Extract names and times of individuals of interest in a tree sequence produced by a slendr model

Extracts a table of metadata information about individuals recorded in a given simulated tree sequence or in a tree sequence which would be produced by a given model

Usage

ts_samples(x)

Arguments

x

Either a tree sequence object of the class slendr_ts, or a compiled slendr model of the class slendr_model

Value

Table of individuals scheduled for sampling across space and time

Details

If a model is provided as x, the function will first simulate a trivially small tree sequence using the built-in msprime engine.

Examples

init_env()

# 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
ts <- ts_read(slendr_ts, model)

# extract the table of individuals scheduled for simulation and sampling
ts_samples(ts)
#> # A tibble: 13 × 3
#>    name   time pop  
#>    <chr> <int> <chr>
#>  1 NEA_1 70000 NEA  
#>  2 NEA_2 40000 NEA  
#>  3 AFR_1     0 AFR  
#>  4 AFR_2     0 AFR  
#>  5 AFR_3     0 AFR  
#>  6 AFR_4     0 AFR  
#>  7 AFR_5     0 AFR  
#>  8 CH_1      0 CH   
#>  9 EUR_1     0 EUR  
#> 10 EUR_2     0 EUR  
#> 11 EUR_3     0 EUR  
#> 12 EUR_4     0 EUR  
#> 13 EUR_5     0 EUR