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

Documentation for Individual class from SLiM

1	Individual

An object of class list of length 28.

This class has the following methods (functions):

containsMutations
countOfMutationsOfType
getValue
relatedness
setSpatialPosition
setValue
sumOfMutationsOfType
uniqueMutationsOfType

This class has the following properties:

age: A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: The age of the individual, measured in generation "ticks”. A newly generated offspring individual will have an age of 0 in the same generation in which is was created. The age of every individual is incremented by one at the same point that the generation counter is incremented. The age of individuals may be changed; usually this only makes sense when setting up the initial state of a model, however.
color: A property of type string. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: The color used to display the individual in SLiMgui. Outside of SLiMgui, this property still exists, but is not used by SLiM. Colors may be specified by name, or with hexadecimal RGB values of the form "#RRGGBB" (see the Eidos manual). If color is the empty string, "", SLiMgui’s default (fitness-based) color scheme is used; this is the default for new Individual objects.
fitnessScaling: A property of type float. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A float scaling factor applied to the individual’s fitness (i.e., the fitness value computed for the individual will be multiplied by this value). This provides a simple, fast way to modify the fitness of an individual; conceptually it is similar to returning a fitness effect for the individual from a fitness(NULL) callback, but without the complexity and performance overhead of implementing such a callback. To scale the fitness of all individuals in a subpopulation by the same factor, see the fitnessScaling property of Subpopulation. The value of fitnessScaling is reset to 1.0 every generation, so that any scaling factor set lasts for only a single generation. This reset occurs immediately after fitness values are calculated, in both WF and nonWF models.
genomes: A property of type Genome object. This property is a constant, so it is not modifiable. Property Description: The pair of Genome objects associated with this individual. If only one of the two genomes is desired, the genome1 or genome2 property may be used.
genome1: A property of type Genome object. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The first Genome object associated with this individual. This property is particularly useful when you want the first genome from each of a vector of individuals, as often arises in haploid models.
genome2: A property of type Genome object. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The second Genome object associated with this individual. This property is particularly useful when you want the second genome from each of a vector of individuals, as often arises in haploid models.
index: A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The index of the individual in the individuals vector of its Subpopulation.
migrant: A property of type logical. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: Set to T if the individual migrated during the current generation, F otherwise. In WF models, this flag is set at the point when a new child is generated if it is a migrant (i.e., if its source subpopulation is not the same as its subpopulation), and remains valid, with the same value, for the rest of the individual’s lifetime. In nonWF models, this flag is F for all new individuals, is set to F in all individuals at the end of the reproduction generation cycle stage, and is set to T on all individuals moved to a new subpopulation by takeMigrants(); the T value set by takeMigrants() will remain until it is reset at the end of the next reproduction generation cycle stage.
pedigreeID: A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: If pedigree tracking is turned on with initializeSLiMOptions(keepPedigrees=T), pedigreeID is a unique non-negative identifier for each individual in a simulation, never re-used throughout the duration of the simulation run. This property is also available when tree- sequence recording is enabled. If neither pedigree tracking nor tree-sequence recording is enabled, this property is unavailable.
pedigreeParentIDs: A property of type integer. This property is a constant, so it is not modifiable. Property Description: If pedigree tracking is turned on with initializeSLiMOptions(keepPedigrees=T), pedigreeParentIDs contains the values of pedigreeID that were possessed by the parents of an individual; it is thus a vector of two values. If pedigree tracking is not on, this property is unavailable. Parental values may be -1 if insufficient generations have elapsed for that information to be available (because the simulation just started, or because a subpopulation is new).
pedigreeGrandparentIDs: A property of type integer. This property is a constant, so it is not modifiable. Property Description: If pedigree tracking is turned on with initializeSLiMOptions(keepPedigrees=T), pedigreeGrandparentIDs contains the values of pedigreeID that were possessed by the grandparents of an individual; it is thus a vector of four values. If pedigree tracking is not on, this property is unavailable. Grandparental values may be -1 if insufficient generations have elapsed for that information to be available (because the simulation just started, or because a subpopulation is new).
sex: A property of type string. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The sex of the individual. This will be "H" if sex is not enabled in the simulation (i.e., for hermaphrodites), otherwise "F" or "M" as appropriate.
