removeMutations: SLiM method removeMutations
In rdinnager/slimrlang: Write SLiM Population Genetics Simulation Scripts in R

Description Usage Arguments Details Value Copyright Author(s)

Documentation for SLiM function removeMutations, which is a method of the SLiM class Genome. 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.

1	removeMutations(mutations, substitute)

`mutations`	An object of type null or Mutation object. The default value is `NULL`. See details for description.
`substitute`	An object of type logical. Must be of length 1 (a singleton). The default value is `F`. See details for description.

Remove the mutations in mutations from the target genome(s), if they are present (if they are not present, they will be ignored). If NULL is passed for mutations (which is the default), then all mutations will be removed from the target genomes; in this case, substitute must be F (a specific vector of mutations to be substituted is required). Note that the Mutation objects removed remain valid, and will still be in the simulation’s mutation registry (i.e. will be returned by SLiMSim’s mutations property), until the next generation. Changing this will normally affect the fitness values calculated at the end of the current generation; if you want current fitness values to be affected, you can call SLiMSim’s method recalculateFitness() – but see the documentation of that method for caveats. The optional parameter substitute was added in SLiM 2.2, with a default of F for backward compatibility. If substitute is T, Substitution objects will be created for all of the removed mutations so that they are recorded in the simulation as having fixed, just as if they had reached fixation and been removed by SLiM’s own internal machinery. This will occur regardless of whether the mutations have in fact fixed, regardless of the convertToSubstitution property of the relevant mutation types, and regardless of whether all copies of the mutations have even been removed from the simulation (making it possible to create Substitution objects for mutations that are still segregating). It is up to the caller to perform whatever checks are necessary to preserve the integrity of the simulation’s records. Typically substitute will only be set to T in the context of calls like sim.subpopulations.genomes.removeMutations(muts, T), such that the substituted mutations are guaranteed to be entirely removed from circulation. As mentioned above, substitute may not be T if mutations is NULL.

An object of type void.

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/

Benjamin C Haller (bhaller@benhaller.com) and Philipp W Messer (messer@cornell.edu)

rdinnager/slimrlang documentation built on June 20, 2020, 8:17 p.m.