tests/testthat/test-find_peaks_fast2.R

In metabodecon: Deconvolution and Alignment of 1d NMR Spectra

library(testthat)

test_that("find_peaks works", {

    # Inputs (Second Derivative (d) and Peak Center Indices (pd))
    x <- c(1,   2,   3,  4,   5,   6 ,  7,   8,   9,  10,  11,  12,  13)
    y <- c(100, 100, 98, 92, 84,  77,  72,  68,  63,  56,  50,  42,  33)
    # plot(x, y)
    d <- calc_second_derivative(y)
    expect_equal(d, c(NA, -2, -4, -2,   1,   2,  1,   -1,  -2,   1,  -2,  -1,  NA))
    #
    #        Nearest maximum or root right
    #        right of PC1 (Peak Center 1).
    #        ==> Right Border for PC1.
    #                |
    #                |     Nearest maximum or root right of
    #                |     PC2 AND nearest maximum or root
    #                |     left of PC3 ==> Right Border for
    #                |     PC2 AND left border for PC3.
    #                |                 |
    #     ___________|_________________|____________
    #  2 |           |    ###          |            |
    #  1 |           | #########      R2L3          |
    # -1 | __ #########         #L2###    ###### __ |
    # -1 |    #########            PC2    ######    |
    # -2 |    #######R1                   PC3       |
    # -3 |       ###                                |
    # -4 |       PC1                                |
    #    |__________________________________________|
    #       1  2  3  4  5  6  7  8  9  10  11 12 13
    #
    pc <- get_peak_centers_fast(d)
    rb <- get_right_borders_fast(d, pc)
    lb <- get_left_borders_fast(d, pc)
    sc <- get_peak_scores_fast(d, pc, lb, rb)
    pk <- data.frame(left = lb, center = pc, right = rb, score = sc)
    peaks <- find_peaks2(y)
    expect_equal(pc, c(3, 9, 11))
    expect_equal(rb, c(4, 10, NA))
    expect_equal(lb, c(NA, 8, 10))
    expect_equal(peaks, pk)
})