coal_model {coala} | R Documentation |
Create a Coalescent Model
Description
This creates a basic coalescent model to which more features, loci,
parameters and summary statistics can be added later. Data under the model
can be simulated using the simulate
function.
Usage
coal_model(sample_size, loci_number = 0, loci_length = 1000, ploidy = 1)
Arguments
sample_size |
Defines the number of populations and the number of individual sampled from each population. Given as an integer vector where each entry gives the number of individuals sampled from the corresponding population. |
loci_number |
You can optionally add a number of loci with equal length to the model. This gives to number of loci to add. |
loci_length |
This gives the length of the loci to add. |
ploidy |
The number of chromosomes that will be simulated per individual. |
Value
The basic coalescent model which can be extended with features, parameters, loci and summary statistics.
See Also
The 'coala-intro' vignette for a general description on how to extend models.
For checking which simulators can be used for this model:
check_model
For adding mutation or for a list of other features:
feat_mutation
For adding loci: locus_single
,
locus_averaged
, locus_trio
For a generating DNA sequences or for a list of summary statistics:
sumstat_dna
Examples
# A model with one population and 20 unlinked loci:
model <- coal_model(10, 20) +
feat_mutation(5) +
sumstat_tajimas_d()
check_model(model)
simulate(model)
# A model with two populations:
model <- coal_model(c(13, 18), 5) +
feat_migration(.5, symmetric = TRUE) +
sumstat_trees()
check_model(model)
simulate(model)
# A model with 10 populations:
model <- coal_model(rep(2, 10), 5) +
feat_migration(.5, symmetric = TRUE) +
sumstat_trees()
check_model(model)
simulate(model)
# A model with recombination:
model <- coal_model(20, 1, 1000) +
feat_recombination(10) +
feat_mutation(5) +
sumstat_four_gamete()
check_model(model)
simulate(model)