dadi-user

Hi Ryan, I have two main questions related with model fit/comparison, and I'd appreciate your

Hello Isaac, If I'm reading the old paper correctly (and quickly), your ancestral population size

Hello Sarah, Neither of these residual plots shows strong underprediction of singletons, son I'm

Hi Hana, Regarding the uncertainties and step size, what you're looking for is (rough)

Hello Reuben, I'm not sure what you mean by “collapse at the same place”. The drop at frequency

Hi Emma, We typically just constrain the sigma to be positive and not huge (maybe < 10). In regard

Hello Clemens, I've not used Stacks before, but based on another user's reports… I would use

Hi Diego and Ryan, I came across this post because I'm interested in giving a try to CLAIC to

Hi Sarah, For L, what we're trying to calculate is the amount of sequence from which SNPs could

Dear Ryan, thanks for your reply. That point about random variance within residuals seems reasonable.

Hello Maycon, If the bounds of the more complex model were a superset of the less complex model, then

Hi Ryan, Thanks for your fast reply! That was the result of a single fit. What you say about the

Yes, that should work. On Mar 4, 2026, at 4:53 AM, Maycon Oliveira <oliveira...@gmail.com>

Hi Maycon, I've pushed a fix to the GitHub source code and PyPi. The fix should be on conda-forge

Hello Cameron, Retaining one SNP per RAD locus is a typical approach that I find sensible. That seems

Hello Maycon, Yes, the sparseness is due to many zeros in your data. You can project down to fill it

Thank you for the help! On Mon, Jan 19, 2026 at 1:42 PM Ryan Gutenkunst <rgute...@gmail.com>

Thanks, Ryan! This is very helpful. On Sunday, January 11, 2026 at 4:22:27 AM UTC+5:30 Ryan

Hi Ryan, Thanks for the response. I started using dadi-cli for my analysis and had some questions

Given that neither models fits the data well, and your data don't show evidence of the expected

Hello Abby, I'm sorry I don't have a very satisfying answer. My group's approach is

Hello dadi users! The 2025 Genomic History Inference Strategies Tournament (GHIST) is live at https:/

Hello Skye, No apologies needed. This is generally confusing. :-) For symmetric versus asymmetric

Hello Emma, Sorry for the slow reply. This is a subtle issue, and I don't think we have a great

Hello Fred, Sorry for the slow reply. I've been on vacation. I'm not deeply familiar with the

Hi Ryan, Thank you so much for your quick reply, I really appreciate it. Amazing, now it is clear.

Hi, I am writing to seek your expertise regarding an issue I've encountered while using dadi for

Hi Sarah, Replies below On Jul 1, 2025, at 11:20 AM, Sarah Babaei <sarahba...@gmail.com>

Hello Panagiotis, There is not currently a way to specify the optimization method in dadi-cli. If you

Hi Ryan, Thanks for clarifying down-projection, it really doesn't seem to be useful in this case.