tests/testthat/test-nmfkc.R

In nmfkc: Non-Negative Matrix Factorization with Kernel Covariates

test_that("workwell", {
  X <- cbind(c(1,0,1),c(0,1,0))
  B <- cbind(c(1,0),c(0,1),c(1,1))
  Y <- X %*% B
  res <- nmfkc::nmfkc(Y,rank=2,epsilon=1e-12,maxit=50000,print.dims = FALSE)
  tolerance <- 1e-3
  expect_equal(Y,res$XB, tolerance = tolerance)
})

test_that("X.init = kmeans++ works and is reproducible", {
  Y <- t(iris[, -5])
  r1 <- nmfkc(Y, rank = 3, X.init = "kmeans++", seed = 1, verbose = FALSE, print.dims = FALSE)
  r2 <- nmfkc(Y, rank = 3, X.init = "kmeans++", seed = 1, verbose = FALSE, print.dims = FALSE)
  expect_true(r1$r.squared > 0.9)
  expect_equal(r1$XB, r2$XB)                       # reproducible with fixed seed
  expect_true(all(r1$X >= 0))                      # basis stays non-negative
  # alias
  r3 <- nmfkc(Y, rank = 3, X.init = "kmeanspp", seed = 1, verbose = FALSE, print.dims = FALSE)
  expect_equal(r1$XB, r3$XB)
})

test_that(".kmeanspp.seed returns k distinct-ish centres of right shape", {
  set.seed(1)
  pts <- matrix(rnorm(200), nrow = 40, ncol = 5)   # 40 points in R^5
  s <- nmfkc:::.kmeanspp.seed(pts, 4)
  expect_equal(dim(s), c(4L, 5L))
  expect_true(all(is.finite(s)))
})

test_that("X.L2.smooth is off by default, smooths rows, and stays monotone", {
  set.seed(1)
  P <- 24; N <- 30; Q <- 2
  Xt <- matrix(abs(rnorm(P * Q)), P, Q)
  B  <- matrix(abs(rnorm(Q * N)), Q, N)
  Y  <- Xt %*% B + matrix(abs(rnorm(P * N, 0, 0.1)), P, N)
  rough <- function(X) sum((X[-1, ] - X[-nrow(X), ])^2) / sum(X^2)
  r0 <- nmfkc(Y, rank = Q, seed = 1, verbose = FALSE, print.dims = FALSE)
  r0b <- nmfkc(Y, rank = Q, seed = 1, X.L2.smooth = 0, verbose = FALSE, print.dims = FALSE)
  rS <- nmfkc(Y, rank = Q, seed = 1, X.L2.smooth = 1000, verbose = FALSE, print.dims = FALSE)
  expect_equal(r0$X, r0b$X)                              # default == explicit 0
  expect_lt(rough(rS$X), rough(r0$X))                    # smoothing reduces roughness
  o <- rS$objfunc.iter; o <- o[is.finite(o)]
  expect_true(all(diff(o) <= 1e-6))                      # MU stays monotone
})