nmr_batman_options {AlpsNMR} | R Documentation |
Batman Options helper
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 )
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) |
A batman_options object with the Batman Options
Other batman functions:
nmr_batman
bopts <- nmr_batman_options()