tests/testthat/test_binning.R

In rformassspectrometry/MsCoreUtils: Core Utils for Mass Spectrometry Data

test_that(".fix_breaks works", {
    rtr <- c(1, 12)
    brks <- seq(rtr[1], rtr[2], by = 4)
    ## brks do not include rtr
    expect_true(all(rtr[2] > brks))
    brks_f <- .fix_breaks(brks, rtr)
    expect_true(rtr[2] <= max(brks_f))

    ## Next unit tests taken from breaks_Spectrum.
    ## Issue #191
    ints <- 1:4
    brks <- seq(min(ints), max(ints), by = 1)
    expect_equal(.fix_breaks(brks, range(ints)), 1:5)
    expect_true(any(.fix_breaks(1:2, range(ints)) < 4))
    expect_equal(.fix_breaks(seq(1, 4, by = 2), range(ints)),
                 c(1, 3, 5))

    ## Test with values smaller than 1
    rng <- c(0.1, 0.4)
    brks <- seq(rng[1], rng[2], by = 0.04)
    .fix_breaks(brks, rng)
})

test_that("bin works", {
    set.seed(123)
    vals <- abs(rnorm(20, mean = 40))
    xs <- seq(1:length(vals)) + rnorm(length(vals), sd = 0.001)

    res <- bin(vals, xs, size = 1)
    brks <- seq(0, 20, by = 1)
    for (i in 1:(length(brks) - 1)) {
        idx <- which(xs > brks[i] & xs < brks[i +1])
        if (length(idx))
            expect_equal(res$x[i], max(vals[idx]))
        else expect_equal(res$x[i], 0)
    }

    ## Ensure that all values are within.
    xs <- seq(1:length(vals))
    brks <- seq(1, 20, by = 3)
    ## brks does not contain all values.
    expect_true(max(brks) < max(xs))
    res <- bin(vals, xs, size = 3, FUN = sum)
    ## The largest bin should contain all values larger than max(brks)
    expect_equal(res$x[length(res$x)], sum(vals[xs >= max(brks)]))
    ## without reporting mid points.
    res_2 <- bin(vals, xs, size = 3, FUN = sum, returnMids = FALSE)
    expect_true(is.numeric(res_2))
    expect_equal(res$x, res_2)

    ## Ensure y is ordered (if .check = TRUE), throw error if its not
    ## Issue #108 https://github.com/rformassspectrometry/MsCoreUtils/issues/108
    expect_error(bin(1:5, 5:1))
    expect_no_error(bin(1:5, 5:1, .check = FALSE))

    ## Check exceptions
    expect_error(bin(1:3, 1:5))
    expect_error(bin(1:3, 1:5), FUN = other)
})

test_that("breaks_ppm works", {
    res <- breaks_ppm(2, 23, by = 1, ppm = 0)
    expect_equal(res, seq(2, 23, by = 1))

    res <- breaks_ppm(10, 23.3, by = 0.1, ppm = 50)
    expect_true(res[length(res)] > 23.3)
    expect_true(res[length(res) - 1L] < 23.3)
    diffs <- diff(res)
    expect_true(diffs[2] > diffs[1])
})