Fix 201 qc ae map raw

R/AE_Assess.R

@@ -13,6 +13,7 @@
 #' - `SiteID` - Site ID
 #' - `Count` - Number of Adverse Events
 #' - `Exposure` - Number of days of exposure
+#' - `Rate` - Rate of Exposure (Count / Exposure)
 #'
 #' The Assessment
 #' - \code{\link{Transform_EventCount}} creates `dfTransformed`.
@@ -47,7 +48,8 @@ AE_Assess <- function( dfInput, vThreshold=NULL, cLabel="", cMethod="poisson",bD
         "cLabel is not character" = is.character(cLabel),
         "cMethod is not 'poisson' or 'wilcoxon'" = cMethod %in% c("poisson","wilcoxon"),
         "bDataList is not logical" = is.logical(bDataList),
-        "One or more of these columns: SubjectID, SiteID, Count, Exposure, and Rate not found in dfInput"=all(c("SubjectID","SiteID", "Count","Exposure", "Rate") %in% names(dfInput))
+        "One or more of these columns: SubjectID, SiteID, Count, Exposure, and Rate not found in dfInput"=all(c("SubjectID","SiteID", "Count","Exposure", "Rate") %in% names(dfInput)),
+        "cMethod must be length 1" = length(cMethod) == 1
     )
     lAssess <- list()
     lAssess$dfInput <- dfInput

R/AE_Map_Raw.R

@@ -20,8 +20,8 @@
 #'
 #' Note that the function can generate data summaries for specific types of AEs, but passing filtered ADAE data to dfADAE.
 #'
-#' @param dfAE AE dataset with columns SUBJID and rows for each AE record
-#' @param dfRDSL Subject-level Raw Data (RDSL) required columns: SubjectID, SiteID, value specified in strExposureCol
+#' @param dfAE AE dataset with required column SUBJID and rows for each AE record
+#' @param dfRDSL Subject-level Raw Data (RDSL) with required columns: SubjectID, SiteID, value specified in strExposureCol
 #' @param strExposureCol Name of exposure column. 'TimeOnTreatment' by default
 #'
 #' @return Data frame with one record per person data frame with columns: SubjectID, SiteID, Count (number of AEs), Exposure (Time on Treatment in Days), Rate (AE/Day)
@@ -40,7 +40,8 @@ AE_Map_Raw <- function( dfAE, dfRDSL, strExposureCol="TimeOnTreatment"){
         "SUBJID column not found in dfAE"="SUBJID" %in% names(dfAE),
         "strExposureCol is not character"=is.character(strExposureCol),
         "SubjectID, SiteID and strExposureCol columns not found in dfRDSL"=all(c("SubjectID","SiteID",strExposureCol) %in% names(dfRDSL)),
-        "NAs found in Subject ID column of dfAE" = all(!is.na(dfAE$SUBJID))
+        "NAs found in SUBJID column of dfAE" = all(!is.na(dfAE$SUBJID)),
+        "NAs found in Subject ID column of dfRDSL" = all(!is.na(dfRDSL$SubjectID))
     )
 
     dfInput <-  dfRDSL %>%

tests/testthat/test_AE_Assess.R

@@ -22,19 +22,17 @@ test_that("incorrect inputs throw errors",{
     expect_error(AE_Assess(ae_input, cLabel=123))
     expect_error(AE_Assess(ae_input, cMethod="abacus"))
     expect_error(AE_Assess(ae_input, bDataList="Yes"))
+    expect_error(AE_Assess(ae_input %>% select(-SubjectID)))
+    expect_error(AE_Assess(ae_input %>% select(-SiteID)))
+    expect_error(AE_Assess(ae_input %>% select(-Count)))
+    expect_error(AE_Assess(ae_input %>% select(-Exposure)))
+    expect_error(AE_Assess(ae_input %>% select(-Rate)))
+    expect_error(AE_Assess(ae_input, cMethod=c("wilcoxon", "poisson")))
 })
 
