context("UtilFigureOfMerit ROC dataset dataset02: FOM = Wilcoxon")
test_that("ROC dataset dataset02: FOM = Wilcoxon", {
dataset <- dataset02
FOM = "Wilcoxon"
fn <- paste0(test_path(), "/goodValues361/FOM/UtilFigureOfMeritROC-", FOM, ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ret <- UtilFigureOfMerit(dataset, FOM = FOM)
saveRDS(ret, file = fn)
}
ret1 <- readRDS(fn)
ret2 <- UtilFigureOfMerit(dataset, FOM = FOM)
for (i in 1:dim(ret1)[1]) {
for (j in 1:dim(ret1)[2])
expect_equal(as.numeric(ret1[[i,j]]), as.numeric(ret2[[i,j]]))
}
})
context("UtilFigureOfMerit FROC dataset: wAFROC1, dataset with no non-diseased cases")
test_that("FROC dataset: wAFROC1, dataset with no non-diseased cases", {
fileName <- system.file("extdata", "/toyFiles/FROC/frocLocatClass.xlsx", package = "RJafroc", mustWork = TRUE)
x <- DfReadDataFile(fileName = fileName, newExcelFileFormat = T)
fn <- paste0(test_path(), "/goodValues361/FOM/UtilFigureOfMeritFROC-", "wAFROC1a", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ret <- UtilFigureOfMerit(x, FOM = "wAFROC1")
saveRDS(ret, file = fn)
}
ret1 <- readRDS(fn)
ret2 <- UtilFigureOfMerit(x, FOM = "wAFROC1")
for (i in 1:length(ret1)) {
expect_equal(as.numeric(ret1[[i]]), as.numeric(ret2[[i]]))
}
})
context("UtilFigureOfMerit: wAFROC1, same FOM with new and old excel formats frocLocatClass.xlsx file")
test_that("UtilFigureOfMerit: wAFROC1, same FOM with new and old excel formatsfrocLocatClass.xlsx file", {
fileName <- system.file("extdata", "/toyFiles/FROC/frocLocatClass.xlsx", package = "RJafroc", mustWork = TRUE)
x1 <- DfReadDataFile(fileName = fileName, newExcelFileFormat = F)
x2 <- DfReadDataFile(fileName = fileName, newExcelFileFormat = T)
ret1 <- UtilFigureOfMerit(x1, FOM = "wAFROC1")
ret2 <- UtilFigureOfMerit(x2, FOM = "wAFROC1")
for (i in 1:length(ret1)) {
expect_equal(as.numeric(ret1[[i]]), as.numeric(ret2[[i]]))
}
})
context("UtilFigureOfMerit: wAFROC1, same FOM with new and old excel formats frocCr.xlsx file")
test_that("UtilFigureOfMerit: wAFROC1, same FOM with new and old excel formats frocCr.xlsx file", {
fileName <- system.file("extdata", "/toyFiles/FROC/frocCr.xlsx", package = "RJafroc", mustWork = TRUE)
x1 <- DfReadDataFile(fileName = fileName, newExcelFileFormat = F)
x2 <- DfReadDataFile(fileName = fileName, newExcelFileFormat = T)
ret1 <- UtilFigureOfMerit(x1, FOM = "wAFROC1")
ret2 <- UtilFigureOfMerit(x2, FOM = "wAFROC1")
for (i in 1:length(ret1)) {
expect_equal(as.numeric(ret1[[i]]), as.numeric(ret2[[i]]))
}
})
context("UtilFigureOfMerit FROC dataset: all FOMs except ...")
