Merge pull request #35 from Gilead-BioStats/PD_multmethods_dbs

lThreshold or dThreshold was not hooked up in AE_Assess. I hooked th…
Gilead-BioStats · Jan 19, 2022 · e6c8d99 · e6c8d99
2 parents 0eedbcb + c18946b
commit e6c8d99
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Showing 2 changed files with 22 additions and 9 deletions.
diff --git a/R/AE_Assess.R b/R/AE_Assess.R
@@ -1,7 +1,7 @@
 #' AE Assessment 
 #' 
 #' @param dfInput input data
-#' @param lThreshold list of threshold values 
+#' @param vThreshold list of threshold values default c(-5,5) for method = "poisson", c(.0001,NA) for method = Wilcoxon
 #' @param nCutoff optional parameter to control the auto-thresholding 
 #' @param cLabel Assessment label 
 #' @param method valid methods are "poisson" (the default), or  "wilcoxon" 
@@ -16,16 +16,18 @@
 #'
 #' @export
 
-AE_Assess <- function( dfInput, dThreshold=NULL, cLabel="", method="poisson", bDataList=FALSE){
+AE_Assess <- function( dfInput, vThreshold=NULL, cLabel="", method="poisson", bDataList=FALSE){
     lAssess <- list()
     lAssess$dfInput <- dfInput
     lAssess$dfTransformed <- gsm::Transform_EventCount( lAssess$dfInput )
     if(method == "poisson"){
+      if(is.null(vThreshold))vThreshold = c(-5,5)
         lAssess$dfAnalyzed <- gsm::Analyze_Poisson( lAssess$dfTransformed) 
-        lAssess$dfFlagged <- gsm::Flag( lAssess$dfAnalyzed , strColumn = 'Residuals', vThreshold =c(-5,5))
+        lAssess$dfFlagged <- gsm::Flag( lAssess$dfAnalyzed , strColumn = 'Residuals', vThreshold = vThreshold)
     } else if(method=="wilcoxon"){
+      if(is.null(vThreshold))vThreshold = c(0.0001,NA)
         lAssess$dfAnalyzed <- gsm::Analyze_Wilcoxon( lAssess$dfTransformed) 
-        lAssess$dfFlagged <- gsm::Flag( lAssess$dfAnalyzed ,  strColumn = 'PValue', vThreshold =c(0.0001,NA))
+        lAssess$dfFlagged <- gsm::Flag( lAssess$dfAnalyzed ,  strColumn = 'PValue', vThreshold = vThreshold)
     }
 
     lAssess$dfSummary <- gsm::Summarize( lAssess$dfFlagged, cAssessment="Safety", cLabel= cLabel)

diff --git a/R/PD_Assess.R b/R/PD_Assess.R
@@ -1,21 +1,32 @@
 #' Protocol Deviation Assessment using Poisson Regression
 #' 
-#' @param dfInput input data
-#' @param lThreshold list of threshold values 
+#' @param dfInput input data 
+#' @param vThreshold list of threshold values default c(-5,5) for method = "poisson", c(.0001,NA) for method = Wilcoxon
 #' @param nCutoff optional parameter to control the auto-thresholding 
 #' @param cLabel Assessment label 
+#' @param method valid methods are "poisson" (the default), or  "wilcoxon" 
 #' @param bDataList Should all assessment datasets be returned as a list? If False (the default), only the finding data frame is returned
 #'
 #' @return Finding data frame with columns for "SiteID", "N", "PValue", "Flag". 
 #' 
 #' @export
 
-PD_Assess <- function( dfInput, lThreshold=NULL, nCutoff=1, cLabel="", bDataList=FALSE){
+PD_Assess <- function( dfInput, vThreshold=NULL, nCutoff=1, cLabel="",method="poisson", bDataList=FALSE){
     lAssess <- list()
     lAssess$dfInput <- dfInput
     lAssess$dfTransformed <- gsm::Transform_EventCount( lAssess$dfInput )
-    lAssess$dfAnalyzed <- gsm::Analyze_Poisson( lAssess$dfTransformed) 
-    lAssess$dfFlagged <- gsm::Flag( lAssess$dfAnalyzed , strColumn = 'Residuals', vThreshold =c(-5,5)) 
+
+    if(method == "poisson"){
+      if(is.null(vThreshold))vThreshold = c(-5,5)
+      lAssess$dfAnalyzed <- gsm::Analyze_Poisson( lAssess$dfTransformed) 
+      lAssess$dfFlagged <- gsm::Flag( lAssess$dfAnalyzed , strColumn = 'Residuals', vThreshold =vThreshold)
+    } else if(method=="wilcoxon"){
+      if(is.null(vThreshold))vThreshold = c(0.0001,NA)
+      lAssess$dfAnalyzed <- gsm::Analyze_Wilcoxon( lAssess$dfTransformed) 
+      lAssess$dfFlagged <- gsm::Flag( lAssess$dfAnalyzed ,  strColumn = 'PValue', vThreshold =vThreshold)
+    }
+
+
     lAssess$dfSummary <- gsm::Summarize( lAssess$dfFlagged, cAssessment="Safety", cLabel= cLabel)
 
     if(bDataList){