spatialPosition: A property of type float. This property is a constant, so it is not modifiable. Property Description: The spatial position of the individual. The length of the spatialPosition property (the number of coordinates in the spatial position of an individual) depends upon the spatial dimensionality declared with initializeSLiMOptions(). If the spatial dimensionality is zero (as it is by default), it is an error to access this property. The elements of this property are identical to the values of the x, y, and z properties (if those properties are encompassed by the spatial dimensionality of the simulation). In other words, if the declared dimensionality is "xy", the individual.spatialPosition property is equivalent to c(individual.x, individual.y); individual.z is not used since it is not encompassed by the simulation’s dimensionality. This property cannot be set, but the setSpatialPosition() method may be used to achieve the same thing.
subpopulation: A property of type Subpopulation object. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The Subpopulation object to which the individual belongs.
tag: A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A user-defined integer value (as opposed to tagF, which is of type float). The value of tag is initially undefined, and it is an error to try to read it; if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code. The value of tag is not used by SLiM; it is free for you to use. See also the getValue() and setValue() methods, for another way of attaching state to individuals. Note that the Individual objects used by SLiM are (conceptually) new with every generation, so the tag value of each new offspring generated in each generation will be initially undefined. If you set a tag value for an offspring individual inside a modifyChild() callback, that tag value will be preserved as the offspring individual becomes a parent (across the generation boundary, in other words). If you take advantage of this, however, you should be careful to set up initial values for the tag values of all offspring, otherwise undefined initial values might happen to match the values that you are trying to use to tag particular individuals. A rule of thumb in programming: undefined values should always be assumed to take on the most inconvenient value possible.
tagF: A property of type float. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A user-defined float value (as opposed to tag, which is of type integer). The value of tagF is initially undefined, and it is an error to try to read it; if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code. The value of tagF is not used by SLiM; it is free for you to use. See also the getValue() and setValue() methods, for another way of attaching state to individuals. Note that at present, although many classes in SLiM have an integer-type tag property, only Individual has a float-type tagF property, because attaching model state to individuals seems to be particularly common and useful. If a tagF property would be helpful on another class, it would be easy to add. See the description of the tag property above for additional comments.
uniqueMutations: A property of type Mutation object. This property is a constant, so it is not modifiable. Property Description: All of the Mutation objects present in this individual. Mutations present in both genomes will occur only once in this property, and the mutations will be given in sorted order by position, so this property is similar to sortBy(unique(individual.genomes.mutations), "position"). It is not identical to that call, only because if multiple mutations exist at the exact same position, they may be sorted differently by this method than they would be by sortBy(). This method is provided primarily for speed; it executes much faster than the Eidos equivalent above. Indeed, it is faster than just individual.genomes.mutations, and gives uniquing and sorting on top of that, so it is advantageous unless duplicate entries for homozygous mutations are actually needed.
x: A property of type float. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A user-defined float value. The value of x is initially undefined (i.e., has an effectively random value that could be different every time you run your model); if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code, typically in a modifyChild() callback. The value of x is not used by SLiM unless the optional "continuous space” facility is enabled with the dimensionality parameter to initializeSLiMOptions(), in which case x will be understood to represent the x coordinate of the individual in space. If continuous space is not enabled, you may use x as an additional tag value of type float.
y: A property of type float. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A user-defined float value. The value of y is initially undefined (i.e., has an effectively random value that could be different every time you run your model); if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code, typically in a modifyChild() callback. The value of y is not used by SLiM unless the optional "continuous space” facility is enabled with the dimensionality parameter to initializeSLiMOptions(), in which case y will be understood to represent the y coordinate of the individual in space (if the dimensionality is "xy" or "xyz"). If continuous space is not enabled, or the dimensionality is not "xy" or "xyz", you may use y as an additional tag value of type float.
z: A property of type float. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A user-defined float value. The value of z is initially undefined (i.e., has an effectively random value that could be different every time you run your model); if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code, typically in a modifyChild() callback. The value of z is not used by SLiM unless the optional "continuous space” facility is enabled with the dimensionality parameter to initializeSLiMOptions(), in which case z will be understood to represent the z coordinate of the individual in space (if the dimensionality is "xyz"). If continuous space is not enabled, or the dimensionality is not "xyz", you may use z as an additional tag value of type float.