gsm v2.2.1 release candidate

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gsm
 Title: Good Statistical Monitoring
-Version: 2.2.0.9999
+Version: 2.2.1
 Authors@R: c(
     person("George", "Wu", , "george.wu@gilead.com", role = c("aut", "cre")),
     person("Jeremy", "Wildfire", , "jwildfire@gmail.com", role = "aut"),

NEWS.md

@@ -1,3 +1,14 @@
+# gsm v2.2.1
+
+This patch release primarily addresses minor report updates bug fixes. Specifically:
+
+- Reduce size of flags over time table by only displaying the most recent 12 periods
+- Return an object of class `function` from `GetStrFunctionIfNamespaced()`
+- Generalize all `Flag_*()` functions to a single `Flag()` function
+- Use `log4r` framework set up in v2.2.0 for `stopif()`/`stopifnot()` calls
+- Add Subject Disposition field to Study Completion domain
+
+
 # gsm v2.2.0
 
 This minor release prepares the gsm to be used as part of a more sophisticated pipeline, through the addition of 

R/Analyze_NormalApprox.R

@@ -36,8 +36,7 @@ Analyze_NormalApprox <- function(
   dfTransformed,
   strType = "binary"
 ) {
-
-  stop_if(cnd = !is.data.frame(dfTransformed), message ="dfTransformed is not a data.frame")
+  stop_if(cnd = !is.data.frame(dfTransformed), message = "dfTransformed is not a data.frame")
   stop_if(
     cnd = !all(c("GroupID", "GroupLevel", "Denominator", "Numerator", "Metric") %in% names(dfTransformed)),
     message = "One or more of these columns not found: GroupID, GroupLevel, Denominator, Numerator, Metric"

R/Flag.R

@@ -46,11 +46,10 @@
 Flag <- function(
   dfAnalyzed,
   strColumn = "Score",
-  vThreshold = c(-3,-2,2,3),
-  vFlag = c(-2,-1,0,1,2),
-  vFlagOrder = c(2,-2,1,-1,0)
+  vThreshold = c(-3, -2, 2, 3),
+  vFlag = c(-2, -1, 0, 1, 2),
+  vFlagOrder = c(2, -2, 1, -1, 0)
 ) {
-
   stop_if(cnd = !is.data.frame(dfAnalyzed), message = "dfAnalyzed is not a data frame")
   stop_if(cnd = !is.character(strColumn), message = "strColumn is not character")
   stop_if(cnd = !is.numeric(vThreshold), message = "vThreshold is not numeric")
@@ -59,23 +58,25 @@ Flag <- function(
   stop_if(cnd = length(strColumn) != 1, message = "strColumn must be length of 1")
   stop_if(cnd = !(strColumn %in% names(dfAnalyzed)), message = "strColumn not found in dfAnalyzed")
   stop_if(cnd = !is.numeric(vFlag), message = "vFlag must be numeric")
-  stop_if(cnd = length(vFlag) != length(vThreshold)+1, message = "Improper number of Flag values provided")
+  stop_if(cnd = length(vFlag) != length(vThreshold) + 1, message = "Improper number of Flag values provided")
   stop_if(cnd = !is.numeric(vFlagOrder) & !is.null(vFlagOrder), message = "vFlagOrder must be numeric or NULL")
 
   dfFlagged <- dfAnalyzed
 
   # generate flag values for dfAnalyzed[strColumn] based on vThresold and vFlag
   dfFlagged$Flag <- cut(
-      dfFlagged[[strColumn]],
-      breaks = c(-Inf, vThreshold, Inf),
-      labels = vFlag,
-      right = FALSE
-  ) %>% as.character() %>% as.numeric() #Parse from factor to numeric
+    dfFlagged[[strColumn]],
+    breaks = c(-Inf, vThreshold, Inf),
+    labels = vFlag,
+    right = FALSE
+  ) %>%
+    as.character() %>%
+    as.numeric() # Parse from factor to numeric
 
