Extract genotype table from the tree sequence
Value
Data frame object of the class tibble containing genotypes
of simulated individuals in columns
Examples
check_dependencies(python = TRUE, quit = TRUE) # dependencies must be present
init_env()
#> The interface to all required Python modules has been activated.
# load an example model with an already simulated tree sequence
slendr_ts <- system.file("extdata/models/introgression_slim.trees", package = "slendr")
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))
# load the tree-sequence object from disk, recapitate it, simplify it, and mutate it
ts <- ts_read(slendr_ts, model) %>%
ts_recapitate(Ne = 10000, recombination_rate = 1e-8) %>%
ts_simplify() %>%
ts_mutate(mutation_rate = 1e-8)
# extract the genotype matrix (this could take a long time consume lots
# of memory!)
gts <- ts_genotypes(ts)
#> 4 multiallelic sites (0.176% out of 2272 total) detected and removed