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dadi-user

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Sarah Babaei, Ryan Gutenkunst4

Mar 11

Split Time Interpretation

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

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Split Time Interpretation

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

Mar 11

Marek Šlenker, Ryan Gutenkunst3

Mar 11

Too Red to Be True: Do Bad Residuals Necessarily Reject the Model?

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

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Too Red to Be True: Do Bad Residuals Necessarily Reject the Model?

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

Mar 11

Maycon Oliveira, Ryan Gutenkunst9

Mar 10

dadi-cli runs take very long

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

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dadi-cli runs take very long

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

Mar 10

Isaac Linn, Ryan Gutenkunst3

Mar 9

Running dadi using variant-only vcf as input?

Hi Ryan, Thank you for your response. That aligns with my expectations, but it seems like there's

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Running dadi using variant-only vcf as input?

Hi Ryan, Thank you for your response. That aligns with my expectations, but it seems like there's

Mar 9

Maria Paula Rodriguez, Ryan Gutenkunst4

Mar 6

2D data SFS with very low entries - problems with input for inference?

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

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2D data SFS with very low entries - problems with input for inference?

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

Mar 6

Maycon Oliveira, Ryan Gutenkunst4

Mar 4

Units for time estimates

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

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Units for time estimates

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

Mar 4

Maycon Oliveira, Travis Struck2

Mar 2

dadi-cli GenerateFs --bootstrap generates unfolded FS by default

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

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dadi-cli GenerateFs --bootstrap generates unfolded FS by default

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

Mar 2

Cameron Grey, Ryan Gutenkunst4

Jan 29

Expansion/migration script and random seeding questions

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

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Expansion/migration script and random seeding questions

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

Jan 29

Maycon Oliveira, Ryan Gutenkunst4

Jan 20

Data dimensions after fold()

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

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Data dimensions after fold()

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

Jan 20

Ryan Gutenkunst, Kaden Winspear2

Jan 19

Re: [dadi-user] Projection Choice - 2D models

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

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Re: [dadi-user] Projection Choice - 2D models

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

Jan 19

RAYIS T R, Ryan Gutenkunst3

Jan 13

Some Questions on dadi-cli

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

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Some Questions on dadi-cli

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

Jan 13

Laura Méndez Cuéllar, … RAYIS T R5

Jan 9

AttributeError: 'MaskedArray' object has no attribute 'folded'

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

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AttributeError: 'MaskedArray' object has no attribute 'folded'

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

Jan 9

宋炎峰, … Ryan Gutenkunst10

12/1/25

Inquiry on Performing LRT Between Allotetra & Seg-Allotetra Models in dadi Pipeline

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

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Inquiry on Performing LRT Between Allotetra & Seg-Allotetra Models in dadi Pipeline

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

12/1/25

Abby Williams, Ryan Gutenkunst2

9/6/25

Comparing non-nested models with linked SNPs

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

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Comparing non-nested models with linked SNPs

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

9/6/25

Gutenkunst, Ryan N - (rgutenk)

8/25/25

Other:GenomicHistory.Inference.StrategiesTournament

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

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Other:GenomicHistory.Inference.StrategiesTournament

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

8/25/25

Skye Davis, Ryan Gutenkunst2

8/17/25

Understanding LRT

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

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Understanding LRT

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

8/17/25

Emma Howell, Ryan Gutenkunst2

7/31/25

Testing for distinct marginal DFEs in a joint DFE context

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

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Testing for distinct marginal DFEs in a joint DFE context

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

7/31/25

Ryan Gutenkunst

7/19/25

Re: [dadi-user] Seeking Help with Model Selection Instability in dadi

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

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Re: [dadi-user] Seeking Help with Model Selection Instability in dadi

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

7/19/25

Sofia Hayden Bofill, Ryan Gutenkunst3

7/7/25

Converting migration fraction to number of migrants

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

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Converting migration fraction to number of migrants

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

7/7/25

7/6/25

Seeking Help with Model Selection Instability in dadi

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

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Seeking Help with Model Selection Instability in dadi

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

7/6/25

Sarah Babaei, Ryan Gutenkunst4

7/1/25

2D sfs and results interpretation

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

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2D sfs and results interpretation

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

7/1/25

Panos Zerv, Ryan Gutenkunst2

5/19/25

dadi-cli optimization method

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

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dadi-cli optimization method

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

5/19/25

Linda H, Ryan Gutenkunst5

4/8/25

low theta, strange parameter values

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

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low theta, strange parameter values

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

4/8/25

Hugo D, Ryan Gutenkunst2

4/1/25

Bias in residuals after physical pruning

Hello Hugo, This is a bit perplexing. If you have a well-fitting model with the unprojected data, I

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Bias in residuals after physical pruning

Hello Hugo, This is a bit perplexing. If you have a well-fitting model with the unprojected data, I

4/1/25

HC Lim, Ryan Gutenkunst9

3/29/25

Any implementation of population fusion models?

Hi Ryan, That's correct - giving it a 2D sfs solved the problem (but run didn't converge but

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Any implementation of population fusion models?

Hi Ryan, That's correct - giving it a 2D sfs solved the problem (but run didn't converge but

3/29/25

Hugo D, Ryan Gutenkunst3

3/26/25

Unrealistic parameters conversion

Hi Ryan, Thank you for confirming that there isn't an issue with the computation procedure. You

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Unrealistic parameters conversion

Hi Ryan, Thank you for confirming that there isn't an issue with the computation procedure. You

3/26/25

Maria Paula Rodriguez, Ryan Gutenkunst5

3/18/25

nonparametric bootstrap files contain only zeros

Hi Ryan It worked!! Thank you very much. Maria El mar, 18 mar 2025 a las 13:43, Ryan Gutenkunst (<

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nonparametric bootstrap files contain only zeros

Hi Ryan It worked!! Thank you very much. Maria El mar, 18 mar 2025 a las 13:43, Ryan Gutenkunst (<

3/18/25

Mathilde SALAMON, Ryan Gutenkunst6

1/15/25

Confirming results 1D model growth vs two-epochs vs bottlegrowth

Hello Mathilde, Sorry for the slow reply. I don't know about the complex generation structure;

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Confirming results 1D model growth vs two-epochs vs bottlegrowth

Hello Mathilde, Sorry for the slow reply. I don't know about the complex generation structure;

1/15/25

Lena Zemlemerova, Ryan Gutenkunst2

12/16/24

problems with optimization and convergence

Hello Lena, Sorry for the slow reply. I'm not super familiar with the Portik pipeline, so

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problems with optimization and convergence

Hello Lena, Sorry for the slow reply. I'm not super familiar with the Portik pipeline, so

12/16/24

Morgan L. Lynn, Ryan Gutenkunst2

10/29/24

Folded Spectrum in python is not recognizing some of the individuals in my VCF file

Hello Morgan, This may occur if you often have missing data. For a site to enter the spectrum for 10

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Folded Spectrum in python is not recognizing some of the individuals in my VCF file

Hello Morgan, This may occur if you often have missing data. For a site to enter the spectrum for 10

10/29/24

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