test_that("FROC dataset: all FOMs except ...", {
# cannot use Wilcoxon with FROC dataset
# correct usage is HrAuc
dataset <- dataset01
expect_error(UtilFigureOfMerit(dataset, FOM = "Wilcoxon"))
## cycle through all FOMs possible with FROC data (except the excessive computation time ones)
FOM_arr <- c("HrAuc","wAFROC1","AFROC1","MaxLLF","MaxNLF","MaxNLFAllCases", "HrSp", "HrSe")
for (i in 1:length(FOM_arr)) {
FOM <- FOM_arr[i]
fn <- paste0(test_path(), "/goodValues361/FOM/UtilFigureOfMeritFROC-", FOM, ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ret <- UtilFigureOfMerit(dataset, FOM = FOM)
saveRDS(ret, file = fn)
}
ret1 <- readRDS(fn)
ret2 <- UtilFigureOfMerit(dataset, FOM = FOM)
for (i in 1:length(ret1)) {
expect_equal(as.numeric(ret1[[i]]), as.numeric(ret1[[i]]))
}
}
})
# context("UtilFigureOfMerit FROC data: excessive computation time FOMs")
# test_that("FROC data: excessive computation time FOMs", {
#
# skip_on_cran()
#
# dataset <- dataset01 # FROC
#
# FOM_arr <- c("SongA2","SongA1")
#
# for (i in 1:length(FOM_arr)) {
#
# FOM <- FOM_arr[i]
#
# fn <- paste0(test_path(), "/goodValues361/FOM/UtilFigureOfMeritFROC-", FOM, ".rds")
# if (!file.exists(fn)) {
# warning(paste0("File not found - generating new ",fn))
# ret <- UtilFigureOfMerit(dataset, FOM = FOM)
# saveRDS(ret, file = fn)
# }
#
# ret1 <- readRDS(fn)
# ret2 <- UtilFigureOfMerit(dataset, FOM = FOM)
#
# for (i in 1:length(ret1)) {
# expect_equal(as.numeric(ret1[[i]]), as.numeric(ret1[[i]]))
# }
#
# }
#
# })
context("UtilFigureOfMerit ROI paradigm")
test_that("ROI paradigm", {
dataset <- datasetROI
FOM <- "ROI"
fn <- paste0(test_path(), "/goodValues361/FOM/UtilFigureOfMeritROI", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ret <- UtilFigureOfMerit(dataset, FOM = FOM)
saveRDS(ret, file = fn)
}
ret1 <- readRDS(fn)
ret2 <- UtilFigureOfMerit(dataset, FOM = FOM)
for (i in 1:length(ret1)) {
expect_equal(as.numeric(ret1[[i]]), as.numeric(ret1[[i]]))
}
})
context("UtilFigureOfMerit LROC paradigm: FOM = Wilcoxon, ALROC")
test_that("LROC paradigm: FOM = Wilcoxon, ALROC", {
dataset <- datasetCadLroc
FOM_arr <- c("Wilcoxon", "ALROC", "PCL")
for (i in 1:length(FOM_arr)) {
FOM <- FOM_arr[i]
fn <- paste0(test_path(), "/goodValues361/FOM/UtilFigureOfMeritLROC-", FOM, ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ret <- UtilFigureOfMerit(dataset, FOM = FOM, FPFValue = 0.2)
saveRDS(ret, file = fn)
}
ret1 <- readRDS(fn)
ret2 <- UtilFigureOfMerit(dataset, FOM = FOM, FPFValue = 0.2)
for (i in 1:length(ret1)) {
expect_equal(as.numeric(ret1[[i]]), as.numeric(ret1[[i]]))
}
}
})
context("UtilFigureOfMerit LROC paradigm: FOM = PCL@FPFValue")
test_that("LROC paradigm: FOM = PCL@FPFValue", {
dataset <- datasetCadLroc
FOM <- "PCL"
fn <- paste0(test_path(), "/goodValues361/FOM/UtilFigureOfMeritLROC-", FOM, ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ret <- UtilFigureOfMerit(dataset, FOM = FOM, FPFValue = 0.2)
saveRDS(ret, file = fn)
}
ret1 <- readRDS(fn)
ret2 <- UtilFigureOfMerit(dataset, FOM = FOM, FPFValue = 0.2)
for (i in 1:length(ret1)) {
expect_equal(as.numeric(ret1[[i]]), as.numeric(ret1[[i]]))
}
})
context("UtilFigureOfMerit FROC")
test_that("UtilFigureOfMerit FROC", {
dataset <- datasetX
FOM <- "wAFROC"
fn <- paste0(test_path(), "/goodValues361/FOM/UtilFigureOfMerit-", FOM, ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ret <- UtilFigureOfMerit(dataset, FOM = FOM)
saveRDS(ret, file = fn)
}
ret1 <- readRDS(fn)
ret2 <- UtilFigureOfMerit(dataset, FOM = FOM)
for (i in 1:2) {
expect_equal(ret1[[i]], ret2[[i]])
}
})
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