Documentation for SLiM function initializeRecombinationRate, which is a
method of the SLiM class Initialize.
Note that the R function is a stub, it does not do anything in R (except bring
up this documentation). It will only do
anything useful when used inside a slim_block function further
nested in a slim_script
function call, where it will be translated into valid SLiM code as part of a
full SLiM script.
initializeRecombinationRate(rates, ends, sex)An object of type numeric. See details for description.
An object of type null or integer. The default value is NULL.
See details for description.
An object of type string. Must be of length 1 (a singleton). The
default value is "*". See details for description.
An object of type void.
Documentation for this function can be found in the official SLiM manual: page 653.
Set the recombination rate per base position per gamete. To be precise, this recombination rate is the probability that a breakpoint will occur between one base and the next base; note that this is different from how the mutation rate is defined (see initializeMutationRate()). All rates must be in the interval [0.0, 0.5]. A rate of 0.5 implies complete independence between the adjacent bases, which might be used to implement independent assortment of loci located on different chromosomes (see the example below). Whether a breakpoint occurs between two bases is then, in effect, determined by a binomial draw with a single trial and the given rate as probability (but under the hood SLiM uses a mathematically equivalent but much more efficient strategy). The recombinational process in SLiM will never generate more then one crossover between one base and the next (in one generation/ genome), and a supplied rate of 0.5 will therefore result in an actual probability of 0.5 for a crossover at the relevant position. (Note that this was not true in SLiM 2.x and earlier, however; their implementation of recombination resulted in a crossover probability of about 39.3 inaccurate approximation method. Recombination rates lower than about 0.01 would have been essentially exact, since the approximation error became large only as the rate approached 0.5.) There are two ways to call this function. If the optional ends parameter is NULL (the default), then rates must be a singleton value that specifies a single recombination rate to be used along the entire chromosome. If, on the other hand, ends is supplied, then rates and ends must be the same length, and the values in ends must be specified in ascending order. In that case, rates and ends taken together specify the recombination rates to be used along successive contiguous stretches of the chromosome, from beginning to end; the last position specified in ends should extend to the end of the chromosome (i.e. at least to the end of the last genomic element, if not further). Note that a recombination rate of 1 centimorgan/Mbp corresponds to a recombination rate of 1e-8 in the units used by SLiM. For example, if the following call is made: initializeRecombinationRate(c(0, 0.5, 0), c(5000, 5001, 9999)); then the result is that the recombination rates between bases 0 / 1, 1 / 2, ..., 4999 / 5000 will be 0, the rate between bases 5000 / 5001 will be 0.5, and the rate between bases 5001 / 5002 onward (up to 9998 / 9999) will again be 0. Setting the recombination rate between one specific pair of bases to 0.5 forces recombination to occur with a probability of 0.5 between those bases, which effectively breaks the simulated locus into separate chromosomes at that point; this example effectively has one simulated chromosome from base position 0 to 5000, and another from 5001 to 9999. If the optional sex parameter is "*" (the default), then the supplied recombination rate map will be used for both sexes (which is the only option for hermaphroditic simulations). In sexual simulations sex may be "M" or "F" instead, in which case the supplied recombination map is used only for that sex. In this case, two calls must be made to initializeRecombinationRate(), one for each sex, even if a rate of zero is desired for the other sex; no default recombination map is supplied.
This is documentation for a function in the SLiM software, and has been reproduced 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 Initialize:
Init,
initializeAncestralNucleotides(),
initializeGeneConversion(),
initializeGenomicElementType(),
initializeGenomicElement(),
initializeHotspotMap(),
initializeInteractionType(),
initializeMutationRate(),
initializeMutationTypeNuc(),
initializeMutationType(),
initializeSLiMModelType(),
initializeSLiMOptions(),
initializeSex(),
initializeSpecies(),
initializeTreeSeq()
## This just brings up the documentation:
initializeRecombinationRate()