tests/testthat/test-basics.R

In OHDSI/BigKnn: Large Scale K-Nearest Neighbor Classifier using the Lucene Search Engine

library(testthat)

context("basics")

# Test init
indexFolder <- tempfile("indexFolder")

covariates <- data.frame(
  rowId = c(1, 1, 1, 2, 2, 3),
  covariateId = c(10, 11, 12, 10, 11, 12),
  covariateValue = c(1, 1, 1, 1, 1, 1)
)
cohorts <- data.frame(rowId = c(1, 2, 3))

outcomes <- data.frame(rowId = c(1, 2, 3), y = c(1, 0, 0))

predictionData <- Andromeda::andromeda(
  covariates = covariates,
  outcomes = outcomes,
  cohorts = cohorts
)


test_that("Build simple model", {
  buildKnn(
    outcomes = predictionData$outcomes,
    covariates = predictionData$covariates,
    indexFolder = indexFolder
  )

  expect_true(file.exists(indexFolder))
})

test_that("Simple prediction", {
  prediction <- predictKnn(
    cohorts = predictionData$cohorts,
    covariates = predictionData$covariates,
    indexFolder = indexFolder,
    k = 1,
    weighted = TRUE
  )
  prediction <- prediction[order(prediction$rowId), ]
  expect_equal(prediction$value, outcomes$y)
})

# Test cleanup
unlink(indexFolder)
Andromeda::close(predictionData)