slim-discuss

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Welcome to slim-discuss! Please find general information and downloads for SLiM at http://messerlab.org/slim/. There is a free online SLiM workshop at http://benhaller.com/workshops/workshops.html.

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Ali Hudson, Ben Haller3

7:48 AM

Not progressing to next tick but no error messages...

Hi Ben, Thanks so much! Setting community.tick=1; in the callback where I read the file in

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Not progressing to next tick but no error messages...

Hi Ben, Thanks so much! Setting community.tick=1; in the callback where I read the file in

7:48 AM

Manas G. A., … Ben Haller8

Sep 29

Model with additive fitness effects

Thanks Ben! On Fri, Sep 29, 2023 at 4:21 PM Ben Haller <bha...@mac.com> wrote: Hi Manas and

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Model with additive fitness effects

Thanks Ben! On Fri, Sep 29, 2023 at 4:21 PM Ben Haller <bha...@mac.com> wrote: Hi Manas and

Sep 29

Elissa Suphapun Sorojsrisom, Ben Haller2

Sep 27

Binomial sampling with weights to vector

Hi Elissa! The usual way to do what you're trying to do is to use runif() to generate draws

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Binomial sampling with weights to vector

Hi Elissa! The usual way to do what you're trying to do is to use runif() to generate draws

Sep 27

Gabriele d'Angella, … Peter Ralph6

Sep 20

Output spatial positions together with genetic information

Hi, Gabriele! Yes, that's exactly right - since it's possible for SLiM to put together

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Output spatial positions together with genetic information

Hi, Gabriele! Yes, that's exactly right - since it's possible for SLiM to put together

Sep 20

Rupert Mazzucco, Ben Haller3

Sep 15

Mutations mysteriously lost

Yes, I just realized that myself ... Many thanks Rupert Ben Haller schrieb am Freitag, 15. September

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Mutations mysteriously lost

Yes, I just realized that myself ... Many thanks Rupert Ben Haller schrieb am Freitag, 15. September

Sep 15

Zuxi Cui2

Sep 11

Alternative allele issue with VCF output

Problem solved. This issue is well explained in 26.2.4 in the manual. On Mon, Sep 11, 2023 at 3:14 PM

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Alternative allele issue with VCF output

Problem solved. This issue is well explained in 26.2.4 in the manual. On Mon, Sep 11, 2023 at 3:14 PM

Sep 11

Colin Olito, Ben Haller2

Aug 29

calculating fitness contributions of arbitrary genome regions

Hi Colin! I'm afraid this is not something that SLiM supports directly. You would need to do it

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calculating fitness contributions of arbitrary genome regions

Hi Colin! I'm afraid this is not something that SLiM supports directly. You would need to do it

Aug 29

Tatiana Bellagio, … Yan Wong5

Aug 28

One tree seq for multiple chromosomes

Perfect, just did! Here is the discussion in case any future user is interested in the same topic:

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One tree seq for multiple chromosomes

Perfect, just did! Here is the discussion in case any future user is interested in the same topic:

Aug 28

Janna Fierst, Ben Haller9

Aug 25

load builds up fatally in a polygenic simulation

Ah okay... I had played around with the survival() to keep the population constant but in reading the

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load builds up fatally in a polygenic simulation

Ah okay... I had played around with the survival() to keep the population constant but in reading the

Aug 25

Aude Caizergues, Ben Haller4

Aug 25

Alternative to K

Hi Aude. It sounds like you just need to do some debugging of your model, looking at things like

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Alternative to K

Hi Aude. It sounds like you just need to do some debugging of your model, looking at things like

Aug 25

Francesc Ganau, Ben Haller4

Aug 17

Adding initial allele frequencies without recapitation

Hi Francesc! If CL is the number of sites you want, as your comment says, then your chromosome

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Adding initial allele frequencies without recapitation

Hi Francesc! If CL is the number of sites you want, as your comment says, then your chromosome

Aug 17

Mark Hibbins, Ben Haller6

Aug 15

Introducing a dominant sex modifier

Thanks Ben, that worked a charm! The missing ingredient in my previous attempt was the self.active =

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Introducing a dominant sex modifier

Thanks Ben, that worked a charm! The missing ingredient in my previous attempt was the self.active =

Aug 15

Kevin Bairos-Novak, Ben Haller4

Aug 11

Modelling pleiotropy in a non-WF (Merging recipes 13.5 and 16.7)

Hi Kevin! I'm glad my previous comments were helpful. As for the failure to evolve, I guess it

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Modelling pleiotropy in a non-WF (Merging recipes 13.5 and 16.7)

Hi Kevin! I'm glad my previous comments were helpful. As for the failure to evolve, I guess it

Aug 11

Asad, Ben Haller2

Aug 10

Outputting multiple Tree Sequences from a single SLiM script

Hi Asad! Well, if t is defined to be 50000, then the expression "(t % 50000 == 0)" should

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Outputting multiple Tree Sequences from a single SLiM script

Hi Asad! Well, if t is defined to be 50000, then the expression "(t % 50000 == 0)" should

Aug 10

Manas G. A., Ben Haller2

Aug 7

Forcing neutral dynamics

Hi Manas! There are a few issues here. - First of all, I'm not sure why you're returning exp(

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Forcing neutral dynamics

Hi Manas! There are a few issues here. - First of all, I'm not sure why you're returning exp(

Aug 7

Viv, Ben Haller2

Aug 2

Changing mutation rate mid-simulation

Hi Viv! Check out the setMutationRate() method of Chromosome. :-> Happy modeling! Cheers, -B.

