tests/testthat/test_prepare_results_PCA.R

In explor: Interactive Interfaces for Results Exploration

skip_if_not(require("FactoMineR"))
context("prepare_results.PCA")

data(decathlon)
pca <- FactoMineR::PCA(decathlon, ind.sup = 1:5, quanti.sup = 11:12, quali.sup = 13, graph = FALSE)
res <- prepare_results(pca)

test_that("Eigenvalues are equals", {
  expect_equal(unname(pca$eig[, "percentage of variance"]), res$eig$percent)
})

test_that("Variables results are equal", {
  expect_equal(
    as.vector(round(pca$var$coord[, 1], 3)),
    res$vars[res$vars$Type == "Active" & res$vars$Axis == "1", "Coord", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$var$cos2[, 2], 3)),
    res$vars[res$vars$Type == "Active" & res$vars$Axis == "2", "Cos2", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$var$cor[, 3], 3)),
    res$vars[res$vars$Type == "Active" & res$vars$Axis == "3", "Cor", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$var$contrib[, 5], 3)),
    res$vars[res$vars$Type == "Active" & res$vars$Axis == "5", "Contrib", drop = TRUE]
  )
})

test_that("Quantitative supplementary variables results are equal", {
  expect_equal(
    as.vector(round(pca$quanti.sup$coord[, 1], 3)),
    res$vars[res$vars$Type == "Supplementary" &
      res$vars$Class == "Quantitative" & res$vars$Axis == "1", "Coord", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$quanti.sup$cor[, 3], 3)),
    res$vars[res$vars$Type == "Supplementary" &
      res$vars$Class == "Quantitative" & res$vars$Axis == "3", "Cor", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$quanti.sup$cos2[, 5], 3)),
    res$vars[res$vars$Type == "Supplementary" &
      res$vars$Class == "Quantitative" & res$vars$Axis == "5", "Cos2", drop = TRUE]
  )
})

test_that("Qualitative supplementary variables results are equal", {
  expect_equal(
    as.vector(round(pca$quali.sup$coord[, 1], 3)),
    res$vars[res$vars$Type == "Supplementary" &
      res$vars$Class == "Qualitative" & res$vars$Axis == "1", "Coord", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$quali.sup$v.test[, 3], 2)),
    res$vars[res$vars$Type == "Supplementary" &
      res$vars$Class == "Qualitative" & res$vars$Axis == "3", "V.test", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$quali.sup$cos2[, 5], 3)),
    res$vars[res$vars$Type == "Supplementary" &
      res$vars$Class == "Qualitative" & res$vars$Axis == "5", "Cos2", drop = TRUE]
  )
})

test_that("Individuals results are equal", {
  expect_equal(
    as.vector(round(pca$ind$coord[, 1], 3)),
    data.frame(res$ind)[res$ind$Type == "Active" & res$ind$Axis == "1", "Coord", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$ind$contrib[, 3], 3)),
    data.frame(res$ind)[res$ind$Type == "Active" & res$ind$Axis == "3", "Contrib", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$ind$cos2[, 5], 3)),
    data.frame(res$ind)[res$ind$Type == "Active" & res$ind$Axis == "5", "Cos2", drop = TRUE]
  )
})

test_that("Supplementary individuals results are equal", {
  expect_equal(
    as.vector(round(pca$ind.sup$coord[, 4], 3)),
    data.frame(res$ind)[res$ind$Type == "Supplementary" & res$ind$Axis == "4", "Coord", drop = TRUE]
  )
  expect_equal(
    as.vector(round(pca$ind.sup$cos2[, 2], 3)),
    data.frame(res$ind)[res$ind$Type == "Supplementary" & res$ind$Axis == "2", "Cos2", drop = TRUE]
  )
})