of lower-triangular Cholesky factorisation to generate random-walk Metropolis proposals
Introduction vignette no longer attempts to download a .zip file over HTTPS
Deleted unused Rcpp function randomWalkVoigt