Description Usage Arguments Value See Also Examples
This performs metabolite and wavelet fitting to input NMR spectra with
fixed multiplet position obtained from running batman
, and also
plots fitting results. The user should modify parameters in the copy file "batmanOptions.txt"
in batman
output folder to change the rerun settings.
1 2 3  batmanrerun(BM, figBatmanFit = TRUE, listMeta = FALSE,
figRelCon = FALSE, figMetaFit = FALSE, showPlot)

BM 

figBatmanFit 
Plot metabolites and wavelets fit if set 
listMeta 
Individual metabolite fit will also be shown in the plot if set 
figRelCon 
Plot posterior samples of the relative concentration for listed
metabolites with 95% credible interval if set 
figMetaFit 
If set 
showPlot 
If set 
When batmanrerun
is called with multiplet ppm shifts fixed from the
batman
results, the following objects are added to the batman
result:
sFitRerun 
A matrix t \times 5n of BATMAN rerun fit results (down sampled). For 1 spectrum, it is a matrix with 5 columns: [ppm, original spectrum, metabolites fit, wavelets fit, overall fit]. n is the number of spectra, and t is the number of data points in each spectrum. 
sFitRerunHR 
A matrix t \times 3n of BATMAN rerun fit results in the original resolution (without down sample). For 1 spectrum, it is a matrix with 3 columns: [ppm, original spectrum, metabolites fit]. n is the number of spectra, and t is the number of data points (without down sample) in each spectrum. 
betaRerun 
For batman rerun, a matrix (m \times n) containing the posterior means of relative concentrations for m fitted metabolites and n spectra. 
betaSamRerun 
For batman rerun, a matrix (m \times (s*n)) containing (for the first spectrum) s posterior samples of the relative concentrations in its rows. m is the number of fitted metabolites. n is the number of spectra analyzed. The subsequent columns contain the same data format for the rest n1 spectra. 
betaCIRerun 
For batman rerun, a matrix (m \times 2n) containing the 95% credible interval of the relative concentrations for m fitted metabolites. Every pair of columns is for one spectrum. 
metaTempRerun 
For batman rerun, a matrix (t \times (m*n)) containing the posterior means of m fitted metabolite templates in its columns (down sampled). n is the number of spectra analyzed and t is the number of data points in each spectrum. 
metaTempRerunHR 
For batman rerun, a matrix (t \times (m*n)) containing the posterior means of m fitted metabolite templates in its columns (without down sample). n is the number of spectra analyzed and t is the number of data points (without down sample) in each spectrum. 
metaFitSamRerun 
For batman rerun, a matrix (t \times (s*n)) containing s posterior samples of total metabolites fit in its columns. n is the number of spectra analyzed and t is the number of data points in each spectrum. The remaining n1 spectra metabolites fit results are saved in the same sequence in subsequent columns. 
metaIndFitSamRerun 
For batman rerun, a matrix (t \times (m*s*n)) containing s posterior samples of m individual metabolites fit in its columns. n is the number of spectra analyzed and t is the number of data points in each spectrum. The remaining n1 spectra results are saved in the same sequence in subsequent columns. 
thetaSamRerun 
For batman rerun, a matrix (t \times (s*n)) containing s samples of wavelet fit in its columns. n is the number of spectra analyzed. The remaining n1 spectra wavelet fit results are saved in the same sequence in subsequent columns. 
outputDir 
The directory of output folder with all the output result files. 
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50  library(batman)
## Run batman
if(interactive())
{
bm<batman()
## then call batmanrerun
bm<batmanrerun(bm)
}
#######################################################################
## The following is an example of what will be displayed in R
## and what value the user could input:
#######################################################################
## Rerunning batman for 500 iterations.
## percentage completed...
##   0%
## Size of each spectrum is 382.
## Size of metabolite list is 22.
## Constructing chain data structure...
## time used is 1 seconds.
## Running MCMC...
## ================================================================== 100%
## time used is 65 seconds.
## saving posteriors...
##
## For rerun, time elapsed
## 65.96 seconds.
## Reading in saved data in folder
## .../user_specified_dir/runBATMAN/BatmanOutput/07_Dec_17_35_53
## Completed.
########################################################################
## Alternatively if more than 1 spectrum are included without using fixed
## effect, user will be asked to input whether to parallelize the analysis
## between spectra.
########################################################################
## How many parallel processes (multicores) do you want to run the
## multispectra analysis?
## (Enter 1 for running them sequentially.)
##
## Parallel processing of multi spectra currently cannot display
## the progress bar (or any words), if you input is > 1, please be patient
## for the results :)
##
## 1: 2 ## user input
##
## For rerun, time elapsed
## 64.4
## Reading in saved data in folder
## .../user_specified_dir/runBATMAN/BatmanOutput/07_Dec_17_35_53
## Completed.
#######################################################################

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.