Initialize

Documentation for Initialize class from SLiM

Details

Before a SLiM simulation can be run, the various classes underlying the simulation need to be set up with an initial configuration. Simulation configuration in SLiM is done in initialize() callbacks that run prior to the beginning of simulation execution. Eidos callbacks are discussed more broadly in chapter 26, but for our present purposes, the idea is very simple. In your input file, you can write something like this: initialize() ... The initialize() declaration specifies that the script block is to be executed as an initialize() callback before the simulation starts. The script between the braces would set up various aspects of the simulation by calling initialization functions. These are SLiM functions that may be called only in an initialize() callback, and their names begin with initialize to mark them clearly as such. You may also use other Eidos functionality in these callbacks; for example, you might automate generating a complex genetic structure containing many genes by using a for loop. In general, it is required for a species to set up its genetic structure in an initialize() callback with calls to initializeMutationRate(), initializeRecombinationRate(), initializeMutationType(), initializeGenomicElementType(), and initializeGenomicElement(); species must call all of these, setting up at least one mutation type, at least one genomic element type, and at least one genomic element. The exception to this general rule is for species that have no genetics at all - species that are modeled purely on an ecological/behavioral level. Such species may be defined by calling none of those initialization functions; in this case, SLiM will default to a zero-length chromosome with mutation and recombination rates of zero. A middle ground between these two configuration paths is not allowed; either a species has no genetics, or it fully defines its genetics. One thing worth mentioning is that in the context of an initialize() callback, the sim global representing the species being simulated is not defined. This is because the state of the simulation is not yet constructed fully, and accessing partially constructed state would not be safe. (Similarly, in multispecies models, the community object and the objects representing individual species are not yet defined.) The above initialize() callback syntax implicitly declares a single species, with the default name of sim, and therefore sets up a single-species model. It is also possible to explicitly declare a species, which is done with this extended syntax (using a species name of fox as an example): species fox initialize() ... This sets up a multispecies model (although it might, in fact, declare only a single species, fox; the term "multispecies", in SLiM parlance, really means "explicitly declared species", but multispecies models almost always do contain multiple species, so the distinction is unimportant). See section 1.9 and chapter 19 for further discussion of multispecies models; in most respects they work identically to single-species models, so we will tend to focus on the single-species case in the reference documentation, with a species name of sim, for simplicity and clarity. In single-species models all initialization can be done in a single initialize() callback (or you can have more than one, if you wish). In multispecies models, each species must be initialized with its own callback(s), as shown above. In addition, multispecies models also support an optional community-level initialization callback that is declared as follows: species all initialize() ... These callbacks, technically called non-species-specific initialize() callbacks, provide a place for community-level initialization to occur. They are run before any species-specific initialize() callbacks are run, so you might wish to set up all of your model parameters in one, providing a single location for all parameters. In multispecies models, the initialization functions initializeSLiMModelType() and initializeInteractionType() may only be called from a nonspecies- specific initialize() callback, since those aspects of model configuration span the entire community. In single-species models, these functions may be called from an ordinary initialize() callback for simplicity and backward compatibility. This class has the following methods (functions):

• initializeAncestralNucleotides

• initializeGeneConversion

• initializeGenomicElement

• initializeGenomicElementType

• initializeHotspotMap

• initializeInteractionType

• initializeMutationRate

• initializeMutationType

• initializeMutationTypeNuc

• initializeRecombinationRate

• initializeSex

• initializeSLiMModelType

• initializeSLiMOptions

• initializeSpecies

• initializeTreeSeq

This class has the following properties:

None.

This class has no properties.

See also

Other Initialize: initializeAncestralNucleotides(), initializeGeneConversion(), initializeGenomicElementType(), initializeGenomicElement(), initializeHotspotMap(), initializeInteractionType(), initializeMutationRate(), initializeMutationTypeNuc(), initializeMutationType(), initializeRecombinationRate(), initializeSLiMModelType(), initializeSLiMOptions(), initializeSex(), initializeSpecies(), initializeTreeSeq()