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

Description Usage Arguments Details Value Copyright Author(s)

Documentation for SLiM function recalculateFitness, which is a method of the SLiM class SLiMSim. 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	recalculateFitness(generation)

generation

An object of type null or integer. Must be of length 1 (a singleton). The default value is NULL. See details for description.

Force an immediate recalculation of fitness values for all individuals in all subpopulations. Normally fitness values are calculated at a fixed point in each generation, and those values are cached and used throughout the following generation. If simulation parameters are changed in script in a way that affects fitness calculations, and if you wish those changes to take effect immediately rather than taking effect at the end of the current generation, you may call recalculateFitness() to force an immediate recalculation and recache. The optional parameter generation provides the generation for which fitness() callbacks should be selected; if it is NULL (the default), the simulation’s current generation value, sim.generation, is used. If you call recalculateFitness() in an early() event in a WF model, you may wish this to be sim.generation - 1 in order to utilize the fitness() callbacks for the previous generation, as if the changes that you have made to fitness-influencing parameters were already in effect at the end of the previous generation when the new generation was first created and evaluated (usually it is simpler to just make such changes in a late() event instead, however, in which case calling recalculateFitness() is probably not necessary at all since fitness values will be recalculated immediately afterwards). Regardless of the value supplied for generation here, sim.generation inside fitness() callbacks will report the true generation number, so if your callbacks consult that parameter in order to create generation-specific fitness effects you will need to handle the discrepancy somehow. (Similar considerations apply for nonWF models that call recalculateFitness() in a late() event, which is also not advisable in general.) After this call, the fitness values used for all purposes in SLiM will be the newly calculated values. Calling this method will trigger the calling of any enabled and applicable fitness() callbacks, so this is quite a heavyweight operation; you should think carefully about what side effects might result (which is why fitness recalculation does not just occur automatically after changes that might affect fitness values).

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.