tests/testthat/testChangeWorkflow.R

In Boodogs/zoon-clone: Reproducible, Accessible & Shareable Species Distribution Modelling

context('Changing workflows')

test_that('ChangeWorkflow errors', {
  
  skip_on_cran()

  # Original run
  set.seed(1)
  w1 <- workflow(UKAnophelesPlumbeus,
                 UKAir, 
                 Background(n = 70),
                 LogisticRegression,
                 PrintMap)
    
  expect_error(ChangeWorkflow(w1),
               'At least one module type must be changed')
  
  expect_error(ChangeWorkflow(w1,
                              occurrence = list(UKAnophelesPlumbeus, UKAnophelesPlumbeus),
                              covariate = list(UKAir, UKAir)),
               'Only one module type can be a list of multiple modules')
  
})

test_that('Basic ChangeWorkflow works', {
  
  skip_on_cran()

  # Original run
  set.seed(1)
  w1 <- workflow(UKAnophelesPlumbeus,
                 UKAir, 
                 Background(n = 70),
                 LogisticRegression,
                 PrintMap)
  
  # Change model
  set.seed(1)
  w2 <- workflow(UKAnophelesPlumbeus,
                 UKAir, 
                 Background(n = 70),
                 RandomForest,
                 PrintMap)

  set.seed(1)
  w3 <- ChangeWorkflow(w2, model = LogisticRegression)

  expect_true(all.equal(w1[!names(w1) %in% 'session.info'],
                        w3[!names(w3) %in% 'session.info']))
  expect_true(identical(w2$call,
    "workflow(occurrence = UKAnophelesPlumbeus, covariate = UKAir, process = Background(n = 70), model = RandomForest, output = PrintMap, forceReproducible = FALSE)"))

  
  # Change Process, model and output
  set.seed(1)
  w4 <- workflow(UKAnophelesPlumbeus,
                 UKAir, 
                 BackgroundAndCrossvalid(k=2),
                 RandomForest,
                 PerformanceMeasures)

  set.seed(1)
  w5 <- ChangeWorkflow(w4,
                       process = Background(n = 70), 
                       model = LogisticRegression, 
                       output = PrintMap)
  expect_true(all.equal(w1[!names(w1) %in% 'session.info'],
                        w5[!names(w5) %in% 'session.info']))
  
  
  # Change occurrence and covariate
  set.seed(1)
  sink(file=ifelse(Sys.info()["sysname"] == "Windows",
                   "NUL",
                   "/dev/null"))
  w6 <- workflow(AnophelesPlumbeus,
                 UKBioclim, 
                 Background(n = 70),
                 LogisticRegression,
                 PrintMap,
                 forceReproducible = TRUE)
  sink()
  
  set.seed(1)
  sink(file=ifelse(Sys.info()["sysname"] == "Windows",
                   "NUL",
                   "/dev/null"))           
  w7 <- ChangeWorkflow(w6,
                       occurrence = UKAnophelesPlumbeus,
                       covariate = UKAir,
                       forceReproducible = FALSE)
  sink()
  
  expect_true(all.equal(w1[!names(w1) %in% 'session.info'],
                        w7[!names(w7) %in% 'session.info']))
  
  # Only change output
  # Change Process, model and output
  set.seed(1)
  w7a <- workflow(UKAnophelesPlumbeus,
                  UKAir, 
                  Background(n = 70),
                  LogisticRegression,
                  PerformanceMeasures)
  set.seed(1)
  w7b <- ChangeWorkflow(w7a,
                        output = PrintMap)
  expect_true(all.equal(w1[!names(w1) %in% 'session.info'],
                        w7b[!names(w7b) %in% 'session.info']))
  
})

test_that('ChangeWorkflow - Chains', {
  
  skip_on_cran()
  
  # Original run
  set.seed(1)
  w1 <- workflow(UKAnophelesPlumbeus,
                 UKAir, 
                 Background(n = 70),
                 LogisticRegression,
                 PrintMap)
  