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Changing mutation rate mid-simulation

Hi Viv! Check out the setMutationRate() method of Chromosome. :-> Happy modeling! Cheers, -B.

Aug 2

Max Shpak, Ben Haller2

Aug 2

assigning mutations to specific coordinate range

Hi Max! I suppose I must be missing something, but don't you just want to do: x = rdunif(1, 4999,

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assigning mutations to specific coordinate range

Hi Max! I suppose I must be missing something, but don't you just want to do: x = rdunif(1, 4999,

Aug 2

Ben Haller

Aug 2

Evolution 2023 talk on Multispecies Modeling in SLiM

Hi all. Here's a link to the video for the talk I recently gave at Evolution in Albuquerque.

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Evolution 2023 talk on Multispecies Modeling in SLiM

Hi all. Here's a link to the video for the talk I recently gave at Evolution in Albuquerque.

Aug 2

Daniel Priego E., Ben Haller2

Aug 2

Migration fractions not adding up to 1.0

Hi! I think you've correctly diagnosed the issue. In the debugger, I see the total migration rate

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Migration fractions not adding up to 1.0

Hi! I think you've correctly diagnosed the issue. In the debugger, I see the total migration rate

Aug 2

Peter Ralph

Aug 1

pyslim 1.0.4: minor bugfix

Hi, all - I've just released pyslim 1.0.4 (it's available on pip now; on conda in a day or

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pyslim 1.0.4: minor bugfix

Hi, all - I've just released pyslim 1.0.4 (it's available on pip now; on conda in a day or

Aug 1

meagha...@gmail.com, … Peter Ralph4

Jul 31

Recapitation error using pyslim 1.0.3. and long burn-in period

Thanks! And, ah-ha, as you said, the problem is from having the recapitation time too long ago. It

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Recapitation error using pyslim 1.0.3. and long burn-in period

Thanks! And, ah-ha, as you said, the problem is from having the recapitation time too long ago. It

Jul 31

Zuxi Cui, Ben Haller5

Jul 20

wget nor working

Hi all, Here's a summary of discussion. I found GitHub using a temporary redirected address when

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wget nor working

Hi all, Here's a summary of discussion. I found GitHub using a temporary redirected address when

Jul 20

Svitlana Braichenko, Ben Haller7

Jul 19

Balancing selection with preferred frequency in nucleotide models

Hi Svitlana! Sorry for the slow reply – you got me at a very complicated time, with a SLiM workshop

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Balancing selection with preferred frequency in nucleotide models

Hi Svitlana! Sorry for the slow reply – you got me at a very complicated time, with a SLiM workshop

Jul 19

Aina Colomer, Peter Ralph4

Jul 17

Time Units Mismatch

Ah, that makes sense. No, there is no need to adjust any of the rates to take into account generation

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Time Units Mismatch

Ah, that makes sense. No, there is no need to adjust any of the rates to take into account generation

Jul 17

Peter Ralph

Jul 17

postdoc position available

Hi, all! Here's a postdoc ad that may be of interest to some of you: please pass it on, and

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postdoc position available

Hi, all! Here's a postdoc ad that may be of interest to some of you: please pass it on, and

Jul 17

Abigail Sequeira, Ben Haller6

Jul 13

Assortative mating scheme in nonWF model

Hi all. Just to resolve this thread: the rank() function is now added, and available if you compile

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Assortative mating scheme in nonWF model

Hi all. Just to resolve this thread: the rank() function is now added, and available if you compile

Jul 13

Jingyi Gao, Ben Haller2

Jul 13

Mimicking breeding program in WF model

Hi Jingyi. For this kind of specific control over patterns of mating, a nonWF model is recommended.

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Mimicking breeding program in WF model

Hi Jingyi. For this kind of specific control over patterns of mating, a nonWF model is recommended.

Jul 13

Zuxi Cui, Ben Haller2

Jul 10

Monomorphism from simulation

Hi Terry, It's hard to guess. I guess I'd suggest perhaps saving out a VCF file at each

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Monomorphism from simulation

Hi Terry, It's hard to guess. I guess I'd suggest perhaps saving out a VCF file at each

Jul 10

Zuxi Cui

Jul 7

Subpopulation Recombination Map

Hi there, I'm trying to optimize the simulation of a single human subpopulation by modeling

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Subpopulation Recombination Map

Hi there, I'm trying to optimize the simulation of a single human subpopulation by modeling

Jul 7

Steven Sun, Ben Haller3

Jul 6

Running several replicates through SLiMGui

Thank you! On Thu, Jul 6, 2023 at 4:38 PM Ben Haller <bha...@mac.com> wrote: You could open

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Running several replicates through SLiMGui

Thank you! On Thu, Jul 6, 2023 at 4:38 PM Ben Haller <bha...@mac.com> wrote: You could open

Jul 6