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Automatically exported from code.google.com/p/dadi
License: Other
I have code for measuring the decay of LD (r^2) in ms simulations. This is
useful to have for
validating the model, so I should include it in the dadi distribution.
Original issue reported on code.google.com by [email protected]
on 24 Sep 2009 at 2:49
Working with a folded Spectrum is at present a little tricky. In particular,
refolding a folded
Spectrum wipes out almost all entries, and this can be done implicitly in the
optimizer.
I think the proper solution is to have Spectrum objects record whether or not
they are folded.
1. Add an isfolded member variable to Spectrum objects. (Use Python property
functionality?)
2. Record isfolded status in the saved files.
3. Make optimizer handle folding automatically, folding the model result if the
data is folded, for
example.
4. It doesn't make sense to project a folded Spectrum, because during
projection it is possible for
minor allele status to switch. To deal with this, we need an unfold() method
that will assume each
allele is minor with 50% probability. Then we can raise an exception when
projecting a folded
Spectrum.
Original issue reported on code.google.com by [email protected]
on 18 Sep 2009 at 1:33
This is an issue in bootstrapping, as raised by Jeffrey Lozier.
Original issue reported on code.google.com by [email protected]
on 11 Aug 2013 at 5:22
In the examples/fs_from_data directory, I include an example of loading a
spectrum from a raw
SNP data file. I should standardize this file format, and include the relevant
code in the main line of
dadi.
Original issue reported on code.google.com by [email protected]
on 25 Sep 2009 at 1:18
In plant populations, self-fertilization can be the dominant reproductive
process. Does selfing
change results from a diffusion-based analysis?
Original issue reported on code.google.com by [email protected]
on 6 Apr 2010 at 4:18
The website would benefit from a running list of papers dadi has been used for.
Original issue reported on code.google.com by [email protected]
on 24 Sep 2009 at 2:48
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