Documentation for SLiM function setMutationRate, which is a method of the
SLiM class Chromosome.
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.
setMutationRate(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 663.
Set the mutation rate per base position per gamete. There are two ways to call this method. If the optional ends parameter is NULL (the default), then rates must be a singleton value that specifies a single mutation 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 mutation 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 (as previously determined, during simulation initialization). See the initializeMutationRate() function for further discussion of precisely how these rates and positions are interpreted. If the optional sex parameter is "*" (the default), then the supplied mutation 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 mutation rate map is used only for that sex. Note that whether sex-specific mutation rate maps will be used is set by the way that the simulation is initially configured with initializeMutationRate(), and cannot be changed with this method; so if the simulation was set up to use sex-specific mutation rate maps then sex must be "M" or "F" here, whereas if it was set up not to, then sex must be "*" or unsupplied here. If a simulation needs sexspecific mutation rate maps only some of the time, the male and female maps can simply be set to be identical the rest of the time. The mutation rate intervals are normally a constant in simulations, so be sure you know what you are doing. In nucleotide-based models, setMutationRate() may not be called. If variation in the mutation rate along the chromosome is desired, setHotspotMap() should be used.
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 Chromosome:
Chromosome,
ancestralNucleotides(),
drawBreakpoints(),
setAncestralNucleotides(),
setGeneConversion(),
setHotspotMap(),
setRecombinationRate()