This method simulates cell evolution until a formula does not hold.
Arguments
- formula
The formula that will be satisfied at the end of the simulation.
- quiet
An optional Boolean flag to avoid the progress bar (default: FALSE).
Examples
# set the seed of the random number generator
set.seed(0)
# create a simulation
sim <- SpatialSimulation()
sim$add_mutant(name = "A",
epigenetic_rates = c("+-" = 0.01, "-+" = 0.01),
growth_rates = c("+" = 0.2, "-" = 0.08),
death_rates = c("+" = 0.1, "-" = 0.01))
sim$place_cell("A+", 500, 500)
# get the variable representing the simulation time
v_time <- sim$var("Time")
# get the variable representing the cardinality of A+
va_p <- sim$var("A+")
# get the variable representing the cardinality of A-
va_m <- sim$var("A-")
# get the variable representing the number of epigenetic
# switches from A+
va_ps <- sim$var("A+.switches")
# build a condition stating that the cardinality of A+ doubles
# that of A-
c1 <- va_p >= 2*va_m
# build a condition that holds when there are more than
# 100000 live cells of mutant A
c2 <- va_p + va_m > 1e5
# build a condition that holds when less than 4000 switched
# from A+ have occured
c3 <- va_ps < 4000
# build a condition that holds when 40 time unit have been
# simulated at least
c4 <- v_time >= 40
# build a condition that holds when c4 and at least one
# among c1, c2, and c3 hold
c5 <- c4 & (c1 | c2 | c3)
c5
#> Time>=40 and (|A+|>=2*|A-| or |A+|+|A-|>100000 or 4000>|A+.switches|)
# run the simulation while c5 does not hold
sim$run_until(c5)
#>
[████████████████████████████████████████] 100% [00m:00s] Saving snapshot
sim
#> ── rRACES D S M /var/folders/tb/jqmdpgxs2t5129bny6pb96680000gn/T/rRACES_alberto_fbbf6bd9 ──────────
#>
#> ── Species: 2, with epigenetics
#>
#> ======= ==== ==== ==== ====== ===
#> species λ δ ε counts %
#> ======= ==== ==== ==== ====== ===
#> A- 0.08 0.01 0.01 30 75
#> A+ 0.20 0.10 0.01 10 25
#> ======= ==== ==== ==== ====== ===
#>
#> ── Firings: 73 total
#>
#> Species [A-]: 5 (deaths), 37 (duplications) and 5 (switches)
#> Species [A+]: 8 (deaths), 15 (duplications) and 3 (switches)
#> ✖ The simulation has no samples yet!
sim$get_clock()
#> [1] 40.34598