 
-test_that("incorrect inputs throw errors",{
-  expect_error(AE_Assess(ae_input %>% select(-SubjectID)))
-  expect_error(AE_Assess(ae_input %>% select(-SiteID)))
-  expect_error(AE_Assess(ae_input %>% select(-Count)))
-  expect_error(AE_Assess(ae_input %>% select(-Exposure)))
-  expect_error(AE_Assess(ae_input %>% select(-Rate)))
-})
-
-ae_list <- AE_Assess(ae_input, bDataList=TRUE)
-expect_true(is.list(ae_list))
-expect_equal(names(ae_list),c('dfInput','dfTransformed','dfAnalyzed','dfFlagged','dfSummary'))
-
-
+test_that("Summary created when bDataList = FALSE has correct structure",{
+  ae_summary <- AE_Assess(ae_input, bDataList=FALSE)
+  expect_equal(length(unique(ae_summary$SiteID)) , length(ae_summary$SiteID))
+  expect_equal(names(ae_summary),c( "Assessment", "Label"   ,  "SiteID"  ,   "N"      ,    "PValue"  ,   "Flag"))
+})

tests/testthat/test_AE_Map_Raw.R

@@ -13,6 +13,10 @@ test_that("incorrect inputs throw errors",{
   expect_error(AE_Map_Raw("Hi","Mom"))
 })
 
+test_that("invalid strExposureCol throws error",{
+  expect_error( AE_Map_Raw(dfAE = clindata::raw_ae, dfRDSL = clindata::rawplus_rdsl, strExposureCol= "Bad_Name" ))
+})
+
 
 test_that("error given if required column not found",{
   expect_error(
@@ -119,7 +123,7 @@ test_that("NA values in input data are handled",{
 
   dfExposure3<-tibble::tribble(
     ~SubjectID, ~SiteID, ~TimeOnTreatment,
-    NA,   1, 10,
+    1,   1, 10,
     2,   1, NA,
     3,   NA, 30,
     4,   2, 50
@@ -128,30 +132,41 @@ test_that("NA values in input data are handled",{
 
   dfInput3 <-tibble::tribble(
     ~SubjectID, ~SiteID, ~Count, ~Exposure,~Rate,
-    NA,   1, 0, 10, 0,
+    1,   1, 4, 10, 0.4,
     2,    1,  2, NA, NA,
     3,   NA,  0, 30, 0 ,
     4,    2,  2, 50, .04
   )
 
   expect_equal(dfInput3, AE_Map_Raw(dfAE = dfAE3, dfRDSL = dfExposure3))
 
-
-
-
-
 
 })
 
 
-test_that("dfAE Subject NA value throws error",{
+test_that("dfAE$SUBJID NA value throws error",{
   dfAE4 <- tibble::tribble(~SUBJID, 1,NA,1,1,2,2,4,4)
 
+  dfExposure4<-tibble::tribble(
+    ~SubjectID, ~SiteID, ~TimeOnTreatment,
+    1,   1, 10,
+    2,   1, 20,
+    3,   3, 30,
+    4,   2, 50
+  )
+
+
+  expect_error(AE_Map_Raw(dfAE = dfAE4, dfRDSL = dfExposure4))
+})
+
+test_that("dfRDSL$SubjectID NA value throws error",{
+  dfAE4 <- tibble::tribble(~SUBJID, 1,1,1,1,2,2,4,4)
+
   dfExposure4<-tibble::tribble(
     ~SubjectID, ~SiteID, ~TimeOnTreatment,
     NA,   1, 10,
-    2,   1, NA,
-    3,   NA, 30,
+    2,   1, 20,
+    3,   2, 30,
     4,   2, 50
   )
 

tests/testthat/test_IE_Map_Raw.R

@@ -31,7 +31,6 @@ test_that("error given if required column not found",{
       clindata::rawplus_rdsl
     )
   )
-  #"INVID", "IECAT", "IETESTCD","IETEST", "IEORRES"
   expect_error(
     IE_Map_Raw(
       clindata::raw_ie_a2 ,