Documentation for SLiM function outputFull, 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.
outputFull(
filePath,
binary,
append,
spatialPositions,
ages,
ancestralNucleotides,
pedigreeIDs
)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 logical. Must be of length 1 (a singleton). The
default value is F. 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 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 F. See details for description.
An object of type void.
Documentation for this function can be found in the official SLiM manual: page 722.
Output the state of the entire population (see section 27.1.1 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. When writing to a file, a logical flag, binary, may be supplied as well. If binary is T, the population state will be written as a binary file instead of a text file (binary data cannot be written to the standard output stream). The binary file is usually smaller, and in any case will be read much faster than the corresponding text file would be read. Binary files are not guaranteed to be portable between platforms; in other words, a binary file written on one machine may not be readable on a different machine (but in practice it usually will be, unless the platforms being used are fairly unusual). If binary is F (the default), a text file will be written. Beginning with SLiM 2.3, the spatialPositions parameter may be used to control the output of the spatial positions of individuals in species for which continuous space has been enabled using the dimensionality option of initializeSLiMOptions(). If spatialPositions is F, the output will not contain spatial positions, and will be identical to the output generated by SLiM 2.1 and later. If spatialPositions is T, spatial position information will be output if it is available (see section 27.1.1 for format details). If the species does not have continuous space enabled, the spatialPositions parameter will be ignored. Positional information may be output for all output destinations - the Eidos output stream, a text file, or a binary file. Beginning with SLiM 3.0, the ages parameter may be used to control the output of the ages of individuals in nonWF simulations. If ages is F, the output will not contain ages, preserving backward compatibility with the output format of SLiM 2.1 and later. If ages is T, ages will be output for nonWF models (see section 27.1.1 for format details). In WF simulations, the ages parameter will be ignored. Beginning with SLiM 3.3, the ancestralNucleotides parameter may be used to control the output of the ancestral nucleotide sequence in nucleotide-based models (see section 27.1.1 for format details). If ancestralNucleotides is F, the output will not contain ancestral nucleotide information, and so the ancestral sequence will not be restored correctly if the saved file is loaded with readPopulationFile(). This option is provided because the ancestral sequence may be quite large, for models with a long chromosome (e.g., 1 GB if the chromosome is 109 bases long, when saved in text format, or 0.25 GB when saved in binary format). If the model is not nucleotide-based (as enabled with the nucleotideBased parameter to initializeSLiMOptions()), the ancestralNucleotides parameter will be ignored. Note that in nucleotide-based models the output format will always include the nucleotides associated with any nucleotide-based mutations; the ancestralNucleotides flag governs only the ancestral sequence. Beginning with SLiM 3.5, the pedigreeIDs parameter may be used to request that pedigree IDs be written out (and read in by readFromPopulationFile(), subsequently). This option is turned off (F) by default, to preserve backward compatibility; if it is turned on (T), different file version values will be used, and backward compatibility with previous versions of SLiM will be lost (see section 27.1.1). This option may only be used if SLiM's optional pedigree tracking has been enabled with initializeSLiMOptions(keepPedigrees=T). 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(),
outputFixedMutations(),
outputMutations(),
readFromPopulationFile(),
recalculateFitness(),
registerFitnessEffectCallback(),
registerMateChoiceCallback(),
registerModifyChildCallback(),
registerMutationCallback(),
registerMutationEffectCallback(),
registerRecombinationCallback(),
registerReproductionCallback(),
registerSurvivalCallback(),
simulationFinished(),
skipTick(),
subsetMutations(),
treeSeqCoalesced(),
treeSeqOutput(),
treeSeqRememberIndividuals(),
treeSeqSimplify()