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I am now conducting simulation with demographic model in `demes` with discrete WF model and standard coalescent model.
I performed two simulations:
- msprime simulation with multiple model
- Cond…
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For tree sequences inferred from simulations, we can't directly compare inferred dates to true dates because node sets differ between the inference and the simulation.
Instead, we've been looking …
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Hi Dr. Müller,
Really sorry if I'm mistaken here, but I think there might be an error in the math in the getNeTime function in mascot.parameterdynamics.ExponentialNe, although it's possible I'm mi…
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Alister and Edmon should identify an appropriate workshop or a mid-key conference where we could write up and present the results. I do not think we have material for anything ambitious, but it would …
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Clicking on the CSV button associated with the time-scaled tree (left panel) yields the columns:
* lineage
* mean.diffs
* clock.residual
* num.cases
* num.variants
* min.coldate
* max.coldate
…
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Hello:
I am trying to run Skyfish.
a)compiled locally the dev-coalescent-dev branch (I tried 'development' as the Tutorial suggests but no support for dnAutocorrelatedEvent().
b) ran the constant…
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So I ran a coalescent simulation of the OutOfAfrica model using the following
`
python -m stdpopsim --msprime-model dtwf --msprime-change-model 10 hudson \
HomSap -g HapMapII_GRCh38 -c $chrom…
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**Short description of the problem:**
Simulation with OutOfAfrica_3G09 model generates two haplotypes with a very high amount of shared derived sites causing the diploid individuals constructed b…
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### Author(s) of proposal
Ran Wei
### Name of taxon
Lepisorus
### Rank of taxon
Genus
### Approximate number of species affected
_No response_
### Description of change
Lump…
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When run the gompertz coalescent, after click sample button it appears different values of the tree with the true rootage
The script I use:
N0 ~ LogNormal(meanlog=10, sdlog=0.5);
NInfinity ~ Lo…