addCrossed: SLiM method addCrossed
In rdinnager/slimrlang: Write SLiM Population Genetics Simulation Scripts in R

Description Usage Arguments Details Value Copyright Author(s)

Documentation for SLiM function addCrossed, which is a method of the SLiM class Subpopulation. 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.

1	addCrossed(parent1, parent2, sex)

`parent1`	An object of type Individual object. Must be of length 1 (a singleton). See details for description.
`parent2`	An object of type Individual object. Must be of length 1 (a singleton). See details for description.
`sex`	An object of type null or float or string. Must be of length 1 (a singleton). The default value is `NULL`. See details for description.

Generates a new offspring individual from the given parents by biparental sexual reproduction, queues it for addition to the target subpopulation, and returns it. The new offspring will not be visible as a member of the target subpopulation until the end of the offspring generation life cycle stage. Attempting to use a newly generated offspring individual as a mate, or to reference it as a member of the target subpopulation in any other way, will result in an error. In most models the returned individual is not used, but it is provided for maximal generality and flexibility. The new offspring individual is generated from parent1 and parent2 by crossing them. In sexual models parent1 must be female and parent2 must be male; in hermaphroditic models, parent1 and parent2 are unrestricted. If parent1 and parent2 are the same individual in a hermaphroditic model, that parent self-fertilizes, or "selfs”, to generate the offspring sexually (note this is not the same as clonal reproduction). Such selfing is considered "incidental” by addCrossed(), however; if the preventIncidentalSelfing flag of initializeSLiMOptions() is T, supplying the same individual for parent1 and parent2 is an error (you must check for and prevent incidental selfing if you set that flag in a nonWF model). If non-incidental selfing is desired, addSelfed() should be used instead. The sex parameter specifies the sex of the offspring. A value of NULL means "make the default choice”; in non-sexual models it is the only legal value for sex, and does nothing, whereas in sexual models it causes male or female to be chosen with equal probability. A value of "M" or "F" for sex specifies that the offspring should be male or female, respectively. Finally, a float value from 0.0 to 1.0 for sex provides the probability that the offspring will be male; a value of 0.0 will produce a female, a value of 1.0 will produce a male, and for intermediate values SLiM will draw the sex of the offspring randomly according to the specified probability. Unless you wish the bias the sex ratio of offspring, the default value of NULL should generally be used. Note that any defined, active, and applicable recombination(), mutation(), and modifyChild() callbacks will be called as a side effect of calling this method, before this method even returns. For recombination() and mutation() callbacks, the subpopulation of the parent that is generating a given gamete is used; for modifyChild() callbacks the situation is more complex. In most biparental mating events, parent1 and parent2 will belong to the same subpopulation, and modifyChild() callbacks for that subpopulation will be used, just as in WF models. In certain models (such as models of pollen flow and broadcast spawning), however, biparental mating may occur between parents that are not from the same subpopulation; that is legal in nonWF models, and in that case, modifyChild() callbacks for the subpopulation of parent1 are used (since that is the maternal parent). If the modifyChild() callback process results in rejection of the proposed child (see section 24.4), a new offspring individual will not be generated, and this method will return NULL. To force the generation of an offspring individual from a given pair of parents, you could loop until addCrossed() succeeds, but note that if your modifyChild() callback rejects all proposed children from those particular parents, your model will then hang, so care must be taken with this approach. Usually, nonWF models do not force generation of offspring in this manner; rejection of a proposed offspring by a modifyChild() callback typically represents a phenomenon such as post-mating reproductive isolation or lethal genetic incompatibilities that would reduce the expected litter size, so the default behavior is typically desirable. Note that this method is only for use in nonWF models, in which offspring generation is managed manually by the model script; in such models, addCrossed() must be called only from reproduction() callbacks, and may not be called at any other time. In WF models, offspring generation is managed automatically by the SLiM core.

An object of type null or Individual object. Return will be of length 1 (a singleton)

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/

Benjamin C Haller (bhaller@benhaller.com) and Philipp W Messer (messer@cornell.edu)

rdinnager/slimrlang documentation built on June 20, 2020, 8:17 p.m.