tests/manual/test.sample-prob-long.R

In OncoSimulR: Forward Genetic Simulation of Cancer Progression with Epistasis

## This ain't particularly long, but adds time and is redundant.
## I leave it here for extra checks.


## Testing when no onlyCancer, but of course we have to exit sooner

cat(paste("\n Starting sample-prob-long", date(), "\n"))

p.value.threshold <- 1e-7


test_that("Increasing cPDetect decreases time, Exp" , {
    gi <- rep(0.1, 10)
    names(gi) <- letters[1:10]
    oi <- allFitnessEffects(noIntGenes = gi)
    n <- 800
    max.tries <- 4  
    for(tries in 1:max.tries) {
        sa <- oncoSimulPop(n,
                           oi,
                           model = "Exp",
                           initSize = 1000,
                           keepEvery = -9,
                           detectionProb = c(p2 = NULL, n2 = NULL, cPDetect = 0.01),
                           finalTime = NA,
                           onlyCancer = FALSE,
                           detectionDrivers = 99, mc.cores = 2)
        sb <- oncoSimulPop(n,
                           oi,
                           model = "Exp",
                           initSize = 1000,
                           keepEvery = -9,
                           detectionProb = c(p2 = NULL, n2 = NULL, cPDetect = .2),
                           finalTime = NA,
                           onlyCancer = FALSE,
                           detectionDrivers = 99, mc.cores = 2)
        ta <- unlist(lapply(sa, function(x) x$FinalTime))
        tb <- unlist(lapply(sb, function(x) x$FinalTime))
        print(suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value))
        T1 <- suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value < p.value.threshold)
        if(T1) break;
    }
    cat(paste("\n done tries", tries, "\n"))
    expect_true(T1)
})


test_that("Increasing p2 decreases time, Exp" , {
    gi <- rep(0.1, 10)
    names(gi) <- letters[1:10]
    oi <- allFitnessEffects(noIntGenes = gi)
    n <- 1200
    max.tries <- 4  
    for(tries in 1:max.tries) {
        sa <- oncoSimulPop(n,
                           oi,
                           model = "Exp",
                           initSize = 3000,
                           keepEvery = NA,
                           detectionProb = c(p2 = .1, n2 = 8500, checkSizePEvery = 10,  cPDetect = NULL),
                           finalTime = NA,
                           onlyCancer = FALSE,
                           detectionDrivers = 99, mc.cores = 2)
        sb <- oncoSimulPop(n,
                           oi,
                           model = "Exp",
                           initSize = 3000,
                           keepEvery = NA,
                           detectionProb = c(p2 = .9, n2 = 8500, checkSizePEvery = 10,  cPDetect = NULL),
                           finalTime = NA,
                           onlyCancer = FALSE,
                           detectionDrivers = 99, mc.cores = 2)
        (ta <- unlist(lapply(sa, function(x) x$FinalTime)))
        (tb <- unlist(lapply(sb, function(x) x$FinalTime)))
        print(suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value))
        T1 <- suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value < p.value.threshold)
        if(T1) break;
    }
    cat(paste("\n done tries", tries, "\n"))
    expect_true(T1)
})


test_that("Increasing n2 increases time, Exp" , {
    gi <- rep(0.1, 10)
    names(gi) <- letters[1:10]
    oi <- allFitnessEffects(noIntGenes = gi)
    n <- 1200
    max.tries <- 4  
    for(tries in 1:max.tries) {
        sa <- oncoSimulPop(n,
                           oi,
                           model = "Exp",
                           initSize = 5000,
                           keepEvery = -9,
                           detectionProb = c(p2 = .6, n2 = 8000, cPDetect = NULL),
                           finalTime = NA,
                           onlyCancer = FALSE,
                           detectionDrivers = 99, mc.cores = 2)
        sb <- oncoSimulPop(n,
                           oi,
                           model = "Exp",
                           initSize = 5000,
                           keepEvery = -9,
                           detectionProb = c(p2 = .6, n2 = 6002, cPDetect = NULL),
                           finalTime = NA,
                           onlyCancer = FALSE,
                           detectionDrivers = 99, mc.cores = 2)
        (ta <- unlist(lapply(sa, function(x) x$FinalTime)))
        (tb <- unlist(lapply(sb, function(x) x$FinalTime)))
        print(suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value))
        T1 <- suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value < p.value.threshold)
        if(T1) break;
    }
    cat(paste("\n done tries", tries, "\n"))
    expect_true(T1)
})




test_that("Increasing checkSizePEvery increases time, Exp" , {
    gi <- rep(0.1, 10)
    names(gi) <- letters[1:10]
    oi <- allFitnessEffects(noIntGenes = gi)
    n <- 1200
    max.tries <- 4  
    for(tries in 1:max.tries) {
        sa <- oncoSimulPop(n,
                           oi,
                           model = "Exp",
                           initSize = 2000,
                           keepEvery = -9,
                           detectionProb = c(p2 = .3, n2 = 5000, cPDetect = NULL, checkSizePEvery = 50),
                           finalTime = NA,
                           onlyCancer = FALSE,
                           detectionDrivers = 99, mc.cores = 2)
        sb <- oncoSimulPop(n,
                           oi,
                           model = "Exp",
                           initSize = 2000,
                           keepEvery = -9,
                           detectionProb = c(p2 = .3, n2 = 5000, cPDetect = NULL, checkSizePEvery = 2),
                           finalTime = NA,
                           onlyCancer = FALSE,
                           detectionDrivers = 99, mc.cores = 2)
        (ta <- unlist(lapply(sa, function(x) x$FinalTime)))
        (tb <- unlist(lapply(sb, function(x) x$FinalTime)))
        print(suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value))
        T1 <- suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value < p.value.threshold)
        if(T1) break;
    }
    cat(paste("\n done tries", tries, "\n"))
    expect_true(T1)
})

cat(paste("\n Ending sample-prob-long tests", date(), "\n"))