Nothing
tests/testthat/test_annotateData.R
In clinDataReview: Clinical Data Review Tool
context("Annotate data")
library(haven)
test_that("Data is correctly annotated from one dataset to another", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5),
VISIT = c("Day 1", "Day 1", "Day 2", "Day 2", "Day 1"),
PARAMCD = c("ALS", "ALT", "ALT", "BILI", "BILI"),
stringsAsFactors = FALSE
)
dataDM <- data.frame(
USUBJID = seq.int(5),
SAFFL = "Y",
SEX = c("F", "F", "M", "M", "M"),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
stringsAsFactors = FALSE
)
dataAnnot <- annotateData(
data = dataLB,
annotations = list(data = dataDM)
)
newCols <- setdiff(colnames(dataAnnot), colnames(dataLB))
expect_equivalent(
object = dataDM[match(dataLB$USUBJID, dataDM$USUBJID), newCols],
expected = dataAnnot[, newCols]
)
})
test_that("A warning is generated if the annotation data and data to annotate contain variables with the same name", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5),
SAFFL = "Y"
)
dataDM <- data.frame(
USUBJID = seq.int(5),
SAFFL = "Y"
)
expect_warning(
dataAnnot <- annotateData(
data = dataLB,
annotations = list(data = dataDM)
),
"SAFFL.*already available"
)
})
test_that("Data is correctly annotated with a new variable, computed based on a combination of multiple variables", {
data <- data.frame(
AVAL = c(1, 2, 3, 4, 5),
AVAL2 = 10,
stringsAsFactors = FALSE
)
dataAnnot <- annotateData(
data = data,
annotations = list(vars = "RATIO", varFct = "AVAL / AVAL2")
)
expect_equal(
object = dataAnnot$RATIO,
expected = with(dataAnnot, AVAL / AVAL2),
check.attributes = FALSE
)
})
test_that("Data is correctly annotated with a new variable, from a function of the variables", {
data <- data.frame(
VISIT = c("Day 1", "Day 1", "Day 2", "Day 2", "Day 1"),
stringsAsFactors = FALSE
)
varFct <- "sub('Day .* - (.+)', '\\\\1', VISIT)"
dataAnnot <- annotateData(
data = data,
annotations = list(
vars = "PERIOD",
varFct = varFct
)
)
expect_equal(
object = dataAnnot$PERIOD,
expected = eval(expr = parse(text = varFct), envir = data),
check.attributes = TRUE
)
})
test_that("An error is generated if a new variable is not specified when the data is annotated based on a function of the variables", {
data <- data.frame(
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954)
)
expect_error(
annotateData(
data = data,
annotations = list(
varFct = 'sprintf("%s %s", AGE, YEAR)',
varLabel = "Age and year"
)
),
"'vars' should be specified"
)
})
test_that("Data is correctly annotated with a new variable, from a function of the data, specified as a character", {
data <- data.frame(
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954)
)
dataAnnot <- annotateData(
data = data,
annotations = list(
vars = "AGEYEAR",
varFct = 'function(data) with(data, sprintf("%s %s", data$AGE, data$YEAR))',
varLabel = "Age and year"
)
)
expect_equal(
object = dataAnnot$AGEYEAR,
expected = with(data, sprintf("%s %s", AGE, YEAR)),
check.attributes = TRUE
)
})
test_that("Data is correctly annotated with a new variable, from a function of the data", {
data <- data.frame(
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954)
)
dataAnnot <- annotateData(
data = data,
annotations = list(
vars = "AGEYEAR",
varFct = function(data) with(data, sprintf("%s %s", data$AGE, data$YEAR)),
varLabel = "Age and year"
)
)
expect_equal(
object = dataAnnot$AGEYEAR,
expected = with(data, sprintf("%s %s", AGE, YEAR)),
check.attributes = TRUE
)
})
test_that("A warning is generated if the exported data for annotation is not available in the specified path", {
data <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
expect_warning(
dataAnnot <- annotateData(
data = data,
dataPath = tempfile(),
annotations = list(dataset = "dm")
),
"not annotated with.*dm.*dataset"
)
expect_identical(object = dataAnnot, expected = data)
})
test_that("Data is correctly annotated based on an exported dataset", {
