Documentation for SLiM function initializeMutationType, 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.
initializeMutationType(id, dominanceCoeff, distributionType, ...)An object of type integer or string. Must be of length 1 (a singleton). See details for description.
An object of type numeric. Must be of length 1 (a singleton). See details for description.
An object of type string. Must be of length 1 (a singleton). See details for description.
An object of type NA. NA See details for description.
An object of type MutationType object. Return will be of length 1 (a singleton)
Documentation for this function can be found in the official SLiM manual: page 652.
Add a mutation type at initialization time. The id must not already be used for any mutation type in the simulation. The id parameter may be either an integer giving the ID of the new mutation type, or a string giving the name of the new mutation type (such as "m5" to specify an ID of 5). The dominanceCoeff parameter supplies the dominance coefficient for the mutation type; 0.0 produces no dominance, 1.0 complete dominance, and values greater than 1.0, overdominance. The distributionType may be "f", in which case the ellipsis ... should supply a numeric$ fixed selection coefficient; "e", in which case the ellipsis should supply a numeric$ mean selection coefficient for an exponential distribution; "g", in which case the ellipsis should supply a numeric$ mean selection coefficient and a numeric$ alpha shape parameter for a gamma distribution; "n", in which case the ellipsis should supply a numeric$ mean selection coefficient and a numeric$ sigma (standard deviation) parameter for a normal distribution; "p", in which case the ellipsis should supply a numeric$ mean selection coefficient and a numeric$ scale parameter for a Laplace distribution; "w", in which case the ellipsis should supply a numeric$ λ scale parameter and a numeric$ k shape parameter for a Weibull distribution; or "s", in which case the ellipsis should supply a string$ Eidos script parameter. See section 25.11 for discussion of the various DFEs and their uses. The global symbol for the new mutation type is immediately available; the return value also provides the new object. Note that by default in WF models, all mutations of a given mutation type will be converted into Substitution objects when they reach fixation, for efficiency reasons. If you need to disable this conversion, to keep mutations of a given type active in the simulation even after they have fixed, you can do so by setting the convertToSubstitution property of MutationType to F. In contrast, by default in nonWF models mutations will not be converted into Substitution objects when they reach fixation; convertToSubstitution is F by default in nonWF models. To enable conversion in nonWF models for neutral mutation types with no indirect fitness effects, you should therefore set convertToSubstitution to T. See sections 23.3, 24.5, and 25.11.1 for further discussion regarding the convertToSubstitution property.
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(),
initializeRecombinationRate(),
initializeSLiMModelType(),
initializeSLiMOptions(),
initializeSex(),
initializeSpecies(),
initializeTreeSeq()
## This just brings up the documentation:
initializeMutationType()