Updated tests

.gitignore

@@ -21,8 +21,9 @@ vignettes/*.pdf
 # R Environment Variables
 .Renviron
 
-# Documetns
+# Documents and results
 docs/
+output/
 
 # Mac files
 .DS_STORE
@@ -41,7 +42,7 @@ docs/
 *.a
 *.lib
 
-# C++ files
+# Other C++ files
 **/__history/
 
 # EXPLORE result files

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(aucrocExplore)
+export(aurocEXPLORE)
 export(changeSetting)
 export(getSetting)
 export(predictExplore)

R/MainFunctions.R

@@ -191,7 +191,8 @@ predictExplore <- function(model, test_data) {
 #' @export
 #'
 #' @examples
-aucrocExplore <- function(output_path, train_data, settings_path, file_name, ...) {
+aurocEXPLORE <- function(output_path, train_data, settings_path, file_name, ...) {
+  # TODO: check with latest implementation in PLP
 
   # Range of specificities to check
   specificities <- seq(from = 0.01, to = 0.99, by = 0.02)
@@ -213,8 +214,8 @@ aucrocExplore <- function(output_path, train_data, settings_path, file_name, ...
     sensitivities[s] <- as.numeric(sensitivity)
   }
 
-  aucroc <- simple_auc(TPR = rev(sensitivities), FPR = rev(1 - specificities))
-  plot(1-specificities, sensitivities)
+  auroc <- simple_auc(TPR = rev(sensitivities), FPR = rev(1 - specificities))
+  # plot(1-specificities, sensitivities)
 
-  return(aucroc)
+  return(auroc)
 }

inst/examples/iris.project

@@ -15,8 +15,8 @@ NumberofPartitions=1
 OperatorMethod=EXHAUSTIVE
 CutoffMethod=RVAC
 CutoffFile=/Users/aniekmarkus/Documents/Git/Explore/inst/examples/iris.cutoff
-ClassFeature='class'
-PositiveClass="Iris-versicolor"
+ClassFeature=class
+PositiveClass=Iris-versicolor
 [Restrictions]
 Rule=
 FeatureInclude=

tests/testthat/test-package_tests.R

@@ -1,59 +1,52 @@
 library(testthat)
 library(Explore)
 
-### Tests for EXPLORE using  iris dataset
-data <- farff::readARFF(paste0(getwd(),"/tests/testthat/examples/iris.arff"))
-output_path <- paste0(getwd(),"/tests/testthat/examples/")
-
-for (file_name in c("iris", "train_data")) {
-  settings_path <- paste0(output_path, file_name,".project")
-  settings <- paste0(paste(readLines(settings_path), collapse="\n"),"\n")
-
-  settings <- changeSetting(settings, parameter = "OutputFile", input = paste0(gsub("examples/", "results/" , output_path), file_name, ".result"), default_setting = NA)
-  settings <- changeSetting(settings, parameter = "DataFile", input = paste0(output_path, file_name, ".arff"), default_setting = NA)
-  settings <- changeSetting(settings, parameter = "CutoffFile", input = paste0(output_path, file_name, ".cutoff"), default_setting = NA)
-
-  write.table(settings, 
-              file=settings_path, 
-              quote = FALSE,
-              col.names = FALSE,
-              row.names = FALSE)
-}
+# TODO: check differences variable names with / without ''
+
+### Tests for EXPLORE using iris dataset
+root_folder <- "../.."
+
+data_path <- file.path(root_folder, "inst/examples/iris.arff")
+settings_path <- file.path(root_folder, "inst/examples/iris.project")
+output_path <- file.path(root_folder, "inst/examples/output/")
+
+data <- farff::readARFF(data_path)
 
 test_that("option 1: fully pre-specified settings file works", {
-  model <- Explore::trainExplore(output_path = gsub("examples/", "results/" , output_path), file_name = "iris", settings_path = paste0(output_path, "iris.project"))
+  model <- Explore::trainExplore(output_path = output_path, file_name = "iris", settings_path = settings_path)
+
   expect_equal(class(model), "character")
   expect_false(model == "NA", info = "Test failed because model is NA")
   expect_equal(model, "petallength>2.45ANDpetallength<=4.95ANDpetalwidth<=1.65")
 })
 
 test_that("option 2: pre-specified settings file with input data works", {
-  model <- Explore::trainExplore(output_path = gsub("examples/", "results/" , output_path), train_data = data, settings_path = paste0(output_path, "train_data.project"), ClassFeature = "'class'", PositiveClass = '"Iris-versicolor"',  PrintSettings = "no", PrintPerformance = "no")
+  model <- Explore::trainExplore(output_path = output_path, train_data = data, settings_path = settings_path, ClassFeature = "'class'", PositiveClass = '"Iris-versicolor"')
   expect_equal(class(model), "character")
   expect_false(model == "NA", info = "Test failed because model is NA")
-  expect_equal(model, "'petallength'>2.45AND'petallength'<=4.95AND'petalwidth'<=1.65") # "'sepallength'>4.85"
+  expect_equal(model, "'petallength'>2.45AND'petallength'<=4.95AND'petalwidth'<=1.65") # OR "'sepallength'>4.85" ?
 })
 
 test_that("option 3: only input parameters (no settings file) works", {
-  model <- Explore::trainExplore(output_path = gsub("examples/", "results/" , output_path), file_name = "iris", settings_path = paste0(output_path, "iris.project"))
+  model <- Explore::trainExplore(output_path = output_path, file_name = "iris", train_data = data, ClassFeature = "'class'", PositiveClass = '"Iris-versicolor"')
   expect_equal(class(model), "character")
   expect_false(model == "NA", info = "Test failed because model is NA")
-  expect_equal(model, "petallength>2.45ANDpetallength<=4.95ANDpetalwidth<=1.65")
+  expect_equal(model, "'petallength'>2.45AND'petallength'<=4.95AND'petalwidth'<=1.65")
 })
 
-test_that("prediction (with model option 2)", {
-  model <- Explore::trainExplore(output_path = gsub("examples/", "results/" , output_path), train_data = data, settings_path = paste0(output_path, "train_data.project"), ClassFeature = "'class'", PositiveClass = '"Iris-versicolor"',  PrintSettings = "no", PrintPerformance = "no")
+test_that("prediction", {
+  model <- Explore::trainExplore(output_path = output_path, train_data = data, settings_path = settings_path, ClassFeature = "'class'", PositiveClass = '"Iris-versicolor"')
   prediction <- Explore::predictExplore(model, test_data = data)
-  
+
   expect_equal(class(prediction), "integer")
   expect_equal(length(prediction), nrow(data))
   expect_equal(sum(prediction %in% c(0,1) == FALSE),0)
 })
 
 test_that("compute AUC", {
-  aucroc <- Explore::aucrocExplore(output_path = gsub("examples/", "results/" , output_path), train_data = data, OutputFile = paste0(gsub("examples/", "results/" , output_path), "train_data.result"), settings_path = paste0(output_path, "train_data.project"), ClassFeature = "'class'", PositiveClass = '"Iris-versicolor"')
+  auroc <- Explore::aurocEXPLORE(output_path = output_path, train_data = data, settings_path = settings_path, ClassFeature = "'class'", PositiveClass = '"Iris-versicolor"')
 
-  expect_equal(class(aucroc), "numeric")
-  expect_true(aucroc < 100)
-  expect_true(aucroc > 0)
+  expect_equal(class(auroc), "numeric")
+  expect_true(auroc < 100)
+  expect_true(auroc > 0)
 })