Documentation for SLiM function treeSeqOutput, 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.
treeSeqOutput(path, simplify, includeModel, metadata)An object of type string. Must be of length 1 (a singleton). See details for description.
An object of type logical. Must be of length 1 (a singleton).
The default value is T. See details for description.
An object of type logical. Must be of length 1 (a
singleton). The default value is T. See details for description.
An object of type null. Must be of length 1 (a singleton). The
default value is NULL. See details for description.
An object of type void.
Documentation for this function can be found in the official SLiM manual: page 728.
Outputs the current tree sequence recording tables to the path specified by path. This method may only be called if tree sequence recording has been turned on with initializeTreeSeq(). If simplify is T (the default), simplification will be done immediately prior to output; this is almost always desirable, unless a model wishes to avoid simplification entirely. (Note that if simplification is not done, then all genomes since the last simplification will be marked as samples in the resulting tree sequence.) A binary tree sequence file will be written to the specified path; a filename extension of .trees is suggested for this type of file. Normally, the full SLiM script used to generate the tree sequence is written out to the provenance entry of the tree sequence file, to the model subkey of the parameters top-level key. Supplying F for includeModel suppresses output of the full script; see section 27.4.6 for further discussion. A Dictionary object containing user-generated metadata may be supplied with the metadata parameter. If present, this dictionary will be serialized as JSON and attached to the saved tree sequence under a key named user_metadata, within the SLiM key (see section 27.4.5). If tskit is used to read the tree sequence in Python, this metadata will automatically be deserialized and made available at ts.metadata["SLiM"]["user_metadata"]. This metadata dictionary is not used by SLiM, or by pyslim, tskit, or msprime; you may use it for any purpose you wish. Note that metadata may actually be any subclass of Dictionary, such as a DataFrame. It can even be a Species object such as sim, or a LogFile instance; however, only the keys and values contained by the object's Dictionary superclass state will be serialized into the metadata (properties of the subclass will be ignored). This metadata dictionary can be recovered from the saved file using the treeSeqMetadata() function.
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(),
treeSeqCoalesced(),
treeSeqRememberIndividuals(),
treeSeqSimplify()