data <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataDM <- data.frame(
USUBJID = seq.int(5),
SAFFL = "Y",
SEX = c("F", "F", "M", "M", "M"),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "dm.xpt")
write_xpt(data = dataDM, path = dataPath)
dataAnnot <- annotateData(
data = data,
dataPath = dir,
annotations = list(dataset = "dm")
)
expect_equal(
object = dataAnnot[, colnames(dataDM)],
expected = dataDM[match(dataAnnot$USUBJID, dataDM$USUBJID), ]
)
})
test_that("Data is correctly annotated with a specified variable based on an exported dataset", {
data <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataDM <- data.frame(
USUBJID = seq.int(5),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "dm.xpt")
write_xpt(data = dataDM, path = dataPath)
dataAnnot <- annotateData(
data = data,
dataPath = dir,
annotations = list(dataset = "dm", vars = "AGE")
)
expect_identical(
object = colnames(dataAnnot),
expected = c(colnames(data), "AGE")
)
expect_equal(
object = dataAnnot$AGE,
expected = dataDM[match(data$USUBJID, dataDM$USUBJID), "AGE"]
)
})
test_that("Data is correctly annotated based on a filtered dataset", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
dataDM <- data.frame(
USUBJID = seq.int(5),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
SEX = c("F", "F", "M", "M", "M")
)
dataAnnotFilter <- annotateData(
data = dataLB,
annotations = list(
data = dataDM,
filters = list(var = "SEX", value = "M")
)
)
idsFiltered <- subset(dataDM, SEX == "M")$USUBJID
newCols <- setdiff(colnames(dataDM), colnames(dataLB))
# records filtered have missing info
dataAnnotFilteredMissing <- subset(dataAnnotFilter, !USUBJID %in% idsFiltered, select = newCols)
expect_true(all(is.na(dataAnnotFilteredMissing)))
# selected records have correct info filled
expect_equal(
object = subset(dataAnnotFilter, USUBJID %in% idsFiltered, select = newCols),
expected = subset(dataDM, USUBJID %in% idsFiltered, select = newCols),
check.attributes = FALSE
)
})
test_that("Data is correctly annotated based on multiple annotations", {
data <- data.frame(
USUBJID = seq.int(5),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
SEX = c("F", "F", "M", "M", "M"),
stringsAsFactors = TRUE
)
dataAnnot <- annotateData(
data = data,
annotations = list(
list(
vars = "SEXFCT",
varFct = 'as.factor(SEX)'
),
list(
vars = "AGESTRING",
varFct = 'sprintf("%s %s", AGE, YEAR)',
varLabel = "Age and year"
)
)
)
expect_identical(
object = dataAnnot$SEXFCT,
expected = as.factor(data$SEX)
)
expect_identical(
object = dataAnnot$AGESTRING,
expected = with(data, sprintf("%s %s", AGE, YEAR))
)
})
test_that("An error is generated if the preset annotation option is not available", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
expect_error(
annotateData(data = dataLB, annotations = "demographic"),
"Data is not annotated, because 'annotations' should be one of"
)
})
test_that("A warning is generated if the data is annotated with the preset 'demographics' option but no such data is available", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
expect_warning(
annotateData(dataLB, annotations = "demographics"),
"Data is not annotated with demographics data because no such data"
)
})
test_that("Data is correctly annotated based on the preset 'demographics' option", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataDM <- data.frame(
USUBJID = seq.int(5),
SEX = c("F", "F", "M", "M", "M"),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "dm.xpt")
write_xpt(data = dataDM, path = dataPath)
dataAnnot <- annotateData(
data = dataLB,
dataPath = dir,
annotations = "demographics"
)
expect_equal(
object = dataAnnot[match(dataLB$USUBJID, dataDM$USUBJID), c("AGE", "SEX")],
expected = dataDM[, c("AGE", "SEX")]
)
})
test_that("A warning is generated if the data is annotated with the preset 'functional groups' option but no parameter code variable is available", {
data <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
expect_warning(
