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lThreshold or dThreshold was not hooked up in AE_Assess. I hooked th… #35

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Jan 19, 2022
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lThreshold or dThreshold was not hooked up in AE_Assess. I hooked th… #35

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10 changes: 6 additions & 4 deletions R/AE_Assess.R
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Original file line number Diff line number Diff line change
@@ -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"
Expand All @@ -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)
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21 changes: 16 additions & 5 deletions R/PD_Assess.R
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Original file line number Diff line number Diff line change
@@ -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){
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