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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/worksh
ops/workshops.html
.
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João Pedro Meireles
,
Ben Haller
4
Jul 2
Giving name to populations
Oh, wait, I see – you're not putting the subpopulations themselves into your Dictionary, just
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Giving name to populations
Oh, wait, I see – you're not putting the subpopulations themselves into your Dictionary, just
Jul 2
Viv
,
Ben Haller
4
Jul 2
Sampling siblings
You could simply call: apply(x, 0, "paste(applyValue, sep=',');") to generate a
unread,
Sampling siblings
You could simply call: apply(x, 0, "paste(applyValue, sep=',');") to generate a
Jul 2
Débora Brandt
, …
Miguel de Navascués
7
Jun 28
output tree sequence for subset of individuals
Thanks, that is very helpful! I might try to use that trick. I just wanted to add a note that I
unread,
output tree sequence for subset of individuals
Thanks, that is very helpful! I might try to use that trick. I just wanted to add a note that I
Jun 28
Peter Laurin
, …
Peter Ralph
6
Jun 27
Not achieving expected diversity metrics in simple diploid and haploid simulations
Thanks I'll try this out! Peter On Thursday, June 27, 2024 at 10:15:05 AM UTC-7 Peter Ralph wrote
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Not achieving expected diversity metrics in simple diploid and haploid simulations
Thanks I'll try this out! Peter On Thursday, June 27, 2024 at 10:15:05 AM UTC-7 Peter Ralph wrote
Jun 27
João Pedro Meireles
, …
Peter Ralph
4
Jun 25
Simulating a reintroduction programme (ex situ to in situ)
Hello Peter and Victor! Thank you so much for your tips and insights! The manipulation of the
unread,
Simulating a reintroduction programme (ex situ to in situ)
Hello Peter and Victor! Thank you so much for your tips and insights! The manipulation of the
Jun 25
Grace Rhodes
, …
Peter Ralph
3
Jun 16
Adapting Gravel et al Recipe to Include Increased Growth Rate In Recent Epoch
I agree with Chase (thanks!). But, let me add one more thing - "what's expected" from
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Adapting Gravel et al Recipe to Include Increased Growth Rate In Recent Epoch
I agree with Chase (thanks!). But, let me add one more thing - "what's expected" from
Jun 16
Ravi Vishwakarma
,
Ben Haller
5
Jun 13
Sampling individuals and calculating microsat expected Heterozygosity
So, Ravi is having trouble posting to the group (if you have difficulties, I recommend using the web
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Sampling individuals and calculating microsat expected Heterozygosity
So, Ravi is having trouble posting to the group (if you have difficulties, I recommend using the web
Jun 13
Padovani, Giada
,
Ben Haller
5
Jun 13
same SpatialMap for two subpopulations
No worries, this feature is a bit hidden – probably somebody else just learned about it because of
unread,
same SpatialMap for two subpopulations
No worries, this feature is a bit hidden – probably somebody else just learned about it because of
Jun 13
Jared Grummer
,
Ben Haller
3
Jun 12
Modeling reproductive skew
Thanks, Ben! I started reading last week and then got sidetracked with some other work. I'll look
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Modeling reproductive skew
Thanks, Ben! I started reading last week and then got sidetracked with some other work. I'll look
Jun 12
Luca Soldini
, …
Peter Ralph
4
Jun 11
Spatial non-WF model - avoiding center
Hi, Luca - the reason seems to be that the spatial position of offspring is not being set explicitly.
unread,
Spatial non-WF model - avoiding center
Hi, Luca - the reason seems to be that the spatial position of offspring is not being set explicitly.
Jun 11
Carlos Sarabia
,
Ben Haller
2
Jun 10
Setting different selection coefficients of the same mutation in different populations
Hi Carlos! Yes, this sort of thing is what a mutationEffect() callback is for (see section 10.2 of
unread,
Setting different selection coefficients of the same mutation in different populations
Hi Carlos! Yes, this sort of thing is what a mutationEffect() callback is for (see section 10.2 of
Jun 10
Mark Hibbins
, …
Ben Haller
3
Jun 7
Mutations with sex-specific DFEs
Thanks Peter! That said, it would be trivial to add an rlaplace() function; I just wait for people to
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Mutations with sex-specific DFEs
Thanks Peter! That said, it would be trivial to add an rlaplace() function; I just wait for people to
Jun 7
Dylan Clark
,
Ben Haller
2
Jun 4
Accidentally sampling genomes from killed individuals
Hi Dylan! No, this is not a concern with your code as designed. As the doc for killIndividuals() says
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Accidentally sampling genomes from killed individuals
Hi Dylan! No, this is not a concern with your code as designed. As the doc for killIndividuals() says
Jun 4
Anushka Jain
,
Ben Haller
2
Jun 3
Simulating HIV sequences
Hi Anushka! So I guess there are two questions here? One is about running MEGAX on your generated
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Simulating HIV sequences
Hi Anushka! So I guess there are two questions here? One is about running MEGAX on your generated
Jun 3
Carlos Sarabia
,
Peter Ralph
2
May 28
