test-interface.R
In shapviz: SHAP Visualizations

S <- matrix(c(1, -1, -1, 1), ncol = 2, dimnames = list(NULL, c("x", "y")))
X <- data.frame(x = c("a", "b"), y = c(100, 10))
shp <- shapviz(S, X, baseline = 4)
mshp <- c(shp = shp, shp2 = shp + shp)

test_that("get_* functions work", {
  expect_equal(4, get_baseline(shp))
  expect_equal(S, get_shap_values(shp))
  expect_equal(X, get_feature_values(shp))

  expect_equal(4, get_baseline(mshp)[[1L]])
  expect_equal(S, get_shap_values(mshp)[[1L]])
  expect_equal(X, get_feature_values(mshp)[[1L]])

  expect_error(get_baseline(3))
  expect_error(get_shap_values("a"))
  expect_error(get_feature_values(c(3, 9)))
})

test_that("dim, nrow, ncol, colnames work", {
  expect_equal(dim(shp), c(2L, 2L))
  expect_equal(nrow(shp), 2L)
  expect_equal(ncol(shp), 2L)
  expect_equal(colnames(shp), colnames(S))
})

test_that("<-dimnames work", {
  shp2 <- shp
  v <- c("a", "b")
  colnames(shp2) <- v
  expect_equal(colnames(shp2), v)
  expect_equal(colnames(get_shap_values(shp2)), v)
  expect_equal(colnames(get_feature_values(shp2)), v)

  v <- c("x", "y")
  dimnames(shp2) <- list(NULL, v)
  expect_equal(colnames(shp2), v)
  expect_equal(colnames(get_shap_values(shp2)), v)
  expect_equal(colnames(get_feature_values(shp2)), v)
})

test_that("subsetting works", {
  expect_equal(dim(shp[, "x"]$S), c(2L, 1L))
  expect_equal(dim(shp[, "x"]$X), c(2L, 1L))
  expect_equal(dim(shp[1L, "x"]$S), c(1L, 1L))
  expect_equal(dim(shp[1L, "x"]$X), c(1L, 1L))
  expect_equal(dim(shp[1L, ]$S), c(1L, 2L))
  expect_equal(dim(shp[1L, ]$X), c(1L, 2L))
  expect_equal(get_baseline(shp[1L, ]), get_baseline(shp))
})

test_that("concatenating with + works", {
  expect_equal(dim((shp + shp)$S), c(4L, 2L))
  expect_equal(dim((shp + shp)$X), c(4L, 2L))
  expect_equal((shp + shp)$baseline, shp$baseline)
  expect_equal(dim((shp + shp + shp)$S), c(6L, 2L))
  expect_equal(dim((shp + shp + shp)$X), c(6L, 2L))

  # mshapviz
  mapply(function(x, dims) {
    expect_equal(dim(x$S), dims)
    expect_equal(dim(x$X), dims)
  }, x = mshp + mshp, dims = list(c(4L, 2L), c(8L, 2L)))
  mapply(function(x, x_sum) expect_equal(x$baseline, x_sum$baseline), x = mshp, x_sum = mshp + mshp)
  mapply(function(x, dims) {
    expect_equal(dim(x$S), dims)
    expect_equal(dim(x$X), dims)
  }, x = mshp + mshp + mshp, dims = list(c(6L, 2L), c(12L, 2L)))
})

test_that("concatenating with rbind works", {
  expect_equal(dim(rbind(shp, shp)$S), c(4L, 2L))
  expect_equal(dim(rbind(shp, shp)$X), c(4L, 2L))
  expect_equal(rbind(shp, shp)$baseline, shp$baseline)
  expect_equal(dim(rbind(shp, shp, shp)$S), c(6L, 2L))
  expect_equal(dim(rbind(shp, shp, shp)$X), c(6L, 2L))

  # mshapviz
  mshp_rbind <- rbind(mshp, mshp)
  expect_equal(dim(mshp_rbind$shp$S), c(4L, 2L))
  expect_equal(dim(mshp_rbind$shp2$S), c(8L, 2L))
  expect_equal(dim(mshp_rbind$shp$X), c(4L, 2L))
  expect_equal(dim(mshp_rbind$shp2$X), c(8L, 2L))
  mapply(function(x, xbind) expect_equal(x$baseline, xbind$baseline), x = mshp, xbind = mshp_rbind)
  mapply(function(x, dims) {
    expect_equal(dim(x$S), dims)
    expect_equal(dim(x$X), dims)
  }, x = rbind(mshp, mshp, mshp), dims = list(c(6L, 2L), c(12L, 2L)))
})

