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Population-scale genomics
As it stands tskit's implementation does not allow for differential emission probs conditional on number of alleles. There are choices here, all of which should be incorporated. 1. Let mismatch...
In #2799 we added an initial version of the backwards algorithm, but ended up including two calls to ``compress()`` per site. This is because we need to call compress immediately...
#2786 added the new ``tsk_tree_position_t`` class which takes care of tracking the edges that need to go in and out of a tree in order to transform it into a...
new (?) statistic to efficiently calculate shared times between every pair of samples at every tree
Hi all, I've been messing around with different ways to calculate the shared time between every pair of samples in many trees, which is a useful metric because it describes...
When the output dimension of a statistic is large, so is the memory consumption. The following example calculates the pairwise distance matrix for all samples from a single tree and...
add_pbs
## Description sorry i messed and delete my local branch, so the pr #2749 was closed automately; i don't know how to reopen, so i opened a new pr; sorry...
PBS (population branch statistics) [^1] is derived from Fst, which can detect positive selection signals in admixted populations . the formula is ``` T = - log(1 – FST) PBS...
To compute a covariance matrix, or do PCA, we currently have to export the genotype matrix. It would be nice to do this using the statistics framework, and totally do-able....
We have a `tree.num_children_array` but not a `tree.num_samples_array`. Is such a thing worth making available? I suspect we need to keep track of the number of samples under each node...
[Here](https://github.com/tskit-dev/tskit/blob/main/python/requirements/CI-docs/requirements.txt#L143) is required 0.5.4 - seems like it might be an issue at some point?