This method builds a dataframe containing forest nodes.
Value
A dataframe representing, for each node
in the forest, the identified (column "cell_id"),
whenever the node is not a root, the ancestor
identifier (column "ancestor"), whenever the
node was sampled, i.e., it is one of the forest
leaves, the name of the sample containing the
node, (column "sample"), the mutant (column
"mutant"), the epistate (column "epistate"),
and the birth time (column "birth_time").
Examples
# set the seed of the random number generator
set.seed(0)
# create a simulation
sim <- SpatialSimulation()
sim$add_mutant(name = "A",
growth_rate = 0.2,
death_rate = 0.01)
sim$place_cell("A", 500, 500)
sim$death_activation_level <- 100
sim$run_up_to_size(species = "A", num_of_cells = 50000)
#>
[████████████████████████████████████████] 100% [00m:00s] Saving snapshot
# sample the region [450,500]x[475,550]
sim$sample_cells("S1", lower_corner=c(450,475), upper_corner=c(500,550))
# build the samples forest
forest <- sim$get_samples_forest()
nodes <- forest$get_nodes()
head(nodes, 5)
#> cell_id ancestor mutant epistate sample birth_time
#> 1 0 NA A <NA> 0.000000
#> 2 1 0 A <NA> 2.870718
#> 3 2 0 A <NA> 2.870718
#> 4 3 1 A <NA> 4.272592
#> 5 4 1 A <NA> 4.272592