library(tools)
contextStr <- "DfReadDataFile jafroc-csv Format"
context(contextStr)
test_that(contextStr, {
# data format:
# A string specifying the format of the data in the file.
# It can be "JAFROC" (the default), "MRMC" or "iMRMC".
# For "MRMC" the format is determined by the data file extension
# as specified in \url{https://perception.lab.uiowa.edu/},
# i.e., .csv or .txt or .lrc.
# For file extension .imrmc the format is described in https://code.google.com/p/imrmc/.
#
# dpc 6/29/19 comment
# ROC is the simplest paradigm and data structure; yet 4 different formats; go
# figure!
#
fileName <- system.file(
"extdata", "RocData.csv", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/csv", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, format = "MRMC")
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, format = "MRMC")
expect_equal(temp, ds)
})
contextStr <- "DfReadDataFile jafroc-lrc Format"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "RocData.lrc", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/lrc", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ds <- DfReadDataFile(fileName, format = "MRMC")
saveRDS(ds, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, format = "MRMC")
expect_equal(temp, ds)
})
contextStr <- "DfReadDataFile jafroc-iMRMC Format"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "RocData.imrmc", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/iMRMC", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ds <- DfReadDataFile(fileName, format = "iMRMC")
saveRDS(ds, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, format = "iMRMC")
expect_equal(temp, ds)
})
contextStr <- "StCadVsRad: Issue T1-RRRC for ROC data #73"
context(contextStr)
test_that(contextStr, {
# See issue 73 on GitHub website
s1 <- dataset09
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/","issue73.imrmc")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
DfSaveDataFile(s1, fn, format="iMRMC")
}
s2 <- DfReadDataFile(fn, format="iMRMC")
expect_equal(s1$ratings, s2$ratings)
expect_equal(s1$lesions, s2$lesions)
expect_equal(s1$descriptions$type, s2$descriptions$type)
expect_equal(s1$descriptions$truthTableStr, s2$descriptions$truthTableStr)
expect_equal(unname(s1$descriptions$readerID), unname(s2$descriptions$readerID))
expect_equal(unname(s1$descriptions$modalityID), unname(s2$descriptions$modalityID))
})
contextStr <- "DfReadDataFile jafroc-MRMC Format"
context(contextStr)
test_that(contextStr, {
fileName <- system.file("extdata", "RocData.txt", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/txt", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ds <- DfReadDataFile(fileName, format = "MRMC")
saveRDS(ds, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, format = "MRMC")
expect_equal(temp, ds)
})
contextStr <- "DfReadDataFile jafroc-oldExcelFormat"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "Roc.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/jafroc-oldExcelFormat", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ds <- DfReadDataFile(fileName, newExcelFileFormat = FALSE)
saveRDS(ds, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = FALSE)
expect_equal(temp, ds)
})
contextStr <- "DfReadDataFile jafroc-newExcelFormat"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "Froc.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/jafroc-newExcelFormat", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ds <- DfReadDataFile(fileName, newExcelFileFormat = FALSE)
saveRDS(ds, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = FALSE)
expect_equal(temp, ds)
})
contextStr <- "DfReadDataFile jafroc-renum"
context(contextStr)
test_that(contextStr, {
# check sequentialNames option
fileName <- system.file(
"extdata", "Froc.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/jafroc-renum", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
ds <- DfReadDataFile(fileName, sequentialNames = TRUE, newExcelFileFormat = FALSE)
saveRDS(ds, file = fn)
}
ds1 <- readRDS(fn)
ds2 <- DfReadDataFile(fileName, sequentialNames = TRUE, newExcelFileFormat = FALSE)
expect_equal(ds2, ds1)
})
contextStr <- "DfReadDataFile bad toy ROC datasets"
context(contextStr)
test_that(contextStr, {
## The failed checks apply to the Truth Sheet only
fileName <- system.file(
"extdata", "/toyFiles/ROC/bad/missing2CellsRow5and7.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
fileName <- system.file(
"extdata", "/toyFiles/ROC/bad/missingEntireRow5.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
fileName <- system.file(
"extdata", "/toyFiles/ROC/bad/missing1CellRow5.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName))
fileName <- system.file(
"extdata", "/toyFiles/ROC/bad/non-integerCaseID.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
fileName <- system.file(
"extdata", "/toyFiles/ROC/bad/non-integerLesionID.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
fileName <- system.file(
"extdata", "/toyFiles/ROC/bad/incorrectWeights.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
fileName <- system.file(
