Merge pull request #157 from pharmaverse/141_QS_tests

add 4 QS tests
pharmaverse · Jul 18, 2023 · 40a4e3b · 40a4e3b
2 parents 0b5a259 + 5d4d464
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diff --git a/tests/testthat/test-check_qs_dup.R b/tests/testthat/test-check_qs_dup.R
@@ -0,0 +1,38 @@
+QS1 <- data.frame(USUBJID = c(rep(101, 5), rep(102, 5)),
+                QSCAT = "DLQI",
+                QSDTC = rep(c("2017-01-01T08:25", "2017-01-05T09:25",
+                 "2017-01-15T10:25","2017-01-20T08:25","2017-01-25T08:25"), 2),
+                VISITNUM = rep(1:5,2),
+                VISIT = rep(c( "Visit 1", "Visit 2", "Visit 3", "UNSCheduled!!!","VIsit 5"), 2),
+                stringsAsFactors = FALSE)
+
+
+test_that("Function returns true when no errors are present", {
+
+    expect_true(check_qs_dup(QS1))
+})
+
+
+test_that("Function returns false when multiple dates, QSDTC, for the same visit", {
+
+    # multiple dates for the same visit in QS
+    QS2 <- QS1
+    QS2$VISIT[QS2$USUBJID == 101] <- "Visit 1"
+
+    expect_false(check_qs_dup(QS2))
+})
+
+
+
+test_that("Function returns true when multiple visit labels for the same date, QSDTC", {
+
+    # multiple visit labels for the same date
+    QS3 <- QS1
+    QS3$QSDTC[QS3$USUBJID == 101] <- "2017-01-01"
+
+    expect_true(check_qs_dup(QS3))
+})
+
+
+
+
diff --git a/tests/testthat/test-check_qs_qsdtc_after_dd.R b/tests/testthat/test-check_qs_qsdtc_after_dd.R
@@ -0,0 +1,98 @@
+AE <- data.frame(USUBJID = c(1,1,1,2,2,2),
+                 AEDTHDTC = c("", "", "2016-01-01", "", "2016-01", "2016-01-01"),
+                 AESTDTC = "2016-01-01",
+                 AEDECOD = LETTERS[1:6],
+                 AETERM = LETTERS[1:6],
+                 stringsAsFactors = FALSE)
+
+DS <- data.frame(USUBJID = c(1,1,1,2,2,2),
+                 DSSTDTC = "2016-01-01",
+                 DSDECOD = c("A", "B", "death", "AC", "BC", "death"),
+                 DSTERM = letters[1:6],
+                 stringsAsFactors = FALSE)
+
+QS <- data.frame(USUBJID = c(1,1,1,2,2,2),
+                 QSDTC   = c("2015-06-30", "2015-09-30", "2015-12-30",
+                             "2015-06-30", "2015-09-30", "2015-12-30"),
+                 QSCAT   = "A",
+                 QSORRES =  LETTERS[1:6],
+                 QSSTAT  = "",
+                 VISIT  =  c("Week 1", "Week 12", "Week 24", "Week 1", "Week 12", "Week 24"),
+                 QSSTRESC = LETTERS[1:6],
+                 stringsAsFactors = FALSE)
+
+
+
+test_that("Function returns true when no errors are present", {
+
+    expect_true(check_qs_qsdtc_after_dd(AE, DS, QS))
+})
+
+
+test_that("Function returns false when QSDTC is after death date for USUBJID", {
+
+    QS1 <- QS
+    QS1$QSDTC[3:5] <- "2016-01-03"
+
+    expect_false(check_qs_qsdtc_after_dd(AE, DS, QS1))
+
+})
+
+
+test_that("Function returns true when no errors are present", {
+
+    QS2 <- QS
+    QS2$QSSTAT[3] <- "Not Done"
+
+    expect_true(check_qs_qsdtc_after_dd(AE, DS, QS2))
+})
+
+
+
+test_that("Function returns true when no errors are present", {
+
+    QS2 <- QS
+    QS2$QSSTAT[3] <- "Not Done"
+
+    expect_true(check_qs_qsdtc_after_dd(AE, DS, QS2))
+})
+
+
+
+test_that("Function returns false when key variable not available", {
+
+    DS1 <- DS
+    DS1$DSSTDTC <- NULL
+
+    expect_false(check_qs_qsdtc_after_dd(AE, DS1, QS))
+})
+
+
+test_that("Function returns false when error is present", {
+
+    AE1 <- data.frame(USUBJID = 1,
+                      AEDTHDTC = "",
+                      AESTDTC = c("2015-11-01", "2016-02-01"),
+                      AEDECOD = "Rash",
