Utility function to tell SLiM to output Nucleotides

Utility function to tell SLiM to output Nucleotides

r_output_nucleotides(
  name = "seqs",
  subpops = FALSE,
  both_genomes = FALSE,
  inds = NULL,
  ...
)

slimr_output_nucleotides(
  name = "seqs",
  subpops = FALSE,
  both_genomes = FALSE,
  inds = NULL,
  ...
)

Arguments

name

Name of output to use to label it in slimr_results object. Default is "seqs".

subpops

Should the subpopulation of each sequence be outputted as well?

both_genomes

Should both genomes be outputted? If `FALSE` only nucleotides from genome1 are outputted

inds

SLiM expression that returns the individuals to get nucleotides from. By default all individuals are returned.

...

Other arguments to be passed to r_output

Value

None

Examples

test_sim <- slim_script(
  slim_block(initialize(), {

    ## tell SLiM to simulate nucleotides
    initializeSLiMOptions(nucleotideBased=T);
    initializeAncestralNucleotides(randomNucleotides(1000));
    initializeMutationTypeNuc("m1", 0.5, "f", 0.0);

    initializeGenomicElementType("g1", m1, 1.0, mmJukesCantor(1e-5));
    initializeGenomicElement(g1, 0, 1000 - 1);
    initializeRecombinationRate(1e-8);

  }),
  slim_block_add_subpops(1, 100),
  slim_block(1, 20, late(), {
    r_output_nucleotides("out", do_every = 10)
  })
)
test_sim
#> <slimr_script[3]>
#> block_init:initialize() {
#>     initializeSLiMOptions(nucleotideBased = T);
#>     initializeAncestralNucleotides(randomNucleotides(1000));
#>     initializeMutationTypeNuc("m1", 0.5, "f", 0);
#>     initializeGenomicElementType("g1", m1, 1, mmJukesCantor(1e-05));
#>     initializeGenomicElement(g1, 0, 1000 - 1);
#>     initializeRecombinationRate(1e-08);
#> }
#> 
#> block_2:1 early() {
#>     sim.addSubpop("p1", 100);
#> }
#> 
#> block_3:1:20 late() {
#>     {paste(sim.subpopulations.individuals.genome1.nucleotides()) -> out}
#> }