nmr_batman_options {AlpsNMR} | 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)

### Value

A batman_options object with the Batman Options

### See Also

Other batman functions: `nmr_batman`

### Examples

    bopts <- nmr_batman_options()

[Package AlpsNMR version 3.2.3 Index]