tests/testthat/test_computeSummaryStatisticsTable-general.R

In inTextSummaryTable: Creation of in-Text Summary Table

context("Compute summary statistics table")

test_that("An error is generated if data is not a data frame", {
			
	# e.g. if we forget to create the 'data' object, 
	# 'data()' function is used instead:
	expect_error(
		computeSummaryStatisticsTable(data),
		"A data.frame should be specified in.*data.*."
	)
	
})

test_that("An message is generated if the data is empty", {
			
	data <- data.frame()
	expect_message(
		res <- computeSummaryStatisticsTable(data),
		"No data to report."
	)
	expect_null(res)
	
})

test_that("A count table for the entire data is created if no variable is specified", {
			
	dataCont <- data.frame(
		x = c(NA, 1, 3, 6, 10), 
		USUBJID = seq.int(5)
	)
	
	# no variable specified: a count table is created
	sumNoVar <- computeSummaryStatisticsTable(dataCont)
	expect_s3_class(sumNoVar, "summaryTable")
	expect_named(sumNoVar, c("isTotal", "statN", "statm", "statPercTotalN", "statPercN"), ignore.order = TRUE)
	expect_equal(
		unname(unlist(subset(sumNoVar, isTotal)[1, c("statN", "statm", "statPercTotalN", "statPercN")])),
		c(5, 5, 5, 100)
	)
	expect_equal(
		subset(sumNoVar, isTotal, select = -isTotal), 
		subset(sumNoVar, !isTotal, select = -isTotal), 
		check.attributes = FALSE
	)
	
})

test_that("An error is generated if the default subject ID variable is not available", {
			
	dataCont <- data.frame(
		x = c(NA, 1, 3, 6, 10),
		`subject identifier` = seq.int(5), 
		check.names = FALSE
	)
	
	expect_error(
		computeSummaryStatisticsTable(dataCont),
		"Subject variable.*not available for the computation of the number of subjects."
	)
	
})

test_that("Counts of subjects are correctly computed when a custom subject ID variable is specified", {
		
	dataCont <- data.frame(
		x = c(NA, 1, 3, 6, 10),
		`subject identifier` = seq.int(5), 
		check.names = FALSE
	)
			
	expect_silent(sumTable <- 
		computeSummaryStatisticsTable(
			data = dataCont, 
			subjectVar = "subject identifier"
		)			
	)
	expect_equal(sumTable$statN, c(5, 5))
	expect_equal(sumTable$statPercTotalN, c(5, 5))
	expect_equal(sumTable$statPercN, c(100, 100))
			
})

test_that("The summary table is correctly filtered", {
			
	data <- data.frame(
		USUBJID = seq.int(5),
		AEDECOD = rep(c("A", "B"), length.out = 5)
	)

	summaryTableFiltered <- computeSummaryStatisticsTable(
		data = data, var = "AEDECOD",
		filterFct = function(x) subset(x, variableGroup == "A")
	)
	expect_equal(
		summaryTableFiltered,
		subset(computeSummaryStatisticsTable(data = data, var = "AEDECOD"), variableGroup == "A"),
		check.attributes = FALSE
	)
	
})

test_that("An error is generated if the filtering function is not correct", {
			
	data <- data.frame(
		USUBJID = seq.int(5),
		AEDECOD = rep(c("A", "B"), length.out = 5)
	)

	expect_error(
		computeSummaryStatisticsTable(
			data = data, var = "AEDECOD",
			filterFct = function(x) subset(x, variableGroup2 == "A")
		)
	)
			
})

test_that("The summary table is correctly filtered when a flag variable is specified", {
	
	# internally, a filterFct is set when varFlag is specified
	# this test checks that if the user specifies additionally 
	# a filterFct, this one is also used.
			
	data <- data.frame(
		USUBJID = seq.int(5),
		AEDECOD = c("A", "A", "B", "B", "B"),
		ANFL = c("Y", "N", "Y", "N", "Y")
	)
	
	summaryTableAll <- computeSummaryStatisticsTable(
		data = data, 
		var = "ANFL", varFlag = "ANFL",
		rowVar = "AEDECOD",
		stats = "n"
	)
			
	summaryTableFiltered <- computeSummaryStatisticsTable(
		data = data, 
		var = "ANFL", varFlag = "ANFL",
		rowVar = "AEDECOD",
		stats = "n",
		filterFct = function(x) subset(x, AEDECOD == "A")
	)
	
	expect_equal(
		summaryTableFiltered,
		subset(summaryTableAll, AEDECOD == "A"),
		check.attributes = FALSE
	)
			
})

test_that("The summary table is correctly computed by a grouping variable", {
		
	data <- data.frame(
		USUBJID = seq.int(5),
		AEDECOD = factor(c("A", "A", "B", "B", "B"), levels = c("B", "A"))
	)	
	
	summaryTableByVar <- computeSummaryStatisticsTable(
		data = data,
		byVar = "AEDECOD"
	)
	
	expect_type(summaryTableByVar, "list")
	expect_length(summaryTableByVar, 2)
	expect_named(summaryTableByVar, paste("AEDECOD:", c("B", "A")))
	
	for(group in unique(data$AEDECOD)){
		expect_equal(
			object = summaryTableByVar[[paste("AEDECOD:", !!group)]],
			expected = computeSummaryStatisticsTable(data = subset(data, AEDECOD == !!group)),
			check.attributes = FALSE
		)
	}
			
})

test_that("The summary table is correctly computed by a grouping variable with specified label", {
			
	data <- data.frame(
		USUBJID = seq.int(5),
		AEDECOD = factor(c("A", "A", "B", "B", "B"), 
			levels = c("B", "A"))
	)	
	
	# correct spec
	summaryTableByVar <- computeSummaryStatisticsTable(
		data = data,
		byVar = "AEDECOD",
		byVarLab = c("AEDECOD" = "Adverse event")
	)
	expect_named(summaryTableByVar, paste("Adverse event:", c("B", "A")))
	
})
	
test_that("The summary table is correctly computed by a grouping variable with default variable name if label is missing", {
		
	data <- data.frame(
		USUBJID = seq.int(5),
		AEDECOD = factor(c("A", "A", "B", "B", "B"), 
			levels = c("B", "A"))
	)
	
	# in case byVarLab specified for other variables
	# var code is used:
	summaryTableByVar <- computeSummaryStatisticsTable(
		data = data,
		byVar = "AEDECOD",
		byVarLab = c("blabla" = "Adverse event")
	)
	expect_named(summaryTableByVar, paste("AEDECOD:", c("B", "A")))
			
})