msprime

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testing matrix bug

1

NOT FOR MERGING-- just trying to isolate the mutation matrix bug

andrewkern

Add python 3.13

1

benjeffery

Hi everyone, I am looking for a method to achieve the task as in the title. This will be used to simulate sequencing read data to reconstruct the trajectory by...

yzliu01

Test_pedigree.py with internal samples

1

I have modified TestSimulateThroughPedigree and the simulate_pedigree function to specify generations of subjects as internal samples. Setting internal_sample_gen=[True, False] on line 562 specifies that founders i.e. parents of a two-generation...

abureau

Documenting the SMC(K) model closes #2382

1

Documenting the smc(k) model. - Added the smc(k) class description and referred to it in the docs - Removed and/or replaced mentions of the old smc and smc' models from...

hossam26644

Change the default Hull offset of the SMCK model to 1

2

Should we change the default hull_offset value of the `SmcKApproxCoalescent` model to **1**? `SmcKApproxCoalescent(hull_offset=1) `is equivalent to the _SMC′_ model, which is generally considered by many to be “equal” to...

hossam26644

Fix/statistical tests above root closes #2428

3

First implementation of statistical tests for simulations above root. @Jerome Can You check that these tests are sufficient before I tidy it up a bit?

hossam26644

Document smc(k)

2

Need some basic documentation for the smc(k) model

jeromekelleher

Statistical tests for stop_at_local_mrca=False

4

We need to do some tests to make sure this is working properly. I think the most powerful test here is to run some simulations with stop_at_local_mrca=True and stop_at_local_mrca=False, and...

jeromekelleher

This is supposed to be an example of where we use ``stop_at_local_mrca=False", but we've set it to "True" https://tskit.dev/msprime/docs/latest/ancestry.html#tracing-ancestry-through-a-pedigree The problems is the example doesn't fully coalesce anywhere, so there's...

jeromekelleher