Run a slendr model in SLiM — slim • slendr

This function will execute a SLiM script generated by the compile function during the compilation of a slendr demographic model.

Usage

slim(
  model,
  sequence_length,
  recombination_rate,
  samples = NULL,
  ts = TRUE,
  path = NULL,
  random_seed = NULL,
  method = c("batch", "gui"),
  verbose = FALSE,
  run = TRUE,
  slim_path = NULL,
  burnin = 0,
  max_attempts = 1,
  spatial = !is.null(model$world),
  coalescent_only = TRUE,
  locations = NULL
)

Arguments

model: Model object created by the compile function
sequence_length: Total length of the simulated sequence (in base-pairs)
recombination_rate: Recombination rate of the simulated sequence (in recombinations per basepair per generation)
samples: A data frame of times at which a given number of individuals should be remembered in the tree-sequence (see schedule_sampling for a function that can generate the sampling schedule in the correct format). If missing, only individuals present at the end of the simulation will be recorded in the final tree-sequence file.
ts: Should a tree sequence be simulated from the model?
path: Path to the directory where simulation result files will be saved. If NULL, this directory will be automatically created as a temporary directory. If TRUE, this path will be also returned by the function. If a string is given, it is assumed to be a path to a directory where simulation results will be saved. In this case, the function will return this path invisibly. Note that if a tree-sequence file should be simulated (along with other files, potentially), that tree-sequence file (named 'slim.trees' by default) will have to be explicitly loaded using ts_read().
random_seed: Random seed (if NULL, a seed will be generated between 0 and the maximum integer number available)
method: How to run the script? ("gui" - open in SLiMgui, "batch" - run on the command line)
verbose: Write the log information from the SLiM run to the console (default FALSE)?
run: Should the SLiM engine be run? If FALSE, the command line SLiM command will be printed (and returned invisibly as a character vector) but not executed.
slim_path: Path to the appropriate SLiM binary (this is useful if the slim binary is not on the $PATH). Note that this argument must be specified if the function is being run on Windows.
burnin: Length of the burnin (in model's time units, i.e. years)
max_attempts: How many attempts should be made to place an offspring near one of its parents? Serves to prevent infinite loops on the SLiM backend. Default value is 1.
spatial: Should the model be executed in spatial mode? By default, if a world map was specified during model definition, simulation will proceed in a spatial mode.
coalescent_only: Should initializeTreeSeq(retainCoalescentOnly = <...>) be set to TRUE (the default) or FALSE? See "retainCoalescentOnly" in the SLiM manual for more detail.
locations: If NULL, locations are not saved. Otherwise, the path to the file where locations of each individual throughout the simulation will be saved (most likely for use with animate_model).

Value

A tree-sequence object loaded via Python-R reticulate interface function ts_read

(internally represented by the Python object tskit.trees.TreeSequence). If the path argument was set, specifying the directory where results should be saved, the function will return this path as a single-element character vector.

Details

The arguments sequence_length and recombination_rate can be omitted for slendr models utilizing customized initialization of genomic architecture. In such cases, users may either provide hard-coded values directly through SLiM's initializeGenomicElement() and initializeRecombinationRate() functions or utilize slendr's templating functionality provided by its substitute() function. When ts = TRUE, the returning value of this function depends on whether or not the path argument was set. If the user did provide the path where output files should be saved, the path is returned (invisibly). This is mostly intended to support simulations of customized user models. If path is not set by the user, it is assumed that a tree-sequence object is desired as a sole return value of the function (when ts = TRUE) and so it is automatically loaded when simulation finishes, or (when ts = FALSE) that only customized files are to be produced by the simulation, in which the user will be loading such files by themselves (and only the path is needed).

Examples

check_dependencies(python = TRUE, slim = TRUE, quit = TRUE) # dependencies must be present

init_env()
#> The interface to all required Python modules has been activated.

# load an example model
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

# afr and eur objects would normally be created before slendr model compilation,
# but here we take them out of the model object already compiled for this
# example (in a standard slendr simulation pipeline, this wouldn't be necessary)
afr <- model$populations[["AFR"]]
eur <- model$populations[["EUR"]]
chimp <- model$populations[["CH"]]

# schedule the sampling of a couple of ancient and present-day individuals
# given model at 20 ky, 10 ky, 5ky ago and at present-day (time 0)
modern_samples <- schedule_sampling(model, times = 0, list(afr, 5), list(eur, 5), list(chimp, 1))
ancient_samples <- schedule_sampling(model, times = c(30000, 20000, 10000), list(eur, 1))

# sampling schedules are just data frames and can be merged easily
samples <- rbind(modern_samples, ancient_samples)

# run a simulation using the SLiM back end from a compiled slendr model object and return
# a tree-sequence object as a result
ts <- slim(model, sequence_length = 1e5, recombination_rate = 0, samples = samples)

# simulated tree-sequence object can be saved to a file using ts_write()...
ts_file <- normalizePath(tempfile(fileext = ".trees"), winslash = "/", mustWork = FALSE)
ts_write(ts, ts_file)
# ... and, at a later point, loaded by ts_read()
ts <- ts_read(ts_file, model)

ts
#> ╔═══════════════════════╗
#> ║TreeSequence           ║
#> ╠═══════════════╤═══════╣
#> ║Trees          │      1║
#> ╟───────────────┼───────╢
#> ║Sequence Length│ 100000║
#> ╟───────────────┼───────╢
#> ║Time Units     │  ticks║
#> ╟───────────────┼───────╢
#> ║Sample Nodes   │  10046║
#> ╟───────────────┼───────╢
#> ║Total Size     │2.6 MiB║
#> ╚═══════════════╧═══════╝
#> ╔═══════════╤═════╤═════════╤════════════╗
#> ║Table      │Rows │Size     │Has Metadata║
#> ╠═══════════╪═════╪═════════╪════════════╣
#> ║Edges      │18361│573.8 KiB│          No║
#> ╟───────────┼─────┼─────────┼────────────╢
#> ║Individuals│12858│  1.2 MiB│         Yes║
#> ╟───────────┼─────┼─────────┼────────────╢
#> ║Migrations │    0│  8 Bytes│          No║
#> ╟───────────┼─────┼─────────┼────────────╢
#> ║Mutations  │    0│  1.2 KiB│          No║
#> ╟───────────┼─────┼─────────┼────────────╢
#> ║Nodes      │18362│682.1 KiB│         Yes║
#> ╟───────────┼─────┼─────────┼────────────╢
#> ║Populations│    4│  2.5 KiB│         Yes║
#> ╟───────────┼─────┼─────────┼────────────╢
#> ║Provenances│    1│ 41.8 KiB│          No║
#> ╟───────────┼─────┼─────────┼────────────╢
#> ║Sites      │    0│ 16 Bytes│          No║
#> ╚═══════════╧═════╧═════════╧════════════╝
#>