Use this function in a slim_block call and it will be
converted in the SLiM script into code to make formatted output.
This output can easily be read into R and even dynamically read
during simulation runs with slim_run from the
slimr package. This function should generally only be
used within a slim_block call
r_output(
slimr_expr,
name,
do_every = 1,
send_to = c("data", "file"),
file_name = tempfile(fileext = ".txt"),
format = c("csv", "fst"),
type = NULL,
expression = NULL,
time_counter = community.tick
)
slimr_output(
slimr_expr,
name,
do_every = 1,
send_to = c("data", "file"),
file_name = tempfile(fileext = ".txt"),
format = c("csv", "fst"),
type = NULL,
expression = NULL,
time_counter = community.tick
)A SLiM expression to generate output. This can either be
a SLiM expression designed to create output, such as outputFull(),
or an object created in the SLiM code, in which case r_output
will automatically concatenate it to a string and output it
The name to use to identify this output.
How often should the output be produced? Expressed
as an integer saying how many generations to run before producing output.
e.g. do_every = 10 means to output every 10 generations of the
simulation.
*deprecated* Where to send the output? This could be used to send the output to be stored in the results object ("data"), or to an external file ("file"). This will no longer be available in future versions in favour of an option to have the results stored as a pointer to an external file (to save memory).
*deprecated* The file name to save output to if send_to = "file"
*deprecated* The file format to save data if send_to = "file", Only "csv" is implemented
but there are plans to support "fst" and "disk.frame".
Provide a custom type to the output. Used mostly for internal purposes.
Provide a custom expression to be included with the output. Used mostly for internal purposes.
Expression used to extract the simulation time from SLiM. By default this uses the global timing mechanism in SLiM version >4.0: `community.tick`. For versions <4.0, use `sim.generation` instead (this parameter is for backwards compatability with old SLiM versions)
An expression with the code to be run in SLiM.
if(slim_is_avail()) {
slim_script(
slim_block(initialize(),
{
initializeMutationRate(1e-7);
initializeMutationType("m1", 0.5, "f", 0.0);
initializeGenomicElementType("g1", m1, 1.0);
initializeGenomicElement(g1, 0, 99999);
initializeRecombinationRate(1e-8);
}),
slim_block(1,
{
sim.addSubpop("p1", 100);
}),
slim_block(100,
{
r_output(p1.outputVCFSample(sampleSize = 10), name = "VCF");
sim.simulationFinished();
})
) %>%
slim_run() -> run_w_out
cat(run_w_out$output_data$data[[1]])
}
#>
#>
#> Simulation finished with exit status: 0
#>
#> Success!
#> #OUT: 100 100 SV p1 10
#> ##fileformat=VCFv4.2
#> ##fileDate=20231221
#> ##source=SLiM
#> ##INFO=<ID=MID,Number=.,Type=Integer,Description="Mutation ID in SLiM">
#> ##INFO=<ID=S,Number=.,Type=Float,Description="Selection Coefficient">
#> ##INFO=<ID=DOM,Number=.,Type=Float,Description="Dominance">
#> ##INFO=<ID=PO,Number=.,Type=Integer,Description="Population of Origin">
#> ##INFO=<ID=TO,Number=.,Type=Integer,Description="Tick of Origin">
#> ##INFO=<ID=MT,Number=.,Type=Integer,Description="Mutation Type">
#> ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele Count">
#> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
#> ##INFO=<ID=MULTIALLELIC,Number=0,Type=Flag,Description="Multiallelic">
#> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT i0 i1 i2 i3 i4 i5 i6 i7 i8 i9
#> 1 61727 . A T 1000 PASS MID=187;S=0;DOM=0.5;PO=1;TO=97;MT=1;AC=2;DP=1000 GT 0|0 0|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0