tests/testthat/test_error.R

In selbouhaddani/OmicsPLS: Data Integration with Two-Way Orthogonal Partial Least Squares

library(OmicsPLS)
context("OmicsPLS main function checking")

set.seed(1234)
X <- matrix(rnorm(10*1e1),10);
Xmiss <- X
Xmiss[sample(length(Xmiss),length(Xmiss)/10)] <- NA

test_that("Normal o2m goes without error", {
  expect_error(o2m(1:10, 1:10, 1, 0, 0), NA)
  expect_error(o2m(diag(1,6,5), diag(1,6,6), 1, 1, 1), NA)
  expect_error(o2m(diag(1,6,5), diag(1,6,6), 1, 1, 1, stripped = TRUE), NA)
  expect_error(o2m(diag(1,6,5), diag(1,6,6), 1, 1, 1, p_thresh = 1, q_thresh = 1), NA)
  expect_error(o2m(diag(1,6,5), diag(1,6,6), 1, 1, 1, p_thresh = 1, q_thresh = 1, stripped = TRUE), NA)
  expect_error(o2m(diag(1,6,5), diag(1,6,6), 1, 1, 1, sparse = TRUE, keepx=1, keepy=1), NA)
  expect_error(o2m(matrix(rnorm(100*10),100), matrix(rnorm(100*11),100), 1, 1, 1, sparse = TRUE, groupx=letters[1:10], groupy=LETTERS[1:11], keepx=5, keepy=5), NA)
  expect_error(print(o2m(1:10%*%t(1:3), 1:10%*%t(1:3), 1, 0, 0, sparse=TRUE, keepx=1, keepy=1)), NA)
  expect_error(print(o2m(1:10%*%t(1:3), 1:10%*%t(1:3), 1, 0, 0, sparse=TRUE, keepx=1, keepy=1, groupx=LETTERS[1:3], groupy=letters[1:3])), NA)
})

test_that("Normal crossval goes without error", {
  expect_error(crossval_o2m(1:10%*%t(1:3), 1:10%*%t(1:3), 1, 0, 0, 2), NA)
  expect_error(crossval_o2m_adjR2(1:10%*%t(1:3), 1:10%*%t(1:3), 1, 0, 0, 2), NA)
  expect_error(crossval_o2m(1:10%*%t(1:3), 1:10%*%t(1:3), 1, 0, 0, 2, 2), NA)
  expect_error(crossval_o2m_adjR2(1:10%*%t(1:3), 1:10%*%t(1:3), 1, 0, 0, 2, 2), NA)
  expect_error(crossval_sparsity(1:10%*%t(1:3), 1:10%*%t(1:3), 1, 0, 0, 2, keepx_seq = 1:2, keepy_seq = 1:2), NA)
  expect_error(crossval_sparsity(matrix(rnorm(100*10),100), matrix(rnorm(100*10),100), 1, 1, 1, 2, keepx_seq = 1:2, keepy_seq = 1:2, groupx=letters[1:10], groupy=LETTERS[1:10]), NA)
})

# test_that("Examples run", {
#   expect_error(example("o2m",package = "OmicsPLS"), NA)
#   expect_error(example("crossval_o2m",package = "OmicsPLS"), NA)
#   expect_error(example("crossval_o2m_adjR2",package = "OmicsPLS"), NA)
#   expect_error(example("orth",package = "OmicsPLS"), NA)
#   expect_error(example("summary.o2m",package = "OmicsPLS"), NA)
#   expect_error(example("loadings.o2m",package = "OmicsPLS"), NA)
# })

