Nothing
context("calculateOL")
################################################################################
# CHANGE LOG
# 22.03.2019: Changed deprecated 'matches' to 'expect_match'.
# 20.01.2014: All tests working.
#
# test_dir("inst/tests/")
# test_file("tests/testthat/test-calculateOL.r")
# test_dir("tests/testthat")
test_that("calculateOL", {
# Load test data.
database <- getDb("ESX 17 Hill")
kitInfo <- getKit("ESX17")
# Load test data.
database2 <- getDb("SGM Norway")
kitInfo2 <- getKit("SGMPlus")
# TEST 01 -------------------------------------------------------------------
# Test excluding virtual alleles, actual frequencies.
# Analyse dataframe.
res <- calculateOL(
kit = kitInfo, db = database,
virtual = FALSE, limit = FALSE, debug = FALSE
)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_true(any(grepl("Kit", names(res))))
expect_true(any(grepl("Marker", names(res))))
expect_true(any(grepl("Database", names(res))))
expect_true(any(grepl("Risk", names(res))))
expect_true(any(grepl("Total", names(res))))
# Check for NA's.
expect_false(any(is.na(res$Kit)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Database)))
expect_false(any(is.na(res$Risk)))
expect_false(any(is.na(res$Total)))
# Check result.
expect_that(ncol(res), equals(5))
expect_that(nrow(res), equals(17))
# Check result.
expect_that(length(unique(res$Total)), equals(1))
expect_that(round(unique(res$Total), 4), equals(0.0609))
# TEST 02 -------------------------------------------------------------------
# Test including virtual alleles, actual frequencies.
# Analyse dataframe.
res <- calculateOL(
kit = kitInfo, db = database,
virtual = TRUE, limit = FALSE, debug = FALSE
)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_true(any(grepl("Kit", names(res))))
expect_true(any(grepl("Marker", names(res))))
expect_true(any(grepl("Database", names(res))))
expect_true(any(grepl("Risk", names(res))))
expect_true(any(grepl("Total", names(res))))
# Check for NA's.
expect_false(any(is.na(res$Kit)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Database)))
expect_false(any(is.na(res$Risk)))
expect_false(any(is.na(res$Total)))
# Check result.
expect_that(ncol(res), equals(5))
expect_that(nrow(res), equals(17))
# Check result.
expect_that(length(unique(res$Total)), equals(1))
expect_that(round(unique(res$Total), 4), equals(0.0185))
# TEST 03 -------------------------------------------------------------------
# Test excluding virtual alleles, using minimum frequency.
# Analyse dataframe.
res <- calculateOL(
kit = kitInfo, db = database,
virtual = FALSE, limit = TRUE, debug = FALSE
)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_true(any(grepl("Kit", names(res))))
expect_true(any(grepl("Marker", names(res))))
expect_true(any(grepl("Database", names(res))))
expect_true(any(grepl("Risk", names(res))))
expect_true(any(grepl("Total", names(res))))
# Check for NA's.
expect_false(any(is.na(res$Kit)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Database)))
expect_false(any(is.na(res$Risk)))
expect_false(any(is.na(res$Total)))
# Check result.
expect_that(ncol(res), equals(5))
expect_that(nrow(res), equals(17))
# Check result.
expect_that(length(unique(res$Total)), equals(1))
expect_that(round(unique(res$Total), 4), equals(0.1096))
# TEST 04 -------------------------------------------------------------------
# Test including virtual alleles, using minimum frequency.
# Analyse dataframe.
res <- calculateOL(
kit = kitInfo, db = database,
virtual = TRUE, limit = TRUE, debug = FALSE
)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_true(any(grepl("Kit", names(res))))
expect_true(any(grepl("Marker", names(res))))
expect_true(any(grepl("Database", names(res))))
expect_true(any(grepl("Risk", names(res))))
expect_true(any(grepl("Total", names(res))))
# Check for NA's.
expect_false(any(is.na(res$Kit)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Database)))
expect_false(any(is.na(res$Risk)))
expect_false(any(is.na(res$Total)))
# Check result.
expect_that(ncol(res), equals(5))
expect_that(nrow(res), equals(17))
# Check result.
expect_that(length(unique(res$Total)), equals(1))
expect_that(round(unique(res$Total), 4), equals(0.0392))
