R : Copyright 2004, The R Foundation for Statistical Computing
Version 1.9.1  (2004-06-21), ISBN 3-900051-00-3

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> rm(list=ls())
> parameter.filename = "Rinput.csv";
> new.parameter.filename = "Routput.csv";
> 
> params = scan(file=parameter.filename,skip=1,what=list(1.0,1.0,1.0,1.0,""),sep=",",strip.white=T)
Read 1 records
> 
> a = as.numeric(params[1])
> b = as.numeric(params[2])
> t0 = as.numeric(params[3])
> V = as.numeric(params[4])
> quadratic.peaks.filename = as.character(params[5])
> 
> 
> peakdata = read.csv(file=quadratic.peaks.filename, header = TRUE, sep = ",", quote="\"", dec=".", fill = TRUE)
> 
> 
> # target mass values are mis (perhaps from reference spectrum)
> # actual mass values are pis
> mis = peakdata[,1]
> pis = peakdata[,2]
> 
> # try to make sure only valid numeric values are input
> mis = mis[is.numeric(mis) & !is.na(mis)]
> pis = pis[is.numeric(pis) & !is.na(pis)]
> 
> 
> # function to minimize
> leastsqssum3pscale = function(pars,masses,tofs,V){
+   a = pars[1]; b = pars[2]; t0 = pars[3];
+   leastsqsum3p = sum( ((masses - V*(a*((tofs - t0)^2)+b))/masses)^2)
+   leastsqsum3p
+ }
> 
> # calculate the tis in the paper, here called tofpis
> # masses too near to zero can cause errors if they correspond
> # to negative times of flight -- in that case need to use
> # parts of the spectrum away from 0
> tofpis = sqrt((pis/V-b)/a)+t0
> pars3 = c(a,b,t0); vals = pars3
> 
> # find minimizing values of a, b, t0
> vals = optim(pars3,leastsqssum3pscale,masses=mis,tofs=tofpis,V=V)$par
> 
> anew = vals[1]; bnew = vals[2]; t0new = vals[3]
> 
> # new m/z values are given by the next line
> #Mz = V*anew*(tofpis - t0new)^2 + V*bnew
> 
> # write out the data
> newdf = data.frame(Avalue = anew, Bvalue = bnew, t0value = t0new, Uvalue = V);
> 
> write.table(file=new.parameter.filename,newdf,sep=",",
+             col.names = TRUE,row.names=F,quote=F)
> 
> q("no")