This function runs a SLiM script, specified as a slimr_script object,
a character vector, or a text file.
slim_run(
x,
slim_path = NULL,
script_file = NULL,
simple_run = FALSE,
capture_output = "file",
keep_all_output = FALSE,
show_output = FALSE,
callbacks = NULL,
cb_args = NULL,
new_grdev = FALSE,
parallel = FALSE,
progress = FALSE,
throw_error = FALSE,
...
)
# S3 method for character
slim_run(
x,
slim_path = NULL,
script_file = NULL,
simple_run = FALSE,
capture_output = "file",
keep_all_output = FALSE,
show_output = FALSE,
callbacks = NULL,
cb_args = NULL,
new_grdev = FALSE,
parallel = FALSE,
progress = FALSE,
throw_error = FALSE,
...
)
# S3 method for slimr_script
slim_run(
x,
slim_path = NULL,
script_file = NULL,
simple_run = FALSE,
capture_output = "file",
keep_all_output = FALSE,
show_output = FALSE,
callbacks = NULL,
cb_args = NULL,
new_grdev = FALSE,
parallel = FALSE,
progress = FALSE,
throw_error = FALSE,
...
)
# S3 method for slimr_script_coll
slim_run(
x,
slim_path = NULL,
script_file = NULL,
simple_run = FALSE,
capture_output = "file",
keep_all_output = FALSE,
show_output = FALSE,
callbacks = NULL,
cb_args = NULL,
new_grdev = FALSE,
parallel = FALSE,
progress = FALSE,
throw_error = FALSE,
...
)Object containing script to run (e.g. a character vector or a slimr_script object)
Path to the SLiM executable. If left NULL slimr will attempt to automatically determine
it, typically by examining environmental variables.
If the script you want to run is in a text file, you can add the pather here. If this is
argument is not NULL argument x will be ignored
Whether to do a "simple run", which just runs the script, capturing all output is capture_output
is TRUE and additionally sending all output to the R console if show_output is TRUE
the script to the R console if show_output is TRUE
If TRUE, output from the script will be captured and included in the returned object. Unless
keep_all_output is TRUE, only non-data output will be kept (e.g. output not produced by a r_output
call)
If there is data produced by r_output calls, should it be captured as well? Ignored if
capture_output is not TRUE
Should output from the script be sent to the R console? Note that SLiM scripts can sometimes produce a large amount of output, which could overwhelm the console if you are not careful, potentially locking it up. Be careful with this option if you are using any of SLiM's output functions that output genomic data. This can be handy though for simply status print outs..
A list of functions to be called during the SLiM run. This can be used to
dynamically transform or visualise output from the simulation while it is running. It should
be of the form function(data, ...) {do something..}. If using r_output
to get formatted data output from SLiM, data will be a four column tibble
containing output from the current iteration of the simulation. Columns are:
A vector of generations processed in the current iteration
Names of the output data.
The SLiM expression used to generate the output
The raw data output from SLiM as a character vector
Additional arguments to be passed to any callback functions. Should be a named list where the names refer to the callback's arguments.
Should a new graphics device window be opened on RStudio? This is mainly useful if you are using
custom callbacks that generate live figures, and want a faster plotting experience. This is because the
default plot viewer in RStudio can be quite slow. Setting this to TRUE also allows record_graphics to work.
If x is a slimr_script_coll, should the elements in x
be run in parallel. For this to work, you must have setup a parallel plan using plan
Should a progress bar be displayed?
Should an error be thrown in R is an error is encountered in SLiM?
If FALSE, the error message from SLiM is stored in the object returned
by slim_run, but execution continues in R. Setting this to TRUE is useful
in a script if subsequent code assumes that the simulation finished successfully.
Additional arguments to be passed to or from other methods.
A slimr_results object which has the following components:
A character vector of raw output. Will be NULL if capture_output is FALSE
The exit status code returned by the SLiM process. 0 means success.
A `tibble` containing output from r_output calls.
A processx object containing information about the SLiM process used during the run.
If an error was encountered during the run, this will be a character vector containing the error message.
The path to the file containing captured output from SLiM during the run.
slim_run(character): Run a SLiM script from character vector
slim_run(slimr_script): Run a SLiM script from slimr_script object
slim_run(slimr_script_coll): Run a SLiM script from slimr_script object
if(slim_is_avail()) {
test_sim <- slim_script(
slim_block_init_minimal(mutation_rate = 1e-6),
slim_block_add_subpops(1, 100),
slim_block(1, 20, late(), {
r_output(sim.outputFull(), "out", do_every = 10)
})
) %>%
slim_run()
test_sim
}
#>
#>
#> Simulation finished with exit status: 0
#>
#> Success!
#> $output
#> [1] "// Initial random seed:"
#> [2] "1530461718"
#> [3] ""
#> [4] "// RunInitializeCallbacks():"
#> [5] "initializeMutationRate(1e-06);"
#> [6] "initializeMutationType(1, 0.5, \"f\", 0);"
#> [7] "initializeGenomicElementType(1, m1, 1);"
#> [8] "initializeGenomicElement(g1, 0, 99999);"
#> [9] "initializeRecombinationRate(1e-08);"
#> [10] ""
#> [11] "// Starting run at tick <start>:"
#> [12] "1 "
#> [13] ""
#> [14] ""
#> [15] "<slimr_out:start>"
#> [16] "<slimr_out:end>"
#> [17] ""
#> [18] "<slimr_out:start>"
#>
#> $exit_status
#> [1] 0
#>
#> $output_data
#> # A tibble: 2 × 5
#> generation name expression type data
#> <int> <chr> <chr> <chr> <chr>
#> 1 10 out sim.outputFull() slim_output "#OUT: 10 10 A\nVersion: 3\nPop…
#> 2 20 out sim.outputFull() slim_output "#OUT: 20 20 A\nVersion: 3\nPop…
#>
#> $process
#> PROCESS 'slim.exe', finished.
#>
#> $error
#> character(0)
#>
#> $output_file
#> [1] "F:\\Rtemp\\RtmpG056mn\\file5a2c5f14277f.txt"
#>
#> attr(,"class")
#> [1] "slimr_results"