nmr_batman_options: Batman Options helper

Description Usage Arguments Value See Also Examples

View source: R/batman_helpers.R

Description

Batman Options helper

Usage

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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)

Value

A batman_options object with the Batman Options

See Also

Other batman functions: nmr_batman

Examples

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bopts <- nmr_batman_options()

AlpsNMR documentation built on April 1, 2021, 6:02 p.m.