test_that("split() works", {
  x_subgroups_a <- split(shp, f = c("1", "2"))
  x_subgroups_b <- c(`1` = shp[1L, ], `2` = shp[2L, ])
  expect_equal(x_subgroups_a, x_subgroups_b)
})

test_that("print() gives no error", {
  capture_output(expect_no_error(print(shp)))
  capture_output(expect_no_error(print(mshp)))
})

test_that("summary() gives no error", {
  capture_output(expect_no_error(summary(shp)))
})

test_that("shapviz() gives error for default method", {
  expect_error(shapviz(1))
})

test_that("column order of X does no matter", {
  expect_equal(shp, shapviz(S, X[, 2:1], baseline = 4))
})

test_that("X can contain additional columns", {
  expect_equal(shp, shapviz(S, X = cbind(X, z = 1:2), baseline = 4))
})

test_that("some input checks fire", {
  expect_error(shapviz(S[1, , drop = FALSE], X))
  expect_error(shapviz(S, X[1, ]))
  expect_error(shapviz(S, X[, 1]))
  expect_error(shapviz(matrix(S, ncol = 2, dimnames = list(NULL, c("d", "e"))), X))
  expect_error(shapviz(matrix(S, ncol = 2, dimnames = list(NULL, NULL)), X))
})

test_that("shapviz works with single row input", {
  shp1 <- shapviz(S[1L, , drop = FALSE], X[1L, , drop = FALSE], baseline = 4)
  expect_s3_class(sv_waterfall(shp1), "ggplot")
  expect_s3_class(sv_force(shp1), "ggplot")
  expect_s3_class(sv_importance(shp1, kind = "beeswarm"), "ggplot")
  expect_s3_class(sv_importance(shp1), "ggplot")
  expect_s3_class(sv_dependence(shp1, "x", color_var = "y"), "ggplot")
  expect_s3_class(sv_dependence(shp1, "x"), "ggplot")
})

test_that("shapviz works with single column input", {
  shp2 <- shapviz(S[, 1L, drop = FALSE], X[, 1L, drop = FALSE])
  expect_s3_class(sv_waterfall(shp2), "ggplot")
  expect_s3_class(sv_force(shp2), "ggplot")
  expect_s3_class(sv_importance(shp2, kind = "both"), "ggplot")
  expect_s3_class(sv_dependence(shp2, "x"), "ggplot")
  expect_s3_class(sv_dependence(shp2, "x", color_var = NULL), "ggplot")
})

# Interactions
test_that("shapviz accepts correct S_inter", {
  S_inter <- array(
    c(1, -1, 0, 0, 0, 0, -1, 1),
    dim = c(2L, 2L, 2L),
    dimnames = list(NULL, c("x", "y"), c("x", "y"))
  )
  expect_silent(shp_inter <- shapviz(S, X = X, baseline = 4, S_inter = S_inter))
  expect_silent(
    shapviz(
      S[1L, , drop = FALSE],
      X = X[1L, ],
      baseline = 4,
      S_inter = S_inter[1L, , , drop = FALSE]
    )
  )
  expect_silent(
    shapviz(S, X = X, baseline = 4, S_inter = S_inter[, c("y", "x"), c("y", "x")])
  )
  expect_identical(
    get_shap_interactions(
      shapviz(S, X = X, baseline = 4, S_inter = S_inter[, c("y", "x"), c("y", "x")])
    ),
    S_inter
  )
  expect_silent(
    shapviz(
      S[, "x", drop = FALSE],
      X = X["x"],
      baseline = 4,
      S_inter = S_inter[, "x", "x", drop = FALSE]
    )
  )
  expect_equal(dim(shp_inter[, "x"]$S_inter), c(2L, 1L, 1L))
  expect_equal(dim(shp_inter[1, ]$S_inter), c(1L, 2L, 2L))
  expect_equal(dim(shp_inter[1, "x"]$S_inter), c(1L, 1L, 1L))
})

test_that("shapviz does not accept S_inter with bad colnames", {
  S_inter_noname <- array(c(1, -1, 0, 0, 0, 0, -1, 1), dim = c(2L, 2L, 2L))
  expect_error(shapviz(S, X = X, baseline = 4, S_inter = S_inter_noname))

  S_inter_badname <- S_inter_noname
  dimnames(S_inter_badname) <- list(NULL, c("x", "z"), c("x", "z"))
  expect_error(shapviz(S, X = X, baseline = 4, S_inter = S_inter_badname))

  dimnames(S_inter_badname) <- list(NULL, c("x", "y"), c("y", "x"))
  expect_error(shapviz(S, X = X, baseline = 4, S_inter = S_inter_badname))
})