dataAnnot <- annotateData(data = data, annotations = "functional_groups_lab"),
"Data is not annotated with functional groups, because no variable"
)
expect_identical(object = dataAnnot, expected = data)
})
test_that("Data is correctly annotated based on the preset 'functional_groups_lab' option", {
data <- data.frame(
USUBJID = seq.int(4),
AVAL = c(1, 2, 3, 4),
PARAMCD = c("ALS", "ALT", "ALP", "CHOL"),
stringsAsFactors = TRUE
)
dataAnnot <- annotateData(
data = data,
annotations = "functional_groups_lab"
)
expect_s3_class(dataAnnot, "data.frame")
expect_identical(
object = colnames(dataAnnot),
expected = c(colnames(data), "LBFCTGRP")
)
expect_s3_class(dataAnnot$LBFCTGRP, "factor")
expect_identical(
object = as.character(dataAnnot$LBFCTGRP),
expected = c("Other", "Liver function", "Liver function", "Lipids")
)
})
test_that("A warning is generated when annotating with the preset 'exposed_subjects' option, but no exposure data is present", {
data <- data.frame(USUBJID = seq.int(5))
expect_warning(
annotateData(
data = data,
dataPath = "path/To/Data",
annotations = "exposed_subjects"
),
"Data is not annotated with exposure data, because no such data"
)
})
test_that("Data is correctly annotated based on the preset 'exposed_subjects' option", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataEX <- data.frame(
USUBJID = seq.int(4),
STDY = c("0103", "0102", "0104", ""),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "ex.xpt")
write_xpt(data = dataEX, path = dataPath)
dataAnnotEx <- annotateData(
data = dataLB,
dataPath = dir,
annotations = "exposed_subjects"
)
# subjects with start date in exposure dataset
expect_setequal(
object = subset(dataAnnotEx, USUBJID %in% seq.int(3))$EXFL,
expected = TRUE
)
# subjects without start date in exposure dataset
expect_setequal(
object = subset(dataAnnotEx, !USUBJID %in% seq.int(3))$EXFL,
expected = FALSE
)
})
test_that("An error is generated when annotating with the preset 'exposed_subjects' option, but this dataset does not contain a subject variable", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataEX <- data.frame(
STDY = c("0103", "0102", "0104", ""),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "ex.xpt")
write_xpt(data = dataEX, path = dataPath)
expect_error(
annotateData(
data = dataLB,
dataPath = dir,
annotations = "exposed_subjects",
subjectVar = "USUBJID"
),
"doesn't contain the subject variable"
)
})
test_that("An error is generated when annotating with the preset 'exposed_subjects' option, but this dataset does not contain a start time variable", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataEX <- data.frame(USUBJID = seq.int(4))
dir <- tempdir("annotation")
dataPath <- file.path(dir, "ex.xpt")
write_xpt(data = dataEX, path = dataPath)
expect_error(
annotateData(
data = dataLB,
dataPath = dir,
annotations = "exposed_subjects",
subjectVar = "USUBJID"
),
"doesn't contain a start time variable"
)
})
test_that("Data is correctly annotated from a filtered subsetted variable by group", {
# extract baseline records
data <- data.frame(
AVISIT = c("Baseline", "Week 4", "Baseline", "Week 4"),
USUBJID = c(1, 1, 2, 2),
AVAL = c(4, 2, 6, 3)
)
annotatedData <- annotateData(
data = data,
annotations = list(
vars = "BASE",
varFct = "AVAL",
varsBy = "USUBJID",
filters = list(var = "AVISIT", value = "Baseline")
)
)
expect_setequal(
object = subset(annotatedData, USUBJID == 1)$BASE,
expected = 4
)
expect_setequal(
object = subset(annotatedData, USUBJID == 2)$BASE,
expected = 6
)
})
test_that("A warning is generated if the variable to group by has replicates", {
data <- data.frame(
AVISIT = c("Baseline", "Week 4", "Baseline", "Week 4"),
USUBJID = c(1, 1, 2, 2),
AVAL = c(4, 2, 6, 3)
)
expect_warning(
annotateData(
data = data,
annotations = list(
vars = "BASE",
varFct = "AVAL",
varsBy = "USUBJID"
)
),
"Duplicated records.*"
)
})
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context("Annotate data")
