Documentation for SLiM function outputFixedMutations, 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.
outputFixedMutations(filePath, append)An object of type null or string. Must be of length 1 (a
singleton). The default value is NULL. See details for description.
An object of type logical. Must be of length 1 (a singleton). The
default value is F. See details for description.
An object of type void.
Documentation for this function can be found in the official SLiM manual: page 721.
Output all fixed mutations - all Substitution objects, in other words (see section 1.5.2) - in a SLiM native format (see section 27.1.2 for output format details). If the optional parameter filePath is NULL (the default), output will be sent to Eidos's output stream (see section 4.2.1). Otherwise, output will be sent to the filesystem path specified by filePath, overwriting that file if append if F, or appending to the end of it if append is T. Mutations which have fixed but have not been turned into Substitution objects - typically because convertToSubstitution has been set to F for their mutation type (see section 25.11.1) - are not output; they are still considered to be segregating mutations by SLiM. In SLiM 3.3 and later, the output format includes the nucleotides associated with any nucleotide-based mutations; see section 27.1.2. Output is generally done in a late() event, so that the output reflects the state of the simulation at the end of a 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(),
outputFull(),
outputMutations(),
readFromPopulationFile(),
recalculateFitness(),
registerFitnessEffectCallback(),
registerMateChoiceCallback(),
registerModifyChildCallback(),
registerMutationCallback(),
registerMutationEffectCallback(),
registerRecombinationCallback(),
registerReproductionCallback(),
registerSurvivalCallback(),
simulationFinished(),
skipTick(),
subsetMutations(),
treeSeqCoalesced(),
treeSeqOutput(),
treeSeqRememberIndividuals(),
treeSeqSimplify()