+                      AETERM = "RASH",
+                      stringsAsFactors = FALSE)
+
+    DS1 <- data.frame(USUBJID = 1,
+                      DSSTDTC = "2016-01",
+                      DSCAT = c("DISPOSITION EVENT", "OTHER"),
+                      DSSCAT = c('STUDY COMPLETION/EARLY DISCONTINUATION', ''),
+                      DSDECOD = "DEATH",
+                      DSTERM = c("DEATH", "DEATH DUE TO PROGRESSIVE DISEASE"),
+                      stringsAsFactors = FALSE)
+
+    QS1 <- data.frame(USUBJID = 1,
+                      QSDTC   = c("2015-06-30", "2016-01-15", "2016-01-15"),
+                      QSCAT   = rep("EQ-5D-5L"),
+                      QSORRES = "1",
+                      QSSTAT  = "",
+                      VISIT  =  c("Week 1", "Week 12", "Week 12"),
+                      QSSTRESC = "1",
+                      stringsAsFactors = FALSE)
+
+    expect_false(check_qs_qsdtc_after_dd(AE1, DS1, QS1))
+})
diff --git a/tests/testthat/test-check_qs_qsdtc_visit_ordinal_error.R b/tests/testthat/test-check_qs_qsdtc_visit_ordinal_error.R
@@ -0,0 +1,63 @@
+# no case
+QS1 <- data.frame(USUBJID = c(rep(101, 5), rep(102, 5)),
+                QSCAT = "DLQI",
+                QSDTC = rep(c("2017-01-01T08:25", "2017-01-05T09:25",
+                 "2017-01-15T10:25","2017-01-20T08:25","2017-01-25T08:25"), 2),
+                VISITNUM = rep(1:5,2),
+                VISIT = rep(c( "Visit 1", "Visit 2", "Visit 3", "UNSCheduled!!!","VIsit 5"), 2),
+                stringsAsFactors = FALSE)
+
+
+test_that("Function returns true when no errors are present", {
+
+    QS2 = QS1
+
+    expect_true(check_qs_qsdtc_visit_ordinal_error(QS1))
+})
+
+
+
+
+
+test_that("Function returns true when no errors are present", {
+    QS2 = QS1
+
+    QS2$QSCAT = "SKINDEX-29"
+
+    QS <- rbind(QS1, QS2)
+
+    expect_true(check_qs_qsdtc_visit_ordinal_error(QS))
+})
+
+
+
+
+test_that("Function returns false when date out of sequence", {
+    QS2 = QS1
+    QS2$QSCAT = "SKINDEX-29"
+
+    QS <- rbind(QS1, QS2)
+
+    # adding cases with earlier date
+    QS$QSDTC[QS$USUBJID == 101 & QS$VISIT == "Visit 3"] <- "2017-01-10T08:25"
+    QS$QSDTC[QS$USUBJID == 102 & QS$VISIT == "Visit 2"] <- "2017-01-01T06:25"
+
+    expect_false(check_qs_qsdtc_visit_ordinal_error(QS))
+})
+
+
+
+
+test_that("Function returns false when duplicated date", {
+    QS2 = QS1
+    QS2$QSCAT = "SKINDEX-29"
+
+    QS <- rbind(QS1, QS2)
+
+    # adding cases with duplicated date
+    QS$QSDTC[QS$USUBJID == 102 & QS$VISIT == "Visit 3"] <- "2017-01-01T06:25"
+
+    expect_false(check_qs_qsdtc_visit_ordinal_error(QS))
+})
+
+
diff --git a/tests/testthat/test-check_qs_qsstat_qsstresc.R b/tests/testthat/test-check_qs_qsstat_qsstresc.R
@@ -0,0 +1,41 @@
+
+
+QS <- data.frame(
+    STUDYID = 1,
+    USUBJID = c(rep(1,6),rep(2,6)),
+    QSSTRESC = 1:12,
+    VISIT = c(rep(1,3),rep(2,3),rep(1,3),rep(2,3)),
+    QSSTAT = rep(c("DONE","NOT DONE"),6),
+    QSCAT = rep(c("INDIVIDUAL","OVERALL","BFI"),4),
+    QSDTC = "2016-01-01",
+    QSTESTCD = "QSALL",
+    stringsAsFactors = FALSE
+)
+
+
+test_that("Function returns false when errors are present", {
+
+    expect_false(check_qs_qsstat_qsstresc(QS))
+})
+
+
+test_that("Function returns false when errors are present", {
+
+    QS1 <- QS
+    QS1$QSSTRESC[4]=" "
+    QS1$QSSTRESC[6]=NA
+    QS1$QSSTRESC[8]="."
+
+    expect_false(check_qs_qsstat_qsstresc(QS1))
+})
+
+
+
+test_that("Function returns false when missing key variable", {
+
+    QS2 <- QS
+    QS2$QSSTRESC=NULL
+
+    expect_false(check_qs_qsstat_qsstresc(QS2))
+})
+