library(haven)
test_that("Data is correctly annotated from one dataset to another", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5),
VISIT = c("Day 1", "Day 1", "Day 2", "Day 2", "Day 1"),
PARAMCD = c("ALS", "ALT", "ALT", "BILI", "BILI"),
stringsAsFactors = FALSE
)
dataDM <- data.frame(
USUBJID = seq.int(5),
SAFFL = "Y",
SEX = c("F", "F", "M", "M", "M"),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
stringsAsFactors = FALSE
)
dataAnnot <- annotateData(
data = dataLB,
annotations = list(data = dataDM)
)
newCols <- setdiff(colnames(dataAnnot), colnames(dataLB))
expect_equivalent(
object = dataDM[match(dataLB$USUBJID, dataDM$USUBJID), newCols],
expected = dataAnnot[, newCols]
)
})
test_that("A warning is generated if the annotation data and data to annotate contain variables with the same name", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5),
SAFFL = "Y"
)
dataDM <- data.frame(
USUBJID = seq.int(5),
SAFFL = "Y"
)
expect_warning(
dataAnnot <- annotateData(
data = dataLB,
annotations = list(data = dataDM)
),
"SAFFL.*already available"
)
})
test_that("Data is correctly annotated with a new variable, computed based on a combination of multiple variables", {
data <- data.frame(
AVAL = c(1, 2, 3, 4, 5),
AVAL2 = 10,
stringsAsFactors = FALSE
)
dataAnnot <- annotateData(
data = data,
annotations = list(vars = "RATIO", varFct = "AVAL / AVAL2")
)
expect_equal(
object = dataAnnot$RATIO,
expected = with(dataAnnot, AVAL / AVAL2),
check.attributes = FALSE
)
})
test_that("Data is correctly annotated with a new variable, from a function of the variables", {
data <- data.frame(
VISIT = c("Day 1", "Day 1", "Day 2", "Day 2", "Day 1"),
stringsAsFactors = FALSE
)
varFct <- "sub('Day .* - (.+)', '\\\\1', VISIT)"
dataAnnot <- annotateData(
data = data,
annotations = list(
vars = "PERIOD",
varFct = varFct
)
)
expect_equal(
object = dataAnnot$PERIOD,
expected = eval(expr = parse(text = varFct), envir = data),
check.attributes = TRUE
)
})
test_that("An error is generated if a new variable is not specified when the data is annotated based on a function of the variables", {
data <- data.frame(
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954)
)
expect_error(
annotateData(
data = data,
annotations = list(
varFct = 'sprintf("%s %s", AGE, YEAR)',
varLabel = "Age and year"
)
),
"'vars' should be specified"
)
})
test_that("Data is correctly annotated with a new variable, from a function of the data, specified as a character", {
data <- data.frame(
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954)
)
dataAnnot <- annotateData(
data = data,
annotations = list(
vars = "AGEYEAR",
varFct = 'function(data) with(data, sprintf("%s %s", data$AGE, data$YEAR))',
varLabel = "Age and year"
)
)
expect_equal(
object = dataAnnot$AGEYEAR,
expected = with(data, sprintf("%s %s", AGE, YEAR)),
check.attributes = TRUE
)
})
test_that("Data is correctly annotated with a new variable, from a function of the data", {
data <- data.frame(
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954)
)
dataAnnot <- annotateData(
data = data,
annotations = list(
vars = "AGEYEAR",
varFct = function(data) with(data, sprintf("%s %s", data$AGE, data$YEAR)),
varLabel = "Age and year"
)
)
expect_equal(
object = dataAnnot$AGEYEAR,
expected = with(data, sprintf("%s %s", AGE, YEAR)),
check.attributes = TRUE
)
})
test_that("A warning is generated if the exported data for annotation is not available in the specified path", {
data <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
expect_warning(
dataAnnot <- annotateData(
data = data,
dataPath = tempfile(),
annotations = list(dataset = "dm")
),
"not annotated with.*dm.*dataset"
)
expect_identical(object = dataAnnot, expected = data)
})
test_that("Data is correctly annotated based on an exported dataset", {
data <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataDM <- data.frame(
USUBJID = seq.int(5),
SAFFL = "Y",
