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

Description Usage Arguments Details Value Copyright Author(s)

Documentation for SLiM function treeSeqRememberIndividuals, 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	treeSeqRememberIndividuals(individuals)

individuals

An object of type Individual object. See details for description.

Permanently adds the individuals specified by individuals to the sample retained across tree sequence table simplification. This method may only be called if tree sequence recording has been turned on with initializeTreeSeq(). All currently living individuals are always retained across simplification; this method does not need to be called, and indeed should not be called, for that purpose. Instead, treeSeqRememberIndividuals() is for permanently adding particular individuals to the retained sample. Typically this would be used, for example, to retain particular individuals that you wanted to be able to trace ancestry back to in later analysis. However, this is not the typical usage pattern for tree sequence recording; most models will not need to call this method. The metadata (age, location, etc) that are stored in the resulting tree sequence are those values present at either (a) the final generation, if the individual is alive at the end of the simulation, or (b) the last time that the individual was remembered, if not. Calling treeSeqRememberIndividuals() on an individual that is already remembered will cause the archived information about the remembered individual to be updated to reflect the individual’s current state. A case where this is particularly important is for the spatial location of individuals in continuous-space models. SLiM automatically remembers the individuals that comprise the first generation of any new subpopulation created with addSubpop(), for easy recapitation and other analysis (see sections 17.2 and 17.10). However, since these first-generation individuals are remembered at the moment they are created, their spatial locations have not yet been set up, and will contain garbage – and those garbage values will be archived in their remembered state. If you need correct spatial locations of first- generation individuals for your post-simulation analysis, you should call treeSeqRememberIndividuals() explicitly on the first generation, after setting spatial locations, to update the archived information with the correct spatial positions.

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.