SLiMv4.2.2 crashing in Linux, not able to open files externally
Hello, Carlos - I've just built 4.2.2 on my linux machine and not encountered any of these issues
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SLiMv4.2.2 crashing in Linux, not able to open files externally
Hello, Carlos - I've just built 4.2.2 on my linux machine and not encountered any of these issues
May 28
Héctor Alessandro López Hérnandez
,
Ben Haller
2
May 21
Tracking allele frequency of m2 in each subpopulation
Hi Héctor! Thanks for the complete code for this question; that makes it much easier to reproduce the
unread,
Tracking allele frequency of m2 in each subpopulation
Hi Héctor! Thanks for the complete code for this question; that makes it much easier to reproduce the
May 21
Héctor Alessandro López Hérnandez
,
Ben Haller
4
May 21
Having problems with a stepping stone model and get printed frequencies
Hi Héctor, Sorry for the slow reply; life is a bit busy right now. Finished teaching a SLiM workshop
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Having problems with a stepping stone model and get printed frequencies
Hi Héctor, Sorry for the slow reply; life is a bit busy right now. Finished teaching a SLiM workshop
May 21
Ben Haller
2
May 10
SLiM 4.2.2 released
Hi folks. Just a quick followup to say: all SLiM installers are now updated to 4.2.2. That includes
unread,
SLiM 4.2.2 released
Hi folks. Just a quick followup to say: all SLiM installers are now updated to 4.2.2. That includes
May 10
font...@gmail.com
,
Ben Haller
5
May 10
logging results of a user defined function that uses a subset of the population as input
Hi João, Here is a minimal example of using addSuppliedColumn() with automatic logging, by setting
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logging results of a user defined function that uses a subset of the population as input
Hi João, Here is a minimal example of using addSuppliedColumn() with automatic logging, by setting
May 10
Ben Haller
May 9
interview on Data Skeptic podcast
Hey campers. I got interviewed about SLiM for a podcast called Data Skeptic: https://dataskeptic.com/
unread,
interview on Data Skeptic podcast
Hey campers. I got interviewed about SLiM for a podcast called Data Skeptic: https://dataskeptic.com/
May 9
Baron Koylass
,
Peter Ralph
5
Apr 30
Setting a starting allele frequency bias
Hi Peter Ralph, Great! I have actually done a combination of both ways you had proposed. I have now
unread,
Setting a starting allele frequency bias
Hi Peter Ralph, Great! I have actually done a combination of both ways you had proposed. I have now
Apr 30
Luis Fernández
,
Ben Haller
2
Apr 26
Microsatellite simulation using a transition matrix
Hi Luis! I wasn't able to run your model, since the .csv files required weren't provided, so
unread,
Microsatellite simulation using a transition matrix
Hi Luis! I wasn't able to run your model, since the .csv files required weren't provided, so
Apr 26
Prothama Manna
,
Ben Haller
2
Apr 26
Neg freq dep selection
Hi Prothama! The constant 1.5 is somewhat arbitrarily chosen, so that with a frequency of 0.0 (or
unread,
Neg freq dep selection
Hi Prothama! The constant 1.5 is somewhat arbitrarily chosen, so that with a frequency of 0.0 (or
Apr 26
Rohini Janivara
,
Ben Haller
4
Apr 26
subset individual method
Hi Rohini! Ah, this question is a bit different, actually, so I'll reply to it as well.
unread,
subset individual method
Hi Rohini! Ah, this question is a bit different, actually, so I'll reply to it as well.
Apr 26
Rohini Janivara
,
Ben Haller
4
Apr 26
Survival from fitness in nonWF models
Hi Rohini! > At the time of writing the email, I wanted information on the > specifics of the
unread,
Survival from fitness in nonWF models
Hi Rohini! > At the time of writing the email, I wanted information on the > specifics of the
Apr 26
Ben Haller
2
Apr 21
SLiM 4.2.1 released
Hi all. Just a quick followup to say that all of the various installers (macOS, Linux, Windows) are
unread,
SLiM 4.2.1 released
Hi all. Just a quick followup to say that all of the various installers (macOS, Linux, Windows) are
Apr 21
Rupert Mazzucco
,
Philipp Messer
3
Apr 19
curious asymmetry in mutation frequencies
No, that is probably it. Many thanks! Rupert Philipp Messer schrieb am Freitag, 19. April 2024 um 14:
unread,
curious asymmetry in mutation frequencies
No, that is probably it. Many thanks! Rupert Philipp Messer schrieb am Freitag, 19. April 2024 um 14:
Apr 19
Daiki Tagami
,
Ben Haller
3
Apr 17
Single crossover
Hi Ben, Thank you very much for your prompt response, and it was super helpful for me. I would also
unread,
Single crossover
Hi Ben, Thank you very much for your prompt response, and it was super helpful for me. I would also
Apr 17
Jared Grummer
,
Ben Haller
8
Apr 17
Recapitation vs. ancestral frequencies from vcf
Hi Ben, Okay, thanks for the reply! Writing out vcfs immediately after reading in sounds like a good
unread,
Recapitation vs. ancestral frequencies from vcf
Hi Ben, Okay, thanks for the reply! Writing out vcfs immediately after reading in sounds like a good
Apr 17
Sherif Negm
, …
Ben Haller
3
Apr 16
Using a custom dispersal density functon for indviduals
Hi Sherif! [ I see Peter has replied, and his answer has the virtue of being short. Here's a
unread,
Using a custom dispersal density functon for indviduals
Hi Sherif! [ I see Peter has replied, and his answer has the virtue of being short. Here's a
Apr 16