   # Apply custom sort order using vFlagOrder
-  if(!is.null(vFlagOrder)){
-    #all values in vFlag should be included in vFlagOrder
-    if(identical(sort(vFlag), sort(vFlagOrder))){
+  if (!is.null(vFlagOrder)) {
+    # all values in vFlag should be included in vFlagOrder
+    if (identical(sort(vFlag), sort(vFlagOrder))) {
       dfFlagged <- dfFlagged %>% arrange(match(.data$Flag, vFlagOrder))
       LogMessage(
         level = "info",
@@ -87,7 +88,7 @@ Flag <- function(
         level = "info",
         message = "Mismatch in vFlagOrder and vFlag values. Aborting Sort and returning unsorted data.",
         cli_detail = "alert_info"
-    )
+      )
     }
   }
 

R/Report_FormatFlag.R

@@ -27,4 +27,3 @@ Report_FormatFlag <- function(flag_value, title = NULL) {
 fa_titled <- function(name, fill, title) {
   fontawesome::fa(name, fill = fill, title = title)
 }
-

R/Summarize.R

@@ -24,7 +24,7 @@
 #' when associated with a workflow.
 #'
 #' @examples
-#' 
+#'
 #' dfTransformed <- Transform_Rate(analyticsInput)
 #' dfAnalyzed <- Analyze_NormalApprox(dfTransformed)
 #' dfFlagged <- Flag(dfAnalyzed)
@@ -37,8 +37,10 @@ Summarize <- function(
   nMinDenominator = NULL
 ) {
   stop_if(cnd = !is.data.frame(dfFlagged), message = "dfFlagged is not a data frame")
-  stop_if(cnd = !all(c("GroupID", "GroupLevel", "Flag", "Score") %in% names(dfFlagged)),
-          message = "One or more of these columns: GroupID, GroupLevel, Flag, Score, not found in dfFlagged" )
+  stop_if(
+    cnd = !all(c("GroupID", "GroupLevel", "Flag", "Score") %in% names(dfFlagged)),
+    message = "One or more of these columns: GroupID, GroupLevel, Flag, Score, not found in dfFlagged"
+  )
 
   if (!("Numerator" %in% colnames(dfFlagged))) {
     dfFlagged$Numerator <- NA

R/Visualize_Score.R

@@ -39,11 +39,11 @@ Visualize_Score <- function(
   bFlagFilter = FALSE,
   strTitle = ""
 ) {
-  stop_if(cnd = !is.character(strTitle), message = "strTitle must be character" )
+  stop_if(cnd = !is.character(strTitle), message = "strTitle must be character")
   stop_if(cnd = !is.logical(bFlagFilter), message = "bFlagFilter must be logical")
   stop_if(cnd = !is.data.frame(dfResults), message = "dfResults must be a data.frame")
-  stop_if(cnd = !(length(strType) == 1), message = "strType must be length 1" )
-  stop_if(cnd = !(strType %in% c("Metric", "Score")), message = "strType must be 'Metric' or 'Score'" )
+  stop_if(cnd = !(length(strType) == 1), message = "strType must be length 1")
+  stop_if(cnd = !(strType %in% c("Metric", "Score")), message = "strType must be 'Metric' or 'Score'")
 
   dfResults$FlagAbs <- abs(dfResults$Flag)
   flagBreaks <- as.character(unique(sort(dfResults$FlagAbs)))

R/Widget_FlagOverTime.R

@@ -48,7 +48,7 @@ Widget_FlagOverTime <- function(
   bDebug = FALSE
 ) {
   stop_if(cnd = !is.data.frame(dfResults), message = "dfResults is not a data.frame")
-  stop_if(cnd = !is.data.frame(dfMetrics),"dfMetrics is not a data.frame")
+  stop_if(cnd = !is.data.frame(dfMetrics), "dfMetrics is not a data.frame")
   stop_if(cnd = !is.character(strGroupLevel), "strGroupLevel is not a character")
   stop_if(cnd = !is.character(strFootnote) && !is.null(strFootnote), "strFootnote is not a character or NULL")
   stop_if(cnd = !is.logical(bDebug), "bDebug is not a logical")

