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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Zuxi Cui, Peter Ralph6

Sep 20

Default fitness formula

Ah-ha. It's because survival is still random (it's binomial, in fact); you can find some more

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Default fitness formula

Ah-ha. It's because survival is still random (it's binomial, in fact); you can find some more

Sep 20

Ben Haller

Sep 14

SLiM 4.0.1 released

Hi everybody! SLiM 4.0.1 has just been released. This is a minor release, mostly to fix a couple of

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SLiM 4.0.1 released

Hi everybody! SLiM 4.0.1 has just been released. This is a minor release, mostly to fix a couple of

Sep 14

Carlos Sarabia, Ben Haller3

Sep 13

SLiM script repeating from a prior state of the simulation rather than asked for, losing population

Dear Ben, I apologize in advance for taking so long to answer. I had left the question in the forum

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SLiM script repeating from a prior state of the simulation rather than asked for, losing population

Dear Ben, I apologize in advance for taking so long to answer. I had left the question in the forum

Sep 13

Zuxi Cui, Ben Haller2

Sep 10

Sample size of output population

Hi Terry. In nonWF models population size is often an emergent property of the model, not a top-down

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Sample size of output population

Hi Terry. In nonWF models population size is often an emergent property of the model, not a top-down

Sep 10

Tom Richards, Ben Haller3

Sep 6

Importing a vector of environmental Optimum conditions ?

Thanks Ben, Very much appreciated!! cheers, Tom On Wednesday, 7 September 2022 at 12:16:24 am UTC+10

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Importing a vector of environmental Optimum conditions ?

Thanks Ben, Very much appreciated!! cheers, Tom On Wednesday, 7 September 2022 at 12:16:24 am UTC+10

Sep 6

Zuxi Cui, Ben Haller7

Aug 30

relation between mating IDs and output IDs

OK. I will try it. Thanks. Terry On Tue, Aug 30, 2022 at 8:04 PM Ben Haller <bhaller@mac.com>

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relation between mating IDs and output IDs

OK. I will try it. Thanks. Terry On Tue, Aug 30, 2022 at 8:04 PM Ben Haller <bhaller@mac.com>

Aug 30

Zuxi Cui, Ben Haller5

Aug 30

createLogFile() function

Great, thanks! On Tue, Aug 30, 2022 at 1:55 PM Ben Haller <bhaller@mac.com> wrote: Yes; see

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createLogFile() function

Great, thanks! On Tue, Aug 30, 2022 at 1:55 PM Ben Haller <bhaller@mac.com> wrote: Yes; see

Aug 30

Ben Haller2

Aug 30

SLiM 4.0 released

Hi folks. Just a quick announcement that, thanks to Russell Dinnage, the "pacman" installer

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SLiM 4.0 released

Hi folks. Just a quick announcement that, thanks to Russell Dinnage, the "pacman" installer

Aug 30

Zuxi Cui2

Aug 29

error with reproduce function

On Mon, Aug 29, 2022 at 5:12 PM Zuxi Cui <zxc307@case.edu> wrote: You are right. There were

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error with reproduce function

On Mon, Aug 29, 2022 at 5:12 PM Zuxi Cui <zxc307@case.edu> wrote: You are right. There were

Aug 29

Olivia Johnson, Ben Haller3

Aug 27

Error when using tree sequence recording in conditional simulations

Hi all. A followup regarding the bug that Olivia reported in SLiM 4.0. It was a trivial error in the

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Error when using tree sequence recording in conditional simulations

Hi all. A followup regarding the bug that Olivia reported in SLiM 4.0. It was a trivial error in the

Aug 27

Svitlana Braichenko, Ben Haller5

Aug 25

Balancing selection with preferred frequency in nucleotide models

Hi Benjamin Thanks, all seems to work! Best Svitlana On Tuesday, 23 August 2022 at 21:51:08 UTC+1 bha

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Balancing selection with preferred frequency in nucleotide models

Hi Benjamin Thanks, all seems to work! Best Svitlana On Tuesday, 23 August 2022 at 21:51:08 UTC+1 bha

Aug 25

Ana Yansi MORALES ARCE, Ben Haller2

Aug 23

epistasis: mutation that modifies the past and current selection coefficients

Hi Ana. You write "The mutationEffect() callback mechanism doesn't work for me because it

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epistasis: mutation that modifies the past and current selection coefficients

Hi Ana. You write "The mutationEffect() callback mechanism doesn't work for me because it

Aug 23

clarka...@gmail.com, r.di...@gmail.com3

Aug 18

Qt platform plugin (Windows users)

Turns out it was a PATH issue as qt found a home off the beaten track. Compiled the new release

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Qt platform plugin (Windows users)

Turns out it was a PATH issue as qt found a home off the beaten track. Compiled the new release

Aug 18

Maeve-Darly Domond, Ben Haller7

Aug 8

Creating Multiple Subpopulations w/ For Loop from 2 Initial Populations

Hi, Thank you Dr. Haller for the assistance! That makes sense. Best, Maeve-Darly Domond On Monday,

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Creating Multiple Subpopulations w/ For Loop from 2 Initial Populations

Hi, Thank you Dr. Haller for the assistance! That makes sense. Best, Maeve-Darly Domond On Monday,

Aug 8

Peter Ralph

Jul 25

Re: tskit union() creates additional subpopulation

I suspect that this is because in your SLiM script to create ts1 you are calling the population p1 ;

