Specify an Eidos function to be included in the SLiM script

slim_function(..., name, return_type = "f$", body)

Arguments

...: List of arguments specified using Eidos's argument syntax (which includes type specification; see details)
name: Name of function being created.
return_type: Type of the functions return, using Eidos' type syntax (see details)
body: SLiM / Eidos code to be executed in the body of the function. Can also be an R function, in which case the body of the R function is used.

Value

A slimr_block object (only useful with the context of a slim_script) call.

Examples

test_sim <- slim_script(
  slim_function("o<Subpopulation>$ subpop1", "o<Subpopulation>$ subpop2",
               name = "calculateFST",
               return_type = "f$", body = function(subpop1, subpop2) {
                 p1_p = sim.mutationFrequencies(subpop1);
                 p2_p = sim.mutationFrequencies(subpop2);
                 mean_p = (p1_p + p2_p) / 2.0;
                 H_t = 2.0 * mean_p * (1.0 - mean_p);
                 H_s = p1_p * (1.0 - p1_p) + p2_p * (1.0 - p2_p);
                 fst = 1.0 - H_s/H_t;
                 fst = fst[isFinite(fst)]; ## exclude muts where mean_p is 0.0 or 1.0
                 return(mean(fst));
               }),
  slim_block_init_minimal(mutation_rate = 1e-6),
  slim_block_add_subpops(2, 100),
  slim_block(1, 20, late(), {
    r_output(calculateFST(p1, p2), "out", do_every = 10)
  })
)
test_sim
#> <slimr_script[4]>
#> block_1:function  (f$)calculateFST(o<Subpopulation>$ subpop1, o<Subpopulation>$ subpop2) {
#>     p1_p = sim.mutationFrequencies(subpop1);
#>     p2_p = sim.mutationFrequencies(subpop2);
#>     mean_p = (p1_p + p2_p)/2;
#>     H_t = 2 * mean_p * (1 - mean_p);
#>     H_s = p1_p * (1 - p1_p) + p2_p * (1 - p2_p);
#>     fst = 1 - H_s/H_t;
#>     fst = fst[isFinite(fst)];
#>     return(mean(fst));
#> }
#> 
#> block_init:initialize() {
#>     initializeMutationRate(1e-06);
#>     initializeMutationType("m1", 0.5, "f", 0);
#>     initializeGenomicElementType("g1", m1, 1);
#>     initializeGenomicElement(g1, 0, 1e+05 - 1);
#>     initializeRecombinationRate(1e-08);
#> }
#> 
#> block_3:1 early() {
#>     {
#>         sim.addSubpop(p1, 100);
#>         sim.addSubpop(p2, 100);
#>     }
#> }
#> 
#> block_4:1:20 late() {
#>     {calculateFST(p1, p2) -> out}
#> }