tests/testthat/test-outliers.R

In sipss/AlpsNMR: Automated spectraL Processing System for NMR

test_that("nmr_pca_outliers_robust works", {
    dataset <- new_nmr_dataset_1D(
        ppm_axis = c(0:10),
        data_1r = matrix(sample(0:43, replace = FALSE), nrow = 4),
        metadata = list(external = data.frame(NMRExperiment = c("10", "20", "30", "40")))
    )
    dataset[["metadata"]][["external"]][["NMRExperiment"]] <- as.character(dataset[["metadata"]][["external"]][["NMRExperiment"]])
    pca_outliers <- nmr_pca_outliers_robust(dataset)

    pca_built <- nmr_pca_build_model(dataset)
    plot_variance <- nmr_pca_plot_variance(pca_built)
    score <- nmr_pca_scoreplot(dataset, pca_built)
    loadings <- nmr_pca_loadingplot(pca_built, 2)

    pca_outliers_no_robust <- nmr_pca_outliers(dataset, pca_built)
    outliers_plot <- nmr_pca_outliers_plot(dataset, pca_outliers_no_robust)

    plot <- nmr_pca_outliers_plot(dataset, pca_outliers)
    dataset <- nmr_pca_outliers_filter(dataset, pca_outliers)


    expect_true(is.numeric(pca_outliers[["outlier_info"]][["Tscores"]]))
    expect_true(is.numeric(pca_outliers_no_robust[["outlier_info"]][["Tscores"]]))

    expect_true(is.matrix(pca_built[["X"]]))
    expect_true(is.list(plot_variance))
    expect_true(is.list(score))
    expect_true(is.list(loadings))
    expect_true(is.list(outliers_plot))
    expect_true(is.list(plot))
    expect_true(is.integer(dataset[["data_1r"]][[1]]))
})