This callback specifies that a code block is providing logic to determine the breakpoints
in the genome for recombination. It is called during the generation of gametes for each gamete
in the generations it is active. This is achieved by setting breakpoints into the pseudo-variable
breakpoints, replacing the default (as integer positions). If breakpoints is modified
the callback must return T. If return(F) is used, SLiM will use the original
breakpoints.
see SLiM Manual: page 604
recombination(subpop_id)The id(s) of the subpopulation(s) to which this callback should apply. Can be an integer 1, 2, etc., or character "p1", "p2", etc.
None
Global variables available in reproduction callbacks:
The focal parent that is generating a gamete
One genome of the focal parent; this is the initial copy strand
The other genome of the focal parent
The subpopulation to which the focal parent belongs
An integer vector of crossover breakpoints
This is documentation for a function in the SLiM software, and has been modified from the official manual, which can be found here: http://benhaller.com/slim/SLiM_Manual.pdf. This documentation is Copyright © 2016-2020 Philipp Messer. All rights reserved. More information about SLiM can be found on the official website: https://messerlab.org/slim/
Other callbacks:
early(),
first(),
fitnessEffect(),
fitness(),
initialize(),
interaction(),
late(),
mateChoice(),
modifyChild(),
mutationEffect(),
mutation(),
reproduction(),
slim_callbacks(),
survival()
slim_block(recombination(), {
if (genome1.containsMarkerMutation(m2, 25000) ==
genome2.containsMarkerMutation(m2, 25000)) {
return(F)
}
inInv = (breakpoints > 25000) & (breakpoints < 75000)
if (!any(inInv)) {
return(F)
}
breakpoints = breakpoints[!inInv]
return(T)
})
#> A slimr_block:
#> <slimr_script[1]>
#> block_1:1:1 recombination() {
#> if (genome1.containsMarkerMutation(m2, 25000) == genome2.containsMarkerMutation(m2, 25000)) {
#> return(F);
#> }
#> inInv = (breakpoints > 25000) & (breakpoints < 75000);
#> if (!any(inInv)) {
#> return(F);
#> }
#> breakpoints = breakpoints[!inInv];
#> return(T);
#> }