  # Replace with a occurrence with chain
  set.seed(1)
  w8 <- workflow(Chain(UKAnophelesPlumbeus, UKAnophelesPlumbeus),
                 UKAir, 
                 Background(n = 70),
                 LogisticRegression,
                 PrintMap)
  
  set.seed(1)
  w9 <- ChangeWorkflow(w1,
                       occurrence = Chain(UKAnophelesPlumbeus, UKAnophelesPlumbeus)
                       )

  expect_true(all.equal(w9[!names(w9) %in% 'session.info'],
                        w8[!names(w8) %in% 'session.info']))
  
  # Replace with a covariate chain
  set.seed(1)
  w10 <- workflow(UKAnophelesPlumbeus,
                  Chain(UKAir, UKAir), 
                  Background(n = 70),
                  LogisticRegression,
                  PrintMap)
  
  set.seed(1)
  w11 <- ChangeWorkflow(w1,
                        covariate = Chain(UKAir, UKAir)
                        )
  
  expect_true(all.equal(w10[!names(w10) %in% 'session.info'],
                        w11[!names(w11) %in% 'session.info']),
              info = paste(all.equal(w10[!names(w10) %in% 'session.info'],
                                     w11[!names(w11) %in% 'session.info']),
                           collapse = ' *** '))
  
  # Replace a chain with a non-chain
  set.seed(1)
  w12 <- ChangeWorkflow(w8,
                        occurrence = UKAnophelesPlumbeus)
  
  expect_true(all.equal(w12[!names(w12) %in% 'session.info'],
                        w1[!names(w1) %in% 'session.info']))

})

test_that('ChangeWorkflow - Lists', {
  
  skip_on_cran()
  
  # Original run
  set.seed(1)
  w1 <- workflow(UKAnophelesPlumbeus,
                 UKAir, 
                 Background(n = 70),
                 LogisticRegression,
                 PrintMap)
  
  # Replace with a occurrence with chain
  set.seed(1)
  w13 <- workflow(list(UKAnophelesPlumbeus, UKAnophelesPlumbeus),
                 UKAir, 
                 Background(n = 70),
                 LogisticRegression,
                 PrintMap)
  
  set.seed(1)
  w14 <- ChangeWorkflow(w1,
                        occurrence = list(UKAnophelesPlumbeus, UKAnophelesPlumbeus)
  )
  
  expect_true(all.equal(w13[!names(w13) %in% 'session.info'],
                        w14[!names(w14) %in% 'session.info']))
  
  # Replace with a covariate chain
  set.seed(1)
  w15 <- workflow(UKAnophelesPlumbeus,
                  list(UKAir, UKAir), 
                  Background(n = 70),
                  LogisticRegression,
                  PrintMap)
  
  set.seed(1)
  w16 <- ChangeWorkflow(w1,
                        covariate = list(UKAir, UKAir)
  )
  
  expect_true(all.equal(w15[!names(w15) %in% 'session.info'],
                        w16[!names(w16) %in% 'session.info']))
  
  # Replace a chain with a non-chain
  set.seed(1)
  w17 <- ChangeWorkflow(w13,
                        occurrence = UKAnophelesPlumbeus)
  
  expect_true(all.equal(w17[!names(w17) %in% 'session.info'],
                        w1[!names(w1) %in% 'session.info']))
  
})

test_that('More complex syntax in remaining modules works', {
  
  skip_on_cran()

  # Original run
  set.seed(1)
  w1 <- workflow(UKAnophelesPlumbeus,
                 UKAir, 
                 Background(n = 70),
                 LogisticRegression,
                 PrintMap)
  
   # Test module with brackets + args
   set.seed(1)
   w18 <- workflow(UKAnophelesPlumbeus,
                   UKAir, 
                   BackgroundAndCrossvalid(k=2),
                   LogisticRegression,
                   PrintMap)
  
   set.seed(1)
   w19 <- ChangeWorkflow(w18, occurrence = UKAnophelesPlumbeus)
  
   expect_true(all.equal(w18[!names(w18) %in% 'session.info'],
                         w19[!names(w19) %in% 'session.info']))
  
   set.seed(1)
   w20 <- ChangeWorkflow(w1, process = BackgroundAndCrossvalid(k = 2))
   
   expect_true(all.equal(w20[!names(w20) %in% 'session.info'],
                         w18[!names(w18) %in% 'session.info']))
   
})