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Merge pull request #199 from pharmaverse/LYW_unit_tests
Lyw unit tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| test_that("Returns true when no errors present",{ | ||
| DM <- data.frame(USUBJID = 1:5, | ||
| ARM = c(letters[1:5]), | ||
| ACTARM = letters[1:5], | ||
| stringsAsFactors = FALSE) | ||
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| expect_true(check_dm_actarm_arm(DM)) | ||
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| }) | ||
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| test_that("Returns false when errors present - 1",{ | ||
| DM <- data.frame(USUBJID = 1:5, | ||
| ARM = c(letters[1:3], letters[5:6]), | ||
| ACTARM = letters[1:5], | ||
| stringsAsFactors = FALSE) | ||
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| expect_false(check_dm_actarm_arm(DM)) | ||
| }) | ||
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| test_that("Returns false when errors present - 2", { | ||
| DM <- data.frame(USUBJID = 1:5, | ||
| ACTARM = c(letters[1:3], letters[5:6]), | ||
| ARM = letters[1:5], | ||
| stringsAsFactors = FALSE) | ||
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| expect_false(check_dm_actarm_arm(DM)) | ||
| }) | ||
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| test_that("Returns false when expected column not present", { | ||
| DM <- data.frame(USUBJID = 1:5, | ||
| ARM = c(letters[1:5]), | ||
| ACTARM = letters[1:5], | ||
| stringsAsFactors = FALSE) | ||
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| DM$ARM <- NULL | ||
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| expect_false(check_dm_actarm_arm(DM)) | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| test_that("Returns true when no errors present", { | ||
| DM <- data.frame( | ||
| USUBJID = 1:10, | ||
| AGE = c(50,60,50,89,19,33,50,40,22,25) | ||
| ) | ||
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| expect_true(check_dm_age_missing(DM)) | ||
| }) | ||
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| test_that("Returns false when errors present - 1", { | ||
| DM <- data.frame( | ||
| USUBJID = 1:10, | ||
| AGE =c(50,60,50,89,NA,33,50,40,22,25) | ||
| ) | ||
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| expect_false(check_dm_age_missing(DM)) | ||
| }) | ||
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| test_that("Returns false when errors present - 2", { | ||
| DM <- data.frame( | ||
| USUBJID = 1:10, | ||
| AGE =c(50,60,50,89,91,33,50,40,22,25) | ||
| ) | ||
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| expect_false(check_dm_age_missing(DM)) | ||
| }) | ||
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| test_that("Returns false when errors present - 3", { | ||
| DM <- data.frame( | ||
| USUBJID = 1:10, | ||
| AGE =c(50,60,50,89,17,33,50,40,22,25) | ||
| ) | ||
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| expect_false(check_dm_age_missing(DM)) | ||
| }) | ||
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| test_that("Returns false when expected column not present", { | ||
| DM <- data.frame( | ||
| USUBJID = 1:10, | ||
| AGE = c(50,60,50,89,19,33,50,40,22,25) | ||
| ) | ||
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| DM$AGE = NULL | ||
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| expect_false(check_dm_age_missing(DM)) | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| test_that("Returns true when no errors present", { | ||
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| DM <- data.frame( | ||
| USUBJID = 1:7, | ||
| DTHFL = 1:7, | ||
| DTHDTC = 1:7 | ||
| ) | ||
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| DM$DTHFL[1] = "" | ||
| DM$DTHDTC[1] = "2020-01-01" | ||
| DM$DTHFL[2] = "N" | ||
| DM$DTHDTC[2] = "2020-01-01" | ||
| DM$DTHFL[3] = "Y" | ||
| DM$DTHDTC[3] = "2020-01-01" | ||
| DM$DTHFL[4] = "Y" | ||
| DM$DTHDTC[4] = "" | ||
| DM$DTHFL[5] = "N" | ||
| DM$DTHDTC[5] = "" | ||
| DM$DTHFL[6] = "Y" | ||
| DM$DTHDTC[6] = "2020" | ||
| DM$DTHFL[7] = "" | ||
| DM$DTHDTC[7] = "" | ||
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| expect_true(check_dm_dthfl_dthdtc(DM[3,])) | ||
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| }) | ||
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| test_that("Returns false when errors present", { | ||
| DM <- data.frame( | ||
| USUBJID = 1:7, | ||
| DTHFL = 1:7, | ||
