nmr_batman_options: Batman Options helper
In sipss/AlpsNMR: Automated spectraL Processing System for NMR

nmr_batman_options

R Documentation

Batman Options helper

Description

Batman Options helper

Usage

nmr_batman_options(
  ppmRange = matrix(c(3, 3.1, 3.6, 3.7, 3.9, 4, 4, 4.1, 6.95, 7.05, 7.6, 7.7, 7.8, 7.9),
    ncol = 2, byrow = TRUE),
  specNo = "1",
  paraProc = 4L,
  negThresh = -0.5,
  scaleFac = 1e+06,
  downSamp = 1,
  hiresFlag = 1,
  randSeed = 100025L,
  nItBurnin = 200L,
  nItPostBurnin = 5000L,
  multFile = 2L,
  thinning = 50L,
  cfeFlag = 0,
  nItRerun = 5000L,
  startTemp = 1000,
  specFreq = 600,
  a = 1e-05,
  b = 1e-09,
  muMean = 1.1,
  muVar = 0.2,
  muVar_prop = 0.002,
  nuMVar = 0.0025,
  nuMVarProp = 0.1,
  tauMean = -0.05,
  tauPrec = 2,
  rdelta = 0.02,
  csFlag = 0
)

Arguments

`ppmRange`	Range of ppm to process
`specNo`	Index of spectra to process
`paraProc`	Number of cores to use
`negThresh`	Truncation threshold for negative intensities
`scaleFac`	Divide each spectrum by this number
`downSamp`	Decimate each spectrum by this factor
`hiresFlag`	Keep High Resolution deconvolved spectra
`randSeed`	A random seed
`nItBurnin`	Number of burn-in iterations
`nItPostBurnin`	Number of iterations after burn-in
`multFile`	Multiplet file (integer)
`thinning`	Save MCMC state every thinning iterations
`cfeFlag`	Same concentration for all spectra (fixed effect)
`nItRerun`	Number of iterations for a batman rerun
`startTemp`	Start temperature
`specFreq`	NMR Spectrometer frequency
`a`	Shape parameter for the gamma distribution (used for lambda, the precision)
`b`	Rate distribution parameter for the gamma distribution (used for lambda, the precision)
`muMean`	Peak width mean in ln(Hz)
`muVar`	Peak width variance in ln(Hz)
`muVar_prop`	Peak width proposed variance in ln(Hz)
`nuMVar`	Peak width metabolite variance in ln(Hz)
`nuMVarProp`	Peak width metabolite proposed variance in ln(Hz)
`tauMean`	mean of the prior on tau
`tauPrec`	inverse of variance of prior on tau
`rdelta`	Truncation of the prior on peak shift (ppm)
`csFlag`	Specify chemical shift for each multiplet in each spectrum? (chemShiftperSpectra.csv file)