Documentation for SLiM function initializeInteractionType, which is a
method of the SLiM class Initialize.
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.
initializeInteractionType(
id,
spatiality,
reciprocal,
maxDistance,
sexSegregation
)An object of type integer or string. Must be of length 1 (a singleton). See details for description.
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 F. See details for description.
An object of type numeric. Must be of length 1 (a singleton).
The default value is INF. See details for description.
An object of type string. Must be of length 1 (a
singleton). The default value is "**". See details for description.
An object of type InteractionType object. Return will be of length 1 (a singleton)
Documentation for this function can be found in the official SLiM manual: page 650.
Add an interaction type at initialization time. The id must not already be used for any interaction type in the simulation. The id parameter may be either an integer giving the ID of the new interaction type, or a string giving the name of the new interaction type (such as "i5" to specify an ID of 5). The spatiality may be "", for non-spatial interactions (i.e., interactions that do not depend upon the distance between individuals); "x", "y", or "z" for one-dimensional interactions; "xy", "xz", or "yz" for two-dimensional interactions; or "xyz" for three-dimensional interactions. The dimensions referenced by spatiality must be defined as spatial dimensions with initializeSLiMOptions(); if the simulation has dimensionality "xy", for example, then interactions in the simulation may have spatiality "", "x", "y", or "xy", but may not reference spatial dimension z and thus may not have spatiality "xz", "yz", or "xyz". If no spatial dimensions have been configured, only non-spatial interactions may be defined. The reciprocal flag may be T, in which case the interaction is guaranteed by the user to be reciprocal: whatever the interaction strength is for exerter B upon receiver A, it will be equal (in magnitude and sign) for exerter A upon receiver B. In principle, this allows the InteractionType to reduce the amount of computation necessary by up to a factor of two (although it may or may not be used). If reciprocal is F, the interaction is not guaranteed to be reciprocal and each interaction will be computed independently. The built-in interaction formulas are all reciprocal, but if you implement an interaction() callback (see section 26.7), you must consider whether the callback you have implemented preserves reciprocality or not. For this reason, the default is reciprocal=F, so that bugs are not inadvertently introduced by an invalid assumption of reciprocality. See below for a note regarding reciprocality in sexual simulations when using the sexSegregation flag. The maxDistance parameter supplies the maximum distance over which interactions of this type will be evaluated; at greater distances, the interaction strength is considered to be zero (for efficiency). The default value of maxDistance, INF (positive infinity), indicates that there is no maximum interaction distance; note that this can make some interaction queries much less efficient, and is therefore not recommended. In SLiM 3.1 and later, a warning will be issued if a spatial interaction type is defined with no maximum distance to encourage a maximum distance to be defined. The sexSegregation parameter governs the applicability of the interaction to each sex, in sexual simulations. It does not affect distance calculations in any way; it only modifies the way in which interaction strengths are calculated. The default, "**", implies that the interaction is felt by both sexes (the first character of the string value) and is exerted by both sexes (the second character of the string value). Either or both characters may be M or F instead; for example, "MM" would indicate a male-male interaction, such as male-male competition, whereas "FM" would indicate an interaction influencing only female receivers that is influenced only by male exerters, such as male mating displays that influence female attraction. This parameter may be set only to "**" unless sex has been enabled with initializeSex(). Note that a value of sexSegregation other than "**" may imply some degree of non-reciprocality, but it is not necessary to specify reciprocal to be F for this reason; SLiM will take the sex-segregation of the interaction into account for you. The value of reciprocal may therefore be interpreted as meaning: in those cases, if any, in which A interacts with B and B interacts with A, is the interaction strength guaranteed to be the same in both directions? The sexSegregation parameter is shorthand for setting sex constraints on the interaction type using the setConstraints() method; see that method for a more extensive set of constraints that may be used. By default, the interaction strength is 1.0 for all interactions within maxDistance. Often it is desirable to change the interaction function using setInteractionFunction(); modifying interaction strengths can also be achieved with interaction() callbacks if necessary (see section 26.7). In any case, interactions beyond maxDistance always have a strength of 0.0, and the interaction strength of an individual with itself is always 0.0, regardless of the interaction function or callbacks. The global symbol for the new interaction type is immediately available; the return value also provides the new object. Note that in multispecies models, initializeInteractionType() must be called from a non-species-specific interaction() callback (declared as species all initialize()), since interactions are managed at the community level.
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 Initialize:
Init,
initializeAncestralNucleotides(),
initializeGeneConversion(),
initializeGenomicElementType(),
initializeGenomicElement(),
initializeHotspotMap(),
initializeMutationRate(),
initializeMutationTypeNuc(),
initializeMutationType(),
initializeRecombinationRate(),
initializeSLiMModelType(),
initializeSLiMOptions(),
initializeSex(),
initializeSpecies(),
initializeTreeSeq()
## This just brings up the documentation:
initializeInteractionType()