R/Widget_GroupOverview.R

@@ -51,10 +51,10 @@ Widget_GroupOverview <- function(
   strGroupLabelKey = "InvestigatorLastName",
   bDebug = FALSE
 ) {
-  stop_if(cnd = !is.data.frame(dfResults),"dfResults is not a data.frame")
-  stop_if(cnd = !is.data.frame(dfMetrics),"dfMetrics is not a data.frame")
-  stop_if(cnd = !is.data.frame(dfGroups),"dfGroups is not a data.frame")
-  stop_if(cnd = !is.character(strGroupSubset),"strGroupSubset is not a character")
+  stop_if(cnd = !is.data.frame(dfResults), "dfResults is not a data.frame")
+  stop_if(cnd = !is.data.frame(dfMetrics), "dfMetrics is not a data.frame")
+  stop_if(cnd = !is.data.frame(dfGroups), "dfGroups is not a data.frame")
+  stop_if(cnd = !is.character(strGroupSubset), "strGroupSubset is not a character")
   stop_if(cnd = !is.character(strGroupLabelKey) && !is.null(strGroupLabelKey), "strGroupLabelKey is not a character or NULL")
   stop_if(cnd = !is.logical(bDebug), "bDebug is not a logical")
 

R/Widget_ScatterPlot.R

@@ -40,12 +40,12 @@ Widget_ScatterPlot <- function(
   strShinyGroupSelectID = "GroupID",
   bDebug = FALSE
 ) {
-  stop_if(cnd = !is.data.frame(dfResults),"dfResults is not a data.frame")
+  stop_if(cnd = !is.data.frame(dfResults), "dfResults is not a data.frame")
   stop_if(cnd = !(is.null(lMetric) || (is.list(lMetric) && !is.data.frame(lMetric))), "lMetric must be a list, but not a data.frame")
-  stop_if(cnd = !(is.null(dfGroups) || is.data.frame(dfGroups)),"dfGroups is not a data.frame")
-  stop_if(cnd = !(is.null(dfBounds) || is.data.frame(dfBounds)),"dfBounds is not a data.frame")
-  stop_if(cnd = !is.logical(bAddGroupSelect),"bAddGroupSelect is not a logical")
-  stop_if(cnd = !is.character(strShinyGroupSelectID),"strShinyGroupSelectID is not a character")
+  stop_if(cnd = !(is.null(dfGroups) || is.data.frame(dfGroups)), "dfGroups is not a data.frame")
+  stop_if(cnd = !(is.null(dfBounds) || is.data.frame(dfBounds)), "dfBounds is not a data.frame")
+  stop_if(cnd = !is.logical(bAddGroupSelect), "bAddGroupSelect is not a logical")
+  stop_if(cnd = !is.character(strShinyGroupSelectID), "strShinyGroupSelectID is not a character")
   stop_if(cnd = !is.logical(bDebug), "bDebug is not a logical")
 
   # define widget inputs

R/Widget_TimeSeries.R

@@ -40,15 +40,14 @@ Widget_TimeSeries <- function(
   strShinyGroupSelectID = "GroupID",
   bDebug = FALSE
 ) {
-
-  stop_if(cnd = !is.data.frame(dfResults),"dfResults is not a data.frame")
+  stop_if(cnd = !is.data.frame(dfResults), "dfResults is not a data.frame")
   stop_if(cnd = !(is.null(lMetric) || (is.list(lMetric) && !is.data.frame(lMetric))), "lMetric must be a list, but not a data.frame")
-  stop_if(cnd = !(is.null(dfGroups) || is.data.frame(dfGroups)),"dfGroups is not a data.frame")
-  stop_if(cnd = length(strOutcome) != 1,"strOutcome must be length 1")
-  stop_if(cnd = !is.character(strOutcome),"strOutcome is not a character")
-  stop_if(cnd = !is.logical(bAddGroupSelect),"bAddGroupSelect is not a logical")
-  stop_if(cnd = !is.character(strShinyGroupSelectID),"strShinyGroupSelectID is not a character")
-  stop_if(cnd = !is.logical(bDebug), "bDebug is not a logical" )
+  stop_if(cnd = !(is.null(dfGroups) || is.data.frame(dfGroups)), "dfGroups is not a data.frame")
+  stop_if(cnd = length(strOutcome) != 1, "strOutcome must be length 1")
+  stop_if(cnd = !is.character(strOutcome), "strOutcome is not a character")
+  stop_if(cnd = !is.logical(bAddGroupSelect), "bAddGroupSelect is not a logical")
+  stop_if(cnd = !is.character(strShinyGroupSelectID), "strShinyGroupSelectID is not a character")
+  stop_if(cnd = !is.logical(bDebug), "bDebug is not a logical")
 
