Nothing
inittime <- Sys.time()
cat(paste("\n Starting warning-mutPropGrowth tests", date(), "\n"))
## RNGkind("Mersenne-Twister")
test_that("mutationPropGrowth warning with Bozic, indiv", {
oi <- allFitnessEffects(orderEffects =
c("F > D" = -0.3, "D > F" = 0.4),
noIntGenes = runif(5, 0.01, 0.06),
geneToModule =
c("Root" = "Root",
"F" = "f1, f2, f3",
"D" = "d1, d2"),
drvNames = c("d1", "d2", "f1", "f2", "f3"))
expect_warning(oiI1 <- oncoSimulIndiv(oi,
sampleEvery = 0.03,
keepEvery = 2,
model = "Bozic",
mutationPropGrowth = TRUE),
"Using fitness Bozic (bozic1) with mutationPropGrowth = TRUE;",
fixed = TRUE)
})
## With seed 5207947 we get a Recoverable exception ti set to
## DBL_MIN. Rerunning. Not if we set the onlyCancer = FALSE. Also, not if
## we use a sampleEvery = 0.1. Setting it to 0.1 still same issue with
## seed 5613635 or 465554. Again, estimate is less < 1/10000. So a rare
## numerical issue. OK. Decrease sampleEvery further, but increase keepEvery for size.
test_that("mutationPropGrowth no warning with Exp, indiv", {
## I once (out of over > 10000) saw it fail. Try to catch it
cat("\n a runif is", runif(1), "\n")
oi <- allFitnessEffects(orderEffects =
c("F > D" = -0.3, "D > F" = 0.4),
noIntGenes = rexp(5, 10),
geneToModule =
c("Root" = "Root",
"F" = "f1, f2, f3",
"D" = "d1, d2"),
drvNames = c("d1", "d2", "f1", "f2", "f3"))
expect_silent(oiI1 <- oncoSimulIndiv(oi,
model = "Exp",
onlyCancer = FALSE, detectionProb = NA,
sampleEvery = 0.03,
keepEvery = 5,
mutationPropGrowth = TRUE,
seed = NULL))
})
test_that("mutationPropGrowth no warning with McFl, indiv", {
oi <- allFitnessEffects(orderEffects =
c("F > D" = -0.3, "D > F" = 0.4),
noIntGenes = rexp(5, 10),
geneToModule =
c("Root" = "Root",
"F" = "f1, f2, f3",
"D" = "d1, d2"),
drvNames = c("d1", "d2", "f1", "f2", "f3"))
expect_silent(oiI1 <- oncoSimulIndiv(oi,
model = "McFL",
mu = 5e-6,
detectionSize = 1e8,
detectionDrivers = 2,
sampleEvery = 0.025,
keepEvery = 2,
onlyCancer = FALSE, detectionProb = NA,
mutationPropGrowth = TRUE))
})
cat(paste("\n Ending warning-mutPropGrowth tests", date(), "\n"))
cat(paste(" Took ", round(difftime(Sys.time(), inittime, units = "secs"), 2), "\n\n"))
rm(inittime)
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