"extdata", "/toyFiles/ROC/bad/non-numeric-weight.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
# fileName <- system.file(
# "extdata", "/toyFiles/ROC/duplicatedRow.xlsx", package = "RJafroc", mustWork = TRUE)
# expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
fileName <- system.file(
"extdata", "/toyFiles/ROC/bad/incorrectSheetName.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
fileName <- system.file("extdata", "toyFiles/ROC/bad/rocCrStrRdrsNonUnique.xlsx",
package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
})
contextStr <- "DfReadDataFile toy FROC crossed datasets"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "/toyFiles/FROC/frocCr.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/frocCr", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
expect_equal(temp, ds)
fileName <- system.file(
"extdata", "/toyFiles/FROC/frocCrStrRdrsTrts.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/frocCrStrRdrsTrts", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
expect_equal(temp, ds)
})
contextStr <- "DfReadDataFile: toy ROC factorial"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "/toyFiles/ROC/rocCr.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/rocCr", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
expect_equal(temp, ds)
# this checks a data file that uses strings for both readers and treatments, i.e., rocCrStrRdrsTrts.xlsx
fileName <- system.file(
"extdata", "/toyFiles/ROC/rocCrStrRdrsTrts.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/rocCrStrRdrsTrts", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
expect_equal(temp, ds)
})
contextStr <- "DfReadDataFile: toy FROC factorial"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "/toyFiles/FROC/frocCr.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/frocCr", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
expect_equal(temp, ds)
# this checks a data file that uses strings for both readers and treatments, i.e., rocCrStrRdrsTrts.xlsx
fileName <- system.file(
"extdata", "/toyFiles/FROC/frocCrStrRdrsTrts.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/frocCrStrRdrsTrts", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE)
expect_equal(temp, ds)
fileName <- system.file(
"extdata", "/toyFiles/FROC/bad/incorrectCaseIDsInTP.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
y <- system.file("extdata", "toyFiles/FROC/bad/frocCrNonCharInReaderID.xlsx",
package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(y, newExcelFileFormat = TRUE))
y <- system.file("extdata", "toyFiles/FROC/bad/frocCrNonCharInModalityID.xlsx",
package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(y, newExcelFileFormat = TRUE))
})
contextStr <- "DfReadDataFile LROC dataset, 1 forced mark per case"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "/toyFiles/LROC/lroc.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/lroc", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE, lrocForcedMark = TRUE)
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE, lrocForcedMark = TRUE)
expect_equal(temp, ds)
# must set lrocForcedMark flag to logical T/F with this LROC dataset
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE))
})
contextStr <- "DfReadDataFile LROC dataset, 1 mark per case NOT enforced, missing a lesion containing case that was not marked"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "/toyFiles/LROC/lroc1.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/lroc1", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE, lrocForcedMark = FALSE)
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE, lrocForcedMark = FALSE)
expect_equal(temp, ds)
# cannot set lrocForcedMark flag with this dataset
expect_error(expect_warning(DfReadDataFile(fileName, newExcelFileFormat = TRUE, lrocForcedMark = TRUE)))
# cannot set lrocForcedMark flag old format dataset
expect_error(expect_warning(DfReadDataFile(fileName, lrocForcedMark = TRUE)))
})
contextStr <- "DfReadDataFile LROC dataset, 1 mark per case NOT enforced, missing a lesion containing case and a normal case that were not marked"
context(contextStr)
test_that(contextStr, {
fileName <- system.file(
"extdata", "/toyFiles/LROC/lroc2.xlsx", package = "RJafroc", mustWork = TRUE)
fn <- paste0(test_path(), "/goodValues361/DfReadDataFile/lroc2", ".rds")
if (!file.exists(fn)) {
warning(paste0("File not found - generating new ",fn))
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE, lrocForcedMark = FALSE)
saveRDS(temp, file = fn)
}
ds <- readRDS(fn)
temp <- DfReadDataFile(fileName, newExcelFileFormat = TRUE, lrocForcedMark = FALSE)
expect_equal(temp, ds)
# cannot set lrocForcedMark flag with this dataset
expect_warning(expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE, lrocForcedMark = TRUE)))
# cannot set LROC flag with FROC or ROC data
{
fileName <- system.file(
"extdata", "/toyFiles/FROC/frocCr.xlsx", package = "RJafroc", mustWork = TRUE)
expect_error(DfReadDataFile(fileName, newExcelFileFormat = TRUE, lrocForcedMark = TRUE))
}
})
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