Documentation for SLiM function killIndividuals, which is a method of the
SLiM class Species.
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.
killIndividuals(individuals)An object of type Individual object. See details for description.
An object of type void.
Documentation for this function can be found in the official SLiM manual: page 720.
Immediately kills the individuals in individuals. This removes them from their subpopulation and gives them an index value of -1. The Individual objects are not freed immediately, since references to them could still exist in local Eidos variables; instead, the individuals are kept in a temporary "graveyard" until they can be freed safely. It therefore continues to be safe to use them and their genomes, except that accessing their subpopulation property will raise an error since they no longer have a subpopulation. Note that the indices and order of individuals and genomes in all source subpopulations will change unpredictably as a side effect of this method. All evaluated interactions are invalidated as a side effect of calling this method. Note that this method is only for use in nonWF models, in which mortality is managed manually by the model script. In WF models, mortality is managed automatically by the SLiM core when the new offspring generation becomes the parental generation and the previous parental generation dies; mortality does not otherwise occur in WF models. In nonWF models, mortality normally occurs during the survival stage of the tick cycle (see section 24.4), based upon the fitness values calculated by SLiM, and survival() callbacks can influence the outcome of that survival stage. Calls to killIndividuals(), on the other hand, can be made at any time during first(), early(), or late() events, and the result cannot be modified by survival() callbacks; the given individuals are simply immediately killed. This method therefore provides an alternative, and relatively rarely used, mortality mechanism that is disconnected from fitness.
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 Species:
Species,
addSubpopSplit(),
addSubpop(),
countOfMutationsOfType(),
individualsWithPedigreeIDs(),
mutationCounts(),
mutationFrequencies(),
mutationsOfType(),
outputFixedMutations(),
outputFull(),
outputMutations(),
readFromPopulationFile(),
recalculateFitness(),
registerFitnessEffectCallback(),
registerMateChoiceCallback(),
registerModifyChildCallback(),
registerMutationCallback(),
registerMutationEffectCallback(),
registerRecombinationCallback(),
registerReproductionCallback(),
registerSurvivalCallback(),
simulationFinished(),
skipTick(),
subsetMutations(),
treeSeqCoalesced(),
treeSeqOutput(),
treeSeqRememberIndividuals(),
treeSeqSimplify()