SEX = c("F", "F", "M", "M", "M"),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "dm.xpt")
write_xpt(data = dataDM, path = dataPath)
dataAnnot <- annotateData(
data = data,
dataPath = dir,
annotations = list(dataset = "dm")
)
expect_equal(
object = dataAnnot[, colnames(dataDM)],
expected = dataDM[match(dataAnnot$USUBJID, dataDM$USUBJID), ]
)
})
test_that("Data is correctly annotated with a specified variable based on an exported dataset", {
data <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataDM <- data.frame(
USUBJID = seq.int(5),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "dm.xpt")
write_xpt(data = dataDM, path = dataPath)
dataAnnot <- annotateData(
data = data,
dataPath = dir,
annotations = list(dataset = "dm", vars = "AGE")
)
expect_identical(
object = colnames(dataAnnot),
expected = c(colnames(data), "AGE")
)
expect_equal(
object = dataAnnot$AGE,
expected = dataDM[match(data$USUBJID, dataDM$USUBJID), "AGE"]
)
})
test_that("Data is correctly annotated based on a filtered dataset", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
dataDM <- data.frame(
USUBJID = seq.int(5),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
SEX = c("F", "F", "M", "M", "M")
)
dataAnnotFilter <- annotateData(
data = dataLB,
annotations = list(
data = dataDM,
filters = list(var = "SEX", value = "M")
)
)
idsFiltered <- subset(dataDM, SEX == "M")$USUBJID
newCols <- setdiff(colnames(dataDM), colnames(dataLB))
# records filtered have missing info
dataAnnotFilteredMissing <- subset(dataAnnotFilter, !USUBJID %in% idsFiltered, select = newCols)
expect_true(all(is.na(dataAnnotFilteredMissing)))
# selected records have correct info filled
expect_equal(
object = subset(dataAnnotFilter, USUBJID %in% idsFiltered, select = newCols),
expected = subset(dataDM, USUBJID %in% idsFiltered, select = newCols),
check.attributes = FALSE
)
})
test_that("Data is correctly annotated based on multiple annotations", {
data <- data.frame(
USUBJID = seq.int(5),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
SEX = c("F", "F", "M", "M", "M"),
stringsAsFactors = TRUE
)
dataAnnot <- annotateData(
data = data,
annotations = list(
list(
vars = "SEXFCT",
varFct = 'as.factor(SEX)'
),
list(
vars = "AGESTRING",
varFct = 'sprintf("%s %s", AGE, YEAR)',
varLabel = "Age and year"
)
)
)
expect_identical(
object = dataAnnot$SEXFCT,
expected = as.factor(data$SEX)
)
expect_identical(
object = dataAnnot$AGESTRING,
expected = with(data, sprintf("%s %s", AGE, YEAR))
)
})
test_that("An error is generated if the preset annotation option is not available", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
expect_error(
annotateData(data = dataLB, annotations = "demographic"),
"Data is not annotated, because 'annotations' should be one of"
)
})
test_that("A warning is generated if the data is annotated with the preset 'demographics' option but no such data is available", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
expect_warning(
annotateData(dataLB, annotations = "demographics"),
"Data is not annotated with demographics data because no such data"
)
})
test_that("Data is correctly annotated based on the preset 'demographics' option", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataDM <- data.frame(
USUBJID = seq.int(5),
SEX = c("F", "F", "M", "M", "M"),
AGE = c(54, 78, 34, 51, 67),
YEAR = c(1967, 1943, 1987, 1970, 1954),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "dm.xpt")
write_xpt(data = dataDM, path = dataPath)
dataAnnot <- annotateData(
data = dataLB,
dataPath = dir,
annotations = "demographics"
)
expect_equal(
object = dataAnnot[match(dataLB$USUBJID, dataDM$USUBJID), c("AGE", "SEX")],
expected = dataDM[, c("AGE", "SEX")]
)
})
test_that("A warning is generated if the data is annotated with the preset 'functional groups' option but no parameter code variable is available", {
data <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
expect_warning(
dataAnnot <- annotateData(data = data, annotations = "functional_groups_lab"),
