[R] Fitdistr() versus nls()

Luca Telloli telloli at cs.unibo.it
Sat Sep 23 12:35:10 CEST 2006

Hello R-Users,
	I'm new to R so I apologize in advance for any big mistake I might  
be doing. I'm trying to fit a set of samples with some probabilistic  
curve, and I have an important question to ask; in particular I have  
some data, from which I calculate manually the CDF, and then I import  
them into R and try to fit: I have the x values (my original samples)  
and the y values (P(X<x)).
	To attempt the fit I've both fitdistr() and nls(), in the way you  
can read in the piece of code at the end of the email. Because the  
fit with all data doesn't work very well, I decided to take a subset  
of samples randomly chosen (for some random x, the correspondant y is  
	The first big problem is that fitdistr and nls, in the way I use  
them in the code, they don't get me similar results. I think I'm  
making a mistake but I can't really understand which one.
	From this first issue, a second one arises because the plot with nls  
is similar (maybe not a great fit bust still...) to my original CDF  
while the plot of fitdistr is basically a straight line of constant  
value y=1. On the other side, the fitdistr outperforms in the  
Kolmogorov-Smirnov test, which for nls has values of probability  
around 0 (not a good score huh?).
	Can u please tell me if there's a major mistake in the code?

Thanks in advance,

cdf.all=read.table("all_failures.cdf", header=FALSE, col.names=c 
("ttr", "cdf"), sep=":" )

plot(allvals.x, allvals.y)

for(it in 1:100){
	#extract random samples
	random=sort(sample(1:length(allvals.x), 15))
	#fit with nls and fitdistr
	fit.exp = fitdistr(somevals.y, "exponential")
	nls.exp <- nls(somevals.y ~ pexp(somevals.x, rate), start=list(rate=. 
0001), model=TRUE)
	#plot what you get out of the two fits
	lines(allvals.x, pexp(allvals.x, coef(fit.exp)), col=it)
	lines(allvals.x, pexp(allvals.x, coef(nls.exp)), col=it)
	#perform kolmogorov-smirnov test on your fit
	ks.exp.nls = ks.test(somevals.y, "pexp", coef(nls.exp))
	ks.exp.fit = ks.test(somevals.y, "pexp", coef(fit.exp))
	bestval.exp.fit = max(bestval.exp.fit, ks.exp.fit$p.value)
	bestval.exp.nls = max(bestval.exp.nls, ks.exp.nls$p.value)


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