Documentation for SLiM function treeSeqCoalesced, 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.
treeSeqCoalesced(void)An object of type . See details for description.
An object of type logical. Return will be of length 1 (a singleton)
Documentation for this function can be found in the official SLiM manual: page 728.
Returns the coalescence state for the recorded tree sequence at the last simplification. The returned value is a logical singleton flag, T to indicate that full coalescence was observed at the last treesequence simplification (meaning that there is a single ancestral individual that roots all ancestry trees at all sites along the chromosome - although not necessarily the same ancestor at all sites), or F if full coalescence was not observed. For simple models, reaching coalescence may indicate that the model has reached an equilibrium state, but this may not be true in models that modify the dynamics of the model during execution by changing migration rates, introducing new mutations programmatically, dictating non-random mating, etc., so be careful not to attach more meaning to coalescence than it is due; some models may require burn-in beyond coalescence to reach equilibrium, or may not have an equilibrium state at all. Also note that some actions by a model, such as adding a new subpopulation, may cause the coalescence state to revert from T back to F (at the next simplification), so a return value of T may not necessarily mean that the model is coalesced at the present moment - only that it was coalesced at the last simplification. This method may only be called if tree sequence recording has been turned on with initializeTreeSeq(); in addition, checkCoalescence=T must have been supplied to initializeTreeSeq(), so that the necessary work is done during each tree-sequence simplification. Since this method does not perform coalescence checking itself, but instead simply returns the coalescence state observed at the last simplification, it may be desirable to call treeSeqSimplify() immediately before treeSeqCoalesced() to obtain up-to-date information. However, the speed penalty of doing this in every tick would be large, and most models do not need this level of precision; usually it is sufficient to know that the model has coalesced, without knowing whether that happened in the current tick or in a recent preceding tick.
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:
Sp,
addSubpopSplit(),
addSubpop(),
countOfMutationsOfType(),
individualsWithPedigreeIDs(),
killIndividuals(),
mutationCounts(),
mutationFrequencies(),
mutationsOfType(),
outputFixedMutations(),
outputFull(),
outputMutations(),
readFromPopulationFile(),
recalculateFitness(),
registerFitnessEffectCallback(),
registerMateChoiceCallback(),
registerModifyChildCallback(),
registerMutationCallback(),
registerMutationEffectCallback(),
registerRecombinationCallback(),
registerReproductionCallback(),
registerSurvivalCallback(),
simulationFinished(),
skipTick(),
subsetMutations(),
treeSeqOutput(),
treeSeqRememberIndividuals(),
treeSeqSimplify()