Data dimensions after fold()

[Maycon Oliveira]

Hello all! I was wondering, what happens to the sample sizes after i call fs.fold() within dadi? To my knowledge, the sample sizes should be updated to reflect the dimensions of the new SFS, but after doing some tests I realize this is not the case currently. Do I have to manually project down the SFS after folding in order to account for this?

[Ryan Gutenkunst]

Hello Maycon,

Folding does not change the sample size, because it is still the same samples. dadi tracks whether a spectrum is folded or not internally and automatically adjusts the model to reflect that. You should not need to do anything to adjust for folded versus unfolded data.

Best,

Ryan

On Jan 19, 2026, at 9:20 AM, Maycon Oliveira <oliveira...@gmail.com> wrote:

Hello all! I was wondering, what happens to the sample sizes after i call fs.fold() within dadi? To my knowledge, the sample sizes should be updated to reflect the dimensions of the new SFS, but after doing some tests I realize this is not the case currently. Do I have to manually project down the SFS after folding in order to account for this?

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[Maycon Oliveira]

Oh, ok. I got confused because on one of my results I got the following (attached) plots which look very sparse, but I guess that's due to many bins with missing counts on my SFS, right? In that case, I believe the correct approach would be to project down the SFS, is that a correct assumption?

[Ryan Gutenkunst]

Hello Maycon,

Yes, the sparseness is due to many zeros in your data. You can project down to fill it out for plotting purposes. You don’t need to project down for the analysis itself.

Best,

Ryan

To view this discussion visit https://groups.google.com/d/msgid/dadi-user/5dd836be-1f9f-40bb-b445-f53cc76314acn%40googlegroups.com.
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