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Re: tskit union() creates additional subpopulation

I suspect that this is because in your SLiM script to create ts1 you are calling the population p1 ;

Jul 25

Daiki Tagami, Ben Haller4

Jul 25

Output of 2D simulation

Hi Daiki, I'm surprised the 40000 subpopulations didn't work for you in SLiMgui; it worked

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Output of 2D simulation

Hi Daiki, I'm surprised the 40000 subpopulations didn't work for you in SLiMgui; it worked

Jul 25

Ben Haller

Jul 24

Bug with mutation frequencies/counts in script

Hi folks. I've just found and fixed a significant bug, which I think merits an email to slim-

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Bug with mutation frequencies/counts in script

Hi folks. I've just found and fixed a significant bug, which I think merits an email to slim-

Jul 24

Max Shpak, … Peter Ralph5

Jul 22

merging multiple tree sequences into a single demographic model

Hm - there will be in SLiM v4 - but, can't you just specify your demography in msprime using the

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merging multiple tree sequences into a single demographic model

Hm - there will be in SLiM v4 - but, can't you just specify your demography in msprime using the

Jul 22

Daiki Tagami, Ben Haller9

Jul 20

Setting birth/death rate

Dear Ben, Thank you very much for your detailed reply on uniform vs poisson distribution. It was very

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Setting birth/death rate

Dear Ben, Thank you very much for your detailed reply on uniform vs poisson distribution. It was very

Jul 20

Peter Ralph

Jul 7

Re: saving tree sequence containing mutation

Hello again, Max! > How can I modify this to generate as output a tree that only contains the muts

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Re: saving tree sequence containing mutation

Hello again, Max! > How can I modify this to generate as output a tree that only contains the muts

Jul 7

Max Shpak, Ben Haller4

Jul 6

mutationFrequencies(): return 0.0 rather than float(0)?

Hi Max. When the allele has been lost, the mutation is no longer part of the simulation; it is

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mutationFrequencies(): return 0.0 rather than float(0)?

Hi Max. When the allele has been lost, the mutation is no longer part of the simulation; it is

Jul 6

Zuxi Cui, Ben Haller7

Jul 6

Question about the randomization of mating

Hi Terry. Recipe 16.12, which I pointed you to before, is a nonWF model and does not use a mateChoice

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Question about the randomization of mating

Hi Terry. Recipe 16.12, which I pointed you to before, is a nonWF model and does not use a mateChoice

Jul 6

Max Shpak, Ben Haller7

Jul 5

recapitation of slim ts gives very low nucleotide diversity

Hi Max, Indeed, yes; thanks for the correction. :-> And to clarify: the sweep recipes in chapter 9

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recapitation of slim ts gives very low nucleotide diversity

Hi Max, Indeed, yes; thanks for the correction. :-> And to clarify: the sweep recipes in chapter 9

Jul 5

Max Shpak, Peter Ralph2

Jun 30

subpopulation information lost in treeSeqOutput?

Hi, Max! The first bit of confusion here is just from terminology: what SLiM calls a "

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subpopulation information lost in treeSeqOutput?

Hi, Max! The first bit of confusion here is just from terminology: what SLiM calls a "

Jun 30

Kadee Lawrence, … Peter Ralph3

Jun 29

Errors with pyslim.recapitate( )

Hi, Kadee! Let's see: there's some kind of mismatch between where the lineages are in the

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Errors with pyslim.recapitate( )

Hi, Kadee! Let's see: there's some kind of mismatch between where the lineages are in the

Jun 29

Max Shpak, Ben Haller2

Jun 23

introducing multiple copies of a mutation and tracking their frequency

Hi Max. Yes, each call to addNewDrawnMutation() will give you a separate mutational lineage with a

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introducing multiple copies of a mutation and tracking their frequency

Hi Max. Yes, each call to addNewDrawnMutation() will give you a separate mutational lineage with a

Jun 23

Max Shpak, Ben Haller2

Jun 23

questions on conditioning selective sweep on fixation (or establishment)

Hi Max! Regarding your first question: The difference is between mutations still being simulated (

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questions on conditioning selective sweep on fixation (or establishment)

Hi Max! Regarding your first question: The difference is between mutations still being simulated (

Jun 23

MARCEL LUCAS SÁNCHEZ, Ben Haller4

Jun 21

How can I lower the computational demand of my SLiM analysis?

Hi Marcel, To your questions, 1. I think I would suggest that you simulate a chromosome that is

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How can I lower the computational demand of my SLiM analysis?

Hi Marcel, To your questions, 1. I think I would suggest that you simulate a chromosome that is

Jun 21

Mayra Banuelos, Ben Haller6

Jun 16

Modeling a single microsatellite surrounded by 100kb bases

Found the bugs! Just in case it is helpful for anyone in the future, the first thing was to set the

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Modeling a single microsatellite surrounded by 100kb bases

Found the bugs! Just in case it is helpful for anyone in the future, the first thing was to set the

Jun 16

DAVID VENDRAMI, … Ben Haller8

Jun 15

non neutral burn-in for large simulation

Hi Benjamin, Dang, that's true! What a silly oversight. Thank you very much for spotting this!

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non neutral burn-in for large simulation

Hi Benjamin, Dang, that's true! What a silly oversight. Thank you very much for spotting this!

Jun 15