"Data is not annotated with functional groups, because no variable"
)
expect_identical(object = dataAnnot, expected = data)
})
test_that("Data is correctly annotated based on the preset 'functional_groups_lab' option", {
data <- data.frame(
USUBJID = seq.int(4),
AVAL = c(1, 2, 3, 4),
PARAMCD = c("ALS", "ALT", "ALP", "CHOL"),
stringsAsFactors = TRUE
)
dataAnnot <- annotateData(
data = data,
annotations = "functional_groups_lab"
)
expect_s3_class(dataAnnot, "data.frame")
expect_identical(
object = colnames(dataAnnot),
expected = c(colnames(data), "LBFCTGRP")
)
expect_s3_class(dataAnnot$LBFCTGRP, "factor")
expect_identical(
object = as.character(dataAnnot$LBFCTGRP),
expected = c("Other", "Liver function", "Liver function", "Lipids")
)
})
test_that("A warning is generated when annotating with the preset 'exposed_subjects' option, but no exposure data is present", {
data <- data.frame(USUBJID = seq.int(5))
expect_warning(
annotateData(
data = data,
dataPath = "path/To/Data",
annotations = "exposed_subjects"
),
"Data is not annotated with exposure data, because no such data"
)
})
test_that("Data is correctly annotated based on the preset 'exposed_subjects' option", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataEX <- data.frame(
USUBJID = seq.int(4),
STDY = c("0103", "0102", "0104", ""),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "ex.xpt")
write_xpt(data = dataEX, path = dataPath)
dataAnnotEx <- annotateData(
data = dataLB,
dataPath = dir,
annotations = "exposed_subjects"
)
# subjects with start date in exposure dataset
expect_setequal(
object = subset(dataAnnotEx, USUBJID %in% seq.int(3))$EXFL,
expected = TRUE
)
# subjects without start date in exposure dataset
expect_setequal(
object = subset(dataAnnotEx, !USUBJID %in% seq.int(3))$EXFL,
expected = FALSE
)
})
test_that("An error is generated when annotating with the preset 'exposed_subjects' option, but this dataset does not contain a subject variable", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataEX <- data.frame(
STDY = c("0103", "0102", "0104", ""),
stringsAsFactors = FALSE
)
dir <- tempdir("annotation")
dataPath <- file.path(dir, "ex.xpt")
write_xpt(data = dataEX, path = dataPath)
expect_error(
annotateData(
data = dataLB,
dataPath = dir,
annotations = "exposed_subjects",
subjectVar = "USUBJID"
),
"doesn't contain the subject variable"
)
})
test_that("An error is generated when annotating with the preset 'exposed_subjects' option, but this dataset does not contain a start time variable", {
dataLB <- data.frame(
USUBJID = seq.int(5),
AVAL = c(1, 2, 3, 4, 5)
)
# export annotation dataset
dataEX <- data.frame(USUBJID = seq.int(4))
dir <- tempdir("annotation")
dataPath <- file.path(dir, "ex.xpt")
write_xpt(data = dataEX, path = dataPath)
expect_error(
annotateData(
data = dataLB,
dataPath = dir,
annotations = "exposed_subjects",
subjectVar = "USUBJID"
),
"doesn't contain a start time variable"
)
})
test_that("Data is correctly annotated from a filtered subsetted variable by group", {
# extract baseline records
data <- data.frame(
AVISIT = c("Baseline", "Week 4", "Baseline", "Week 4"),
USUBJID = c(1, 1, 2, 2),
AVAL = c(4, 2, 6, 3)
)
annotatedData <- annotateData(
data = data,
annotations = list(
vars = "BASE",
varFct = "AVAL",
varsBy = "USUBJID",
filters = list(var = "AVISIT", value = "Baseline")
)
)
expect_setequal(
object = subset(annotatedData, USUBJID == 1)$BASE,
expected = 4
)
expect_setequal(
object = subset(annotatedData, USUBJID == 2)$BASE,
expected = 6
)
})
test_that("A warning is generated if the variable to group by has replicates", {
data <- data.frame(
AVISIT = c("Baseline", "Week 4", "Baseline", "Week 4"),
USUBJID = c(1, 1, 2, 2),
AVAL = c(4, 2, 6, 3)
)
expect_warning(
annotateData(
data = data,
annotations = list(
vars = "BASE",
varFct = "AVAL",
varsBy = "USUBJID"
)
),
"Duplicated records.*"
)
})
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