Description Usage Arguments Value Author(s)
Individual based simulation of the breakdown of contiguous ancestry blocks, with or without selection. Simulations can be started from scratch, or from a predefined input population.
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input_population |
Potential earlier simulated population used as starting point for the simulation. If not provided by the user, the simulation starts from scratch. |
pop_size |
Number of individuals in the population |
number_of_founders |
Number of unique ancestors |
initial_frequencies |
A vector describing the initial frequency of each ancestor. By default, equal frequencies are assumed. If a vector not summing to 1 is provided, the vector is normalized. |
total_runtime |
Number of generations allowed for inbreeding |
morgan |
Length of the chromosome in Morgan (e.g. the number of crossovers during meiosis) |
seed |
Seed of the pseudo-random number generator |
select_matrix |
Selection matrix indicating the markers which are under selection. If not provided by the user, the simulation proceeds neutrally. If provided, each row in the matrix should contain five entries:
|
progress_bar |
Displays a progress_bar if TRUE. Default value is TRUE |
track_junctions |
Track the average number of junctions over time if TRUE |
track_frequency |
If TRUE, every generation the frequency of all ancestors at the marker under selection is tracked. Currently only supports one marker under selection. Alternatively, the user can provide a region for which a fixed number of markers is tracked. The user does this by providing a vector with three entries: |
multiplicative_selection |
Default: TRUE. If TRUE, fitness is calculated for multiple markers by multiplying fitness values for each marker. If FALSE, fitness is calculated by adding fitness values for each marker. |
A list with: population
a population object, and three tibbles with allele frequencies (if track_frequency = TRUE): frequencies
(if track_frequency
= TRUE), initial_frequencies
and final_frequencies
. Each tibble contains four columns, time
, location
, ancestor
and frequency
, which indicates the number of generations, the location along the chromosome of the marker, the ancestral allele at that location in that generation, and finally, the frequency of that allele.
Thijs Janzen
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