# TEST 05 -------------------------------------------------------------------
# Test excluding virtual alleles, actual frequencies.
# Analyse dataframe.
res <- calculateOL(
kit = kitInfo2, db = database2,
virtual = FALSE, limit = FALSE, debug = FALSE
)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_true(any(grepl("Kit", names(res))))
expect_true(any(grepl("Marker", names(res))))
expect_true(any(grepl("Database", names(res))))
expect_true(any(grepl("Risk", names(res))))
expect_true(any(grepl("Total", names(res))))
# Check for NA's.
expect_false(any(is.na(res$Kit)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Database)))
expect_false(any(is.na(res$Risk)))
expect_false(any(is.na(res$Total)))
# Check result.
expect_that(ncol(res), equals(5))
expect_that(nrow(res), equals(11))
# Check result.
expect_that(length(unique(res$Total)), equals(1))
expect_that(round(unique(res$Total), 4), equals(0))
# TEST 06 -------------------------------------------------------------------
# Test including virtual alleles, actual frequencies.
# Analyse dataframe.
res <- calculateOL(
kit = kitInfo2, db = database2,
virtual = TRUE, limit = FALSE, debug = FALSE
)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_true(any(grepl("Kit", names(res))))
expect_true(any(grepl("Marker", names(res))))
expect_true(any(grepl("Database", names(res))))
expect_true(any(grepl("Risk", names(res))))
expect_true(any(grepl("Total", names(res))))
# Check for NA's.
expect_false(any(is.na(res$Kit)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Database)))
expect_false(any(is.na(res$Risk)))
expect_false(any(is.na(res$Total)))
# Check result.
expect_that(ncol(res), equals(5))
expect_that(nrow(res), equals(11))
# Check result.
expect_that(length(unique(res$Total)), equals(1))
expect_that(round(unique(res$Total), 4), equals(0))
# TEST 07 -------------------------------------------------------------------
# Test excluding virtual alleles, using minimum frequency.
# Analyse dataframe.
res <- calculateOL(
kit = kitInfo2, db = database2,
virtual = FALSE, limit = TRUE, debug = FALSE
)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_true(any(grepl("Kit", names(res))))
expect_true(any(grepl("Marker", names(res))))
expect_true(any(grepl("Database", names(res))))
expect_true(any(grepl("Risk", names(res))))
expect_true(any(grepl("Total", names(res))))
# Check for NA's.
expect_false(any(is.na(res$Kit)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Database)))
expect_false(any(is.na(res$Risk)))
expect_false(any(is.na(res$Total)))
# Check result.
expect_that(ncol(res), equals(5))
expect_that(nrow(res), equals(11))
# Check result.
expect_that(length(unique(res$Total)), equals(1))
expect_that(round(unique(res$Total), 4), equals(0))
# TEST 08 -------------------------------------------------------------------
# Test including virtual alleles, using minimum frequency.
# Analyse dataframe.
res <- calculateOL(
kit = kitInfo2, db = database2,
virtual = TRUE, limit = TRUE, debug = FALSE
)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_true(any(grepl("Kit", names(res))))
expect_true(any(grepl("Marker", names(res))))
expect_true(any(grepl("Database", names(res))))
expect_true(any(grepl("Risk", names(res))))
expect_true(any(grepl("Total", names(res))))
# Check for NA's.
expect_false(any(is.na(res$Kit)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Database)))
expect_false(any(is.na(res$Risk)))
expect_false(any(is.na(res$Total)))
# Check result.
expect_that(ncol(res), equals(5))
expect_that(nrow(res), equals(11))
# Check result.
expect_that(length(unique(res$Total)), equals(1))
expect_that(round(unique(res$Total), 4), equals(0))
})
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