R help - Jun 2009 - typo in Lomb-Scargle periodogram implementation in spec.ls() from cts package?

Hello!

I tried to contact author of the package, but I got no reply. That is why I
write it here. This might be useful for those who were using cts for spectral
analysis of non-uniformly spaced data.

In file spec.ls.R from cts_1.0-1.tar.gz lines 59-60 are written as

pgram[k, i, j] <- 0.5 * ((sum(x[1:length(ti)]* cos(2 * pi * freq.temp[k] *
(ti - tao))))^2/sum((cos(2 *
pi * freq.temp[k] * (ti - tao)))^2) + (sum(x[1:length(ti)] *  sin(2 * pi *
freq.temp[k] * (ti - tao))))^2 ===> ) <=== /sum((sin(2 * pi * freq.temp[k]
* (ti - tao)))^2)

Is there a misplaced bracket (shown like ===> ) <===)? Should it be like
the following?

pgram[k, i, j] <- 0.5 * ((sum(x[1:length(ti)]* cos(2 * pi * freq.temp[k] *
(ti - tao))))^2/sum((cos(2 *
pi * freq.temp[k] * (ti - tao)))^2) + (sum(x[1:length(ti)] *  sin(2 * pi *
freq.temp[k] * (ti - tao))))^2/sum((sin(2 * pi * freq.temp[k] * (ti - tao)))^2)
===> ) <==

Here is quick reference
http://en.wikipedia.org/wiki/Least-squares_spectral_analysis#The_Lomb.E2.80.93Scargle_periodogram
. One half coefficient was not applied to entire expression.

Also I find weird next lines (61-62)

pgram[1, i, j] <- 0.5 * (pgram[2, i, j] + pgram[N, i, j])

First of all, such things should not be in the for loop. Second, I don't
quite understand the meaning of it.

P.S. Should I use tapering of my data? If I just try to fit sine and cosine, I
may not use it, however for FFT windowing is a must. What about Lomb-Scargle?

Mikhail

Please report problems in the code to the package maintainer (CCing).

Best,
Uwe Ligges



Mikhail Titov wrote:
> Hello!
> 
> I tried to contact author of the package, but I got no reply. That is why I
write it here. This might be useful for those who were using cts for spectral
analysis of non-uniformly spaced data.
> 
> In file spec.ls.R from cts_1.0-1.tar.gz lines 59-60 are written as
> 
> pgram[k, i, j] <- 0.5 * ((sum(x[1:length(ti)]* cos(2 * pi * freq.temp[k]
* (ti - tao))))^2/sum((cos(2 *
> pi * freq.temp[k] * (ti - tao)))^2) + (sum(x[1:length(ti)] *  sin(2 * pi *
freq.temp[k] * (ti - tao))))^2 ===> ) <=== /sum((sin(2 * pi * freq.temp[k]
* (ti - tao)))^2)
> 
> Is there a misplaced bracket (shown like ===> ) <===)? Should it be
like the following?
> 
> pgram[k, i, j] <- 0.5 * ((sum(x[1:length(ti)]* cos(2 * pi * freq.temp[k]
* (ti - tao))))^2/sum((cos(2 *
> pi * freq.temp[k] * (ti - tao)))^2) + (sum(x[1:length(ti)] *  sin(2 * pi *
freq.temp[k] * (ti - tao))))^2/sum((sin(2 * pi * freq.temp[k] * (ti - tao)))^2)
===> ) <==>
> 
> Here is quick reference
http://en.wikipedia.org/wiki/Least-squares_spectral_analysis#The_Lomb.E2.80.93Scargle_periodogram
. One half coefficient was not applied to entire expression.
> 
> Also I find weird next lines (61-62)
> 
> pgram[1, i, j] <- 0.5 * (pgram[2, i, j] + pgram[N, i, j])
> 
> First of all, such things should not be in the for loop. Second, I
don't quite understand the meaning of it.
> 
> P.S. Should I use tapering of my data? If I just try to fit sine and
cosine, I may not use it, however for FFT windowing is a must. What about
Lomb-Scargle?
> 
> Mikhail
> 
> ______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/r-help
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http://www.R-project.org/posting-guide.html
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