   # Parse `vThreshold` from comma-delimited character string to numeric vector.
   if (!is.null(vThreshold)) {

R/util-CalculatePercentage.R

@@ -3,7 +3,7 @@
 #' @description
 #'
 #' Used to create percentage values on enrollment data, such as site activation and
-#' and participantment enrollment, and pasting together an appropriate n/N (xx.x%) value
+#' and participant enrollment, and pasting together an appropriate n/N (xx.x%) value
 #' as well.
 #'
 #' @param data The input dataframe

R/util-Ingest.R

@@ -35,7 +35,7 @@
 #' @export
 
 Ingest <- function(lSourceData, lSpec, strDomain = "Raw") {
-  stop_if(!is.list(lSourceData),"[ lSourceData ] must be a list.")
+  stop_if(!is.list(lSourceData), "[ lSourceData ] must be a list.")
   stop_if(!is.list(lSpec), "[ lSpec ] must be a list.")
 
   # If there is a domain (specificed with and underscore) in lSourceData/lSpec names, remove it

R/util-MakeBounds.R

@@ -66,7 +66,7 @@ MakeBounds <- function(
       vThreshold <- ParseThreshold(strThreshold = lMetric$Threshold)
       if (!is.null(lMetric$AnalysisType) &&
         tolower(unique(lMetric$AnalysisType)) %in% c("identity")) {
-        dfBounds <- NULL 
+        dfBounds <- NULL
       } else if (!is.null(lMetric$AnalysisType) &&
         tolower(unique(lMetric$AnalysisType)) %in% c("poisson")) {
         dfBounds <- Analyze_Poisson_PredictBounds(

R/util-MakeWorkflowList.R

@@ -33,7 +33,7 @@ MakeWorkflowList <- function(
   if (length(strPackage)) {
     path <- system.file(strPath, package = strPackage)
   }
-  stop_if(!dir.exists(path), "[ strPath ] must exist." )
+  stop_if(!dir.exists(path), "[ strPath ] must exist.")
   path <- tools::file_path_as_absolute(path)
 
   # list all files to loop through to build the workflow list.

R/util-Report.R

@@ -64,33 +64,33 @@ FilterByLatestSnapshotDate <- function(df, strSnapshotDate = NULL) {
 #' @export
 
 FilterByFlags <- function(
-    dfResults,
-    bCurrentlyFlagged = FALSE
+  dfResults,
+  bCurrentlyFlagged = FALSE
 ) {
   dfResultsFlagged <- dfResults %>%
     group_by(.data$GroupID, .data$MetricID) %>%
     mutate(
-        flagsum = sum(abs(.data$Flag), na.rm = TRUE),
-        flaglatest = Flag[SnapshotDate == max(SnapshotDate)]
+      flagsum = sum(abs(.data$Flag), na.rm = TRUE),
+      flaglatest = Flag[SnapshotDate == max(SnapshotDate)]
     ) %>%
     ungroup() %>%
     filter(
       .data$flagsum > 0
     )
 
-    if (bCurrentlyFlagged) {
-      dfResultsFlagged <- dfResultsFlagged %>%
-        filter(
-            .data$flaglatest != 0
-        )
-    }
-
+  if (bCurrentlyFlagged) {
     dfResultsFlagged <- dfResultsFlagged %>%
-        select(-all_of(c(
-            'flagsum', 'flaglatest'
-        )))
+      filter(
+        .data$flaglatest != 0
+      )
+  }
+
+  dfResultsFlagged <- dfResultsFlagged %>%
+    select(-all_of(c(
+      "flagsum", "flaglatest"
+    )))
 
-    return(dfResultsFlagged)
+  return(dfResultsFlagged)
 }
 
 add_Groups_metadata <- function(