| DTHDTC = 1:7 | ||
| ) | ||
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| DM$DTHFL[1] = "" | ||
| DM$DTHDTC[1] = "2020-01-01" | ||
| DM$DTHFL[2] = "N" | ||
| DM$DTHDTC[2] = "2020-01-01" | ||
| DM$DTHFL[3] = "Y" | ||
| DM$DTHDTC[3] = "2020-01-01" | ||
| DM$DTHFL[4] = "Y" | ||
| DM$DTHDTC[4] = "" | ||
| DM$DTHFL[5] = "N" | ||
| DM$DTHDTC[5] = "" | ||
| DM$DTHFL[6] = "Y" | ||
| DM$DTHDTC[6] = "2020" | ||
| DM$DTHFL[7] = "" | ||
| DM$DTHDTC[7] = "" | ||
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| expect_false(check_dm_dthfl_dthdtc(DM)) | ||
| }) | ||
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| test_that("Returns false when expected column not present", { | ||
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| DM <- data.frame( | ||
| USUBJID = 1:7, | ||
| DTHFL = 1:7, | ||
| DTHDTC = 1:7 | ||
| ) | ||
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| DM$DTHFL[1] = "" | ||
| DM$DTHDTC[1] = "2020-01-01" | ||
| DM$DTHFL[2] = "N" | ||
| DM$DTHDTC[2] = "2020-01-01" | ||
| DM$DTHFL[3] = "Y" | ||
| DM$DTHDTC[3] = "2020-01-01" | ||
| DM$DTHFL[4] = "Y" | ||
| DM$DTHDTC[4] = "" | ||
| DM$DTHFL[5] = "N" | ||
| DM$DTHDTC[5] = "" | ||
| DM$DTHFL[6] = "Y" | ||
| DM$DTHDTC[6] = "2020" | ||
| DM$DTHFL[7] = "" | ||
| DM$DTHDTC[7] = "" | ||
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| DM$DTHDTC <- NULL | ||
| expect_false(check_dm_dthfl_dthdtc(DM[3,])) | ||
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| }) | ||
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|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,187 @@ | ||
| test_that("Returns true when no errors present", { | ||
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| USUBJID<- c(1:10) | ||
| DM=data.frame(USUBJID) | ||
| AE=data.frame(USUBJID) | ||
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| EX <- data.frame( | ||
| USUBJID = c(1:8, 6, 8, 10, 10, 10, 10), | ||
| EXOCCUR = rep("Y", times=14), | ||
| EXDOSE = rep(c(1,2), times=7), | ||
| EXSTDTC = c(rep("2012-01-01", 10),"2012-02-04","2012-02-04", "", "2012-02-07"), | ||
| EXTRT = "GDC", | ||
| stringsAsFactors=FALSE | ||
| ) | ||
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| DS <- data.frame( | ||
| USUBJID = c(2,8,8), | ||
| DSDECOD = rep("DEATH", times=3), | ||
| DSSTDTC = c("2012-12-01", NA, "2013-07-01"), | ||
| stringsAsFactors=FALSE | ||
| ) | ||
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| expect_true(check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)) | ||
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| }) | ||
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| test_that("Returns false when errors present - 1", { | ||
| USUBJID<- c(1:10) | ||
| DM=data.frame(USUBJID) | ||
| AE=data.frame(USUBJID) | ||
| AE$USUBJID[3]=NA | ||
| AE$USUBJID[8]=NA | ||
| AE$USUBJID[10]=NA | ||
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| EX <- data.frame( | ||
| USUBJID = c(1:8, 6, 8, 10, 10, 10, 10), | ||
| EXOCCUR = rep("Y", times=14), | ||
| EXDOSE = rep(c(1,2), times=7), | ||
| EXSTDTC = c(rep("2012-01-01", 10),"2012-02-04","2012-02-04", "", "2012-02-07"), | ||
| EXTRT = "GDC", | ||
| stringsAsFactors=FALSE | ||
| ) | ||
|
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| DS <- data.frame( | ||
| USUBJID = c(2,8,8), | ||
| DSDECOD = rep("DEATH", times=3), | ||
| DSSTDTC = c("2012-12-01", NA, "2013-07-01"), | ||
| stringsAsFactors=FALSE | ||
| ) | ||
|
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| expect_false(check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)) | ||
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| }) | ||
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| test_that("Returns false when errors present - 2", { | ||
| USUBJID<- c(1:10) | ||
| DM=data.frame(USUBJID) | ||
| AE=data.frame(USUBJID) | ||
| AE$USUBJID[3]=NA | ||
| AE$USUBJID[8]=NA | ||
| AE$USUBJID[10]=NA | ||
|
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| EX <- data.frame( | ||
| USUBJID = c(1:8, 6, 8, 10, 10, 10, 10), | ||
| EXOCCUR = rep("Y", times=14), | ||
| EXDOSE = rep(c(1,2), times=7), | ||
| EXSTDTC = c(rep("2012-01-01", 10),"2012-02-04","2012-02-04", "", "2012-02-07"), | ||
| EXTRT = "GDC", | ||
| stringsAsFactors=FALSE | ||
| ) | ||
|
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| DS <- data.frame( | ||
| USUBJID = c(2,8,8), | ||
| DSDECOD = rep("DEATH", times=3), | ||