# More tests on interactions
S_inter <- array(
  c(1, -1, 0, 0, 0, 0, -1, 1),
  dim = c(2L, 2L, 2L),
  dimnames = list(NULL, c("x", "y"), c("x", "y"))
)
shp_inter <- shapviz(S, X = X, baseline = 4, S_inter = S_inter)
mshp_inter <- c(shp1 = shp_inter, shp2 = shp_inter + shp_inter)

test_that("get_shap_interactions, +, rbind works for interactions", {
  expect_equal(S_inter, get_shap_interactions(shp_inter))
  expect_equal(length(get_shap_interactions(mshp_inter)), 2L)
  expect_error(get_shap_interactions(4))
  expect_equal(dim((shp_inter + shp_inter)$S_inter)[1L], 2 * dim(shp_inter$S_inter)[1L])
  expect_equal(
    dim(rbind(shp_inter, shp_inter, shp_inter)$S_inter)[1L],
    3 * dim(shp_inter$S_inter)[1L]
  )
})

test_that("dimnames() and replacement work for interactions", {
  shp2 <- shp_inter
  colnames(shp2) <- c("a", "b")
  expect_equal(colnames(shp2), c("a", "b"))
  expect_equal(colnames(get_shap_interactions(shp2)), c("a", "b"))

  dimnames(shp2) <- list(NULL, c("x", "y"))
  expect_equal(colnames(shp2), c("x", "y"))
  expect_equal(colnames(get_shap_interactions(shp2)), c("x", "y"))
})

test_that("split() works for interactions", {
  x_subgroups_a <- split(shp_inter, f = c("1", "2"))
  x_subgroups_b <- c(`1` = shp_inter[1L, ], `2` = shp_inter[2L, ])
  expect_equal(x_subgroups_a, x_subgroups_b)
})

test_that("print() and summary() gives no error (with interactions)", {
  capture_output(expect_no_error(print(shp_inter)))
  capture_output(expect_no_error(print(mshp_inter)))
  capture_output(expect_no_error(summary(shp_inter)))
})

test_that("mshapviz object contains original shapviz objects", {
  expect_equal(mshp_inter[[1L]], shp_inter)
  expect_equal(mshp_inter[[2L]][1:nrow(shp_inter)], shp_inter)
})

test_that("shapviz objects with interactions can be rowbinded", {
  expect_equal(dim(rbind(shp_inter, shp_inter)), dim(shp_inter) * (2:1))
  expect_error(rbind(shp_inter, shp))
})

# Check on mshapviz
test_that("combining non-shapviz objects fails", {
  expect_error(c(shp, 1))
  expect_error(mshapviz(list(1, 2)))
})

test_that("combining incompatible shapviz objects fails", {
  shp2 <- shp[, "x"]
  expect_error(mshapviz(list(shp, shp2)))
  expect_error(c(shp, shp2))
})

# Multiclass with XGBoost
X_pred <- data.matrix(iris[, -5L])
dtrain <- xgboost::xgb.DMatrix(X_pred, label = as.integer(iris[, 5L]) - 1L, nthread = 1)
fit <- xgboost::xgb.train(
  params = list(nthread = 1L),
  data = dtrain,
  nrounds = 1L,
  objective="multi:softprob",
  num_class = 3L
)
shp3 <- shapviz(fit, X_pred = X_pred, which_class = 3L, interactions = TRUE)
mshp <- shapviz(fit, X_pred = X_pred, interactions = TRUE)

test_that("is.shapviz() and is.mshapviz() functions work", {
  expect_true(is.shapviz(shp3))
  expect_true(is.mshapviz(mshp))
  expect_false(is.shapviz(mshp))
  expect_false(is.mshapviz(shp3))
})

test_that("shapviz on class 3 equals mshapviz[[3]] for classification", {
  expect_equal(mshp[[3L]], shp3)
})

test_that("combining shapviz on classes 1, 2, 3 equal mshapviz", {
  shp1 <- shapviz(fit, X_pred = X_pred, which_class = 1L, interactions = TRUE)
  shp2 <- shapviz(fit, X_pred = X_pred, which_class = 2L, interactions = TRUE)
  expect_equal(mshp, c(Class_1 = shp1, Class_2 = shp2, Class_3 = shp3))
  expect_equal(mshp, mshapviz(list(Class_1 = shp1, Class_2 = shp2, Class_3 = shp3)))
})

test_that("single row predictions work with shapviz (see issue #141)", {
  expect_no_error(
    shp1 <- shapviz(fit, X_pred = X_pred[1L, , drop = FALSE], interactions = TRUE)
  )
  shp2 <- shapviz(fit, X_pred = X_pred, interactions = TRUE)
  for (j in names(shp1)) {
    expect_equal(shp1[[j]], shp2[[j]][1L, ])
  }
})