sample_geneology  R Documentation 
This function simulates a geneology where the last generation has population_size
individuals.
sample_geneology(
population_size,
generations,
generations_full = 1L,
generations_return = 3L,
enable_gamma_variance_extension = FALSE,
gamma_parameter_shape = 5,
gamma_parameter_scale = 1/5,
progress = TRUE,
verbose_result = FALSE
)
population_size 
The size of the population. 
generations 
The number of generations to simulate:

generations_full 
Number of full generations to be simulated. 
generations_return 
How many generations to return (pointers to) individuals for. 
enable_gamma_variance_extension 
Enable symmetric Dirichlet (and disable standard WrightFisher). 
gamma_parameter_shape 
Parameter related to symmetric Dirichlet distribution for each man's probability to be father. Refer to details. 
gamma_parameter_scale 
Parameter realted to symmetric Dirichlet distribution for each man's probability to be father. Refer to details. 
progress 
Show progress. 
verbose_result 
Verbose result. 
By the backwards simulating process of the WrightFisher model,
individuals with no descendants in the end population are not simulated.
If for some reason additional full generations should be simulated,
the number can be specified via the generations_full
parameter.
This can for example be useful if one wants to simulate the
final 3 generations although some of these may not get (male) children.
Let \alpha
be the parameter of a symmetric Dirichlet distribution
specifying each man's probability to be the father of an arbitrary
male in the next generation. When \alpha = 5
, a man's relative probability
to be the father has 95\
constant 1 under the standard WrightFisher model and the standard deviation in
the number of male offspring per man is 1.10 (standard WrightFisher = 1).
This symmetric Dirichlet distribution is implemented by drawing
father (unscaled) probabilities from a Gamma distribution with
parameters gamma_parameter_shape
and gamma_parameter_scale
that are then normalised to sum to 1.
To obtain a symmetric Dirichlet distribution with parameter \alpha
,
the following must be used:
`gamma_parameter_shape` = \alpha
and
`gamma_parameter_scale` = 1/\alpha
.
A malan_simulation / list with the following entries:
population
. An external pointer to the population.
generations
. Generations actually simulated, mostly useful when parameter generations = 1
.
founders
. Number of founders after the simulated generations
.
growth_type
. Growth type model.
sdo_type
. Standard deviation in a man's number of male offspring. StandardWF or GammaVariation depending on enable_gamma_variance_extension
.
end_generation_individuals
. Pointers to individuals in end generation.
individuals_generations
. Pointers to individuals in last generations_return
generation (if generations_return = 3
, then individuals in the last three generations are returned).
If verbose_result
is true, then these additional components are also returned:
individual_pids
. A matrix with pid (person id) for each individual.
father_pids
. A matrix with pid (person id) for each individual's father.
father_indices
. A matrix with indices for fathers.
sample_geneology_varying_size()
.
sim < sample_geneology(100, 10)
str(sim, 1)
sim$population
peds < build_pedigrees(sim$population)
peds
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