| DSSTDTC = c("2012-12-01", NA, "2013-07-01"), | ||
| stringsAsFactors=FALSE | ||
| ) | ||
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| EX$EXOCCUR[3]="N" | ||
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| expect_false(check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)) | ||
| }) | ||
|
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| test_that("Returns false when expected column not present - 1", { | ||
| USUBJID<- c(1:10) | ||
| DM=data.frame(USUBJID) | ||
| AE=data.frame(USUBJID) | ||
|
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| EX <- data.frame( | ||
| USUBJID = c(1:8, 6, 8, 10, 10, 10, 10), | ||
| EXOCCUR = rep("Y", times=14), | ||
| EXDOSE = rep(c(1,2), times=7), | ||
| EXSTDTC = c(rep("2012-01-01", 10),"2012-02-04","2012-02-04", "", "2012-02-07"), | ||
| EXTRT = "GDC", | ||
| stringsAsFactors=FALSE | ||
| ) | ||
|
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| DS <- data.frame( | ||
| USUBJID = c(2,8,8), | ||
| DSDECOD = rep("DEATH", times=3), | ||
| DSSTDTC = c("2012-12-01", NA, "2013-07-01"), | ||
| stringsAsFactors=FALSE | ||
| ) | ||
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| EX$EXDOSE=NULL | ||
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| expect_false(check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)) | ||
| }) | ||
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| test_that("Returns false when expected column not present - 2", { | ||
| USUBJID<- c(1:10) | ||
| DM=data.frame(USUBJID) | ||
| AE=data.frame(USUBJID) | ||
|
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| EX <- data.frame( | ||
| USUBJID = c(1:8, 6, 8, 10, 10, 10, 10), | ||
| EXOCCUR = rep("Y", times=14), | ||
| EXDOSE = rep(c(1,2), times=7), | ||
| EXSTDTC = c(rep("2012-01-01", 10),"2012-02-04","2012-02-04", "", "2012-02-07"), | ||
| EXTRT = "GDC", | ||
| stringsAsFactors=FALSE | ||
| ) | ||
|
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| DS <- data.frame( | ||
| USUBJID = c(2,8,8), | ||
| DSDECOD = rep("DEATH", times=3), | ||
| DSSTDTC = c("2012-12-01", NA, "2013-07-01"), | ||
| stringsAsFactors=FALSE | ||
| ) | ||
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| DS$DSDECOD=NULL | ||
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| expect_false(check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)) | ||
| }) | ||
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| test_that("Returns false when expected column not present - 3", { | ||
| USUBJID<- c(1:10) | ||
| DM=data.frame(USUBJID) | ||
| AE=data.frame(USUBJID) | ||
|
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| EX <- data.frame( | ||
| USUBJID = c(1:8, 6, 8, 10, 10, 10, 10), | ||
| EXOCCUR = rep("Y", times=14), | ||
| EXDOSE = rep(c(1,2), times=7), | ||
| EXSTDTC = c(rep("2012-01-01", 10),"2012-02-04","2012-02-04", "", "2012-02-07"), | ||
| EXTRT = "GDC", | ||
| stringsAsFactors=FALSE | ||
| ) | ||
|
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| DS <- data.frame( | ||
| USUBJID = c(2,8,8), | ||
| DSDECOD = rep("DEATH", times=3), | ||
| DSSTDTC = c("2012-12-01", NA, "2013-07-01"), | ||
| stringsAsFactors=FALSE | ||
| ) | ||
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| AE$USUBJID=NULL | ||
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| expect_false(check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)) | ||
| }) | ||
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| test_that("Returns false when expected column not present - 4", { | ||
| USUBJID<- c(1:10) | ||
| DM=data.frame(USUBJID) | ||
| AE=data.frame(USUBJID) | ||
|
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| EX <- data.frame( | ||
| USUBJID = c(1:8, 6, 8, 10, 10, 10, 10), | ||
| EXOCCUR = rep("Y", times=14), | ||
| EXDOSE = rep(c(1,2), times=7), | ||
| EXSTDTC = c(rep("2012-01-01", 10),"2012-02-04","2012-02-04", "", "2012-02-07"), | ||
| EXTRT = "GDC", | ||
| stringsAsFactors=FALSE | ||
| ) | ||
|
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| DS <- data.frame( | ||
| USUBJID = c(2,8,8), | ||
| DSDECOD = rep("DEATH", times=3), | ||
| DSSTDTC = c("2012-12-01", NA, "2013-07-01"), | ||
| stringsAsFactors=FALSE | ||
| ) | ||
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| DM$USUBJID=NULL | ||
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| expect_false(check_dm_usubjid_ae_usubjid(DM, AE, DS, EX)) | ||
| }) | ||
|
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