data(examplesFitnessEffects)
tmp <- oncoSimulIndiv(examplesFitnessEffects[["o3"]],
model = "McFL",
mu = 5e-5,
detectionSize = 1e8,
detectionDrivers = 3,
sampleEvery = 0.025,
max.num.tries = 10,
keepEvery = 5,
initSize = 2000,
finalTime = 3000,
onlyCancer = FALSE,
keepPhylog = TRUE)
## Show only those with N > 10 at end
plotClonePhylog(tmp, N = 10)
## Show only those with N > 1 between times 5 and 1000
plotClonePhylog(tmp, N = 1, t = c(5, 1000))
## Show everything, even if teminal nodes are extinct
plotClonePhylog(tmp, N = 0)
## Show time when first appeared
plotClonePhylog(tmp, N = 10, timeEvents = TRUE)
## Not run:
# ## Show each event
# ## This can take a few seconds
# plotClonePhylog(tmp, N = 10, keepEvents = TRUE)
# ## End(Not run)
## Adjacency matrix
require(igraph)
get.adjacency(plotClonePhylog(tmp, N = 10, returnGraph = TRUE))
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