test_that("Errors in *o2m* are thrown", {
  expect_error(o2m(diag(3),diag(4),1,0,0),                   "rows")
  expect_error(o2m(matrix(1:9,3),matrix(1:9,3),0,1,1),       "n")
  expect_error(o2m(matrix(c(1:8,NA),3),matrix(1:9,3),1,1,1), "NA")
  expect_error(o2m(matrix(1:9,3),matrix(c(1:8,NaN),3),1,1,1),"NaN")
  expect_error(o2m(matrix(1:9,3),matrix(c(1:8,Inf),3),1,1,1),"finite")
  expect_error(o2m(diag(4),diag(4),1.5,0,0),                 "n")
  expect_error(o2m(diag(4),diag(4),1,1.5,0),                 "nx")
  expect_error(o2m(diag(4),diag(4),1,0,1.5),                 "ny")
  expect_error(crossval_o2m(diag(3),diag(4),1,0,0,2)                   )
  expect_error(crossval_o2m(matrix(c(1:8,NA),3),matrix(1:9,3),1,1,1,2) )
  expect_error(crossval_o2m(matrix(1:9,3),matrix(c(1:8,NaN),3),1,1,1,2))
  expect_error(crossval_o2m(matrix(1:9,3),matrix(c(1:8,Inf),3),1,1,1,2))
  expect_error(crossval_o2m(diag(4),diag(4),1.5,0,0,2)                 )
  expect_error(crossval_o2m(diag(4),diag(4),1,1.5,0,2)                 )
  expect_error(crossval_o2m(diag(4),diag(4),1,0,1.5,2)                 )
  expect_error(crossval_o2m(diag(4),diag(4),1,0,0,2,nr_folds = 1)      )
  expect_error(crossval_o2m_adjR2(diag(3),diag(4),1,0,0,2)                   )
  expect_error(crossval_o2m_adjR2(matrix(c(1:8,NA),3),matrix(1:9,3),1,1,1,2))
  expect_error(crossval_o2m_adjR2(matrix(1:9,3),matrix(c(1:8,NaN),3),1,1,1,2))
  expect_error(crossval_o2m_adjR2(matrix(1:9,3),matrix(c(1:8,Inf),3),1,1,1,2))
  expect_error(crossval_o2m_adjR2(diag(4),diag(4),1.5,0,0,2)                 )
  expect_error(crossval_o2m_adjR2(diag(4),diag(4),1,1.5,0,2)                 )
  expect_error(crossval_o2m_adjR2(diag(4),diag(4),1,0,1.5,2)                 )
  expect_warning(crossval_o2m_adjR2(diag(4,10,10),diag(4,10,3),1:2,0:4,0:2,2))
  expect_error(o2m(matrix(rnorm(100*10),100), matrix(rnorm(100*10),100), 1, 1, 1, sparse = TRUE, groupx=letters[1:10], keepx=5, keepy=5), "groupy")
  expect_error(o2m(matrix(rnorm(100*10),100), matrix(rnorm(100*10),100), 1, 1, 1, sparse = TRUE, groupy=letters[1:10], keepx=5, keepy=5), "groupx")
})

test_that("size, ratios and names are correct", {
  expect_equal(o2m(diag(4),diag(4),1,1,0)$R2X,      0.5)
  expect_equal(o2m(diag(4),diag(4),1,0,1)$R2Y,      0.5)
  expect_equal(nrow(o2m(diag(4),diag(4),1,0,0)$W.), 4)
  expect_equal(nrow(o2m(diag(5),diag(5),1,0,0)$C.), 5)
  expect_equal(rownames(o2m(data.frame(a=1:10,b=2:11,c=3:12),data.frame(1:10,2:11,3:12),1,0,0)$W.), letters[1:3])
  expect_equal(rownames(o2m(data.frame(1:10,2:11,3:12),data.frame(a=1:10,b=2:11,c=3:12),1,0,0)$C.), letters[1:3])
})

test_that("S3 Methods are working OK", {
  fit = o2m(data.frame(a=1:10,b=2:11,c=3:12),data.frame(d=1:10,e=2:11,f=3:12),2,0,0)
  cvfit = crossval_o2m(data.frame(a=1:10,b=2:11,c=3:12),data.frame(d=1:10,e=2:11,f=3:12),1:2,0,0,2)
  expect_error(invisible(print(fit)), NA)
  expect_error(invisible(print(cvfit)), NA)
  expect_error(invisible(summary(fit)), NA)
  expect_error(invisible(print(summary(fit))), NA)
  expect_error(invisible(print(summary(o2m(diag(3),diag(3),1,1,1)))), NA)
  expect_error(plot(fit), NA)
  expect_error(plot(fit, use_ggplot2=FALSE, i=1,j=2), NA)
  expect_error(loadings(fit), NA)
  expect_error(loadings(fit,sorted=TRUE), NA)
  expect_error(predict(fit,t(1:3)), NA)
  expect_error(scores(fit), NA)
  expect_error(scores(fit, "Yo"), NA)
  expect_error(rmsep(1:10%*%t(1:3), 1:10%*%t(1:3), fit), NA)
  expect_error(loocv(1:10%*%t(1:3), 1:10%*%t(1:3), 1, 0, 0, fit, app_err = TRUE, kcv=2), NA)
})

test_that("Misc functions are working", {
  expect_error(orth(1:10), NA)
  expect_error(orth(1:10, 1:10, type="SVD"), NA)
  expect_error(adjR2(1:10, 1:10, 1, 0, 0), NA)
  expect_error(impute_matrix(Xmiss, maxit = 1000), NA)
  expect_message(impute_matrix(X), "original matrix")
})
test_that("Internal functions are correct", {
  #expect_warning(pow_o2m(orth(matrix(1:20,5))[,1:2],orth(matrix(1:20,5))[,3:4], 1))
  expect_error(orth_vec(1:10, matrix(rnorm(10*3),10)), NA)
})