changed datasetXModality to datasetX

NEWS.md

@@ -9,21 +9,21 @@ title: "NEWS"
 
 
 ### Commented some code 10/31/23
-* bootstrap and DeLong in `StORAnalysis`
+* bootstrap and DeLong in `StORAnalysis` disabled for XMod analysis
 
 
 
 ### Do global search for questionable code
 * marked as follows
-* ???DPC???
+* ???DPC??? or !!!DPC!!!
 * Renamed `StSignificanceTestingCadVsRad` to `StCadVsRad`
+* Renamed `UtilVarComponentOR` to `UtilOrVarCov`
+* Renamed `UtilVarComponentsDBM` to `UtilDBMVarComp`
 
 
 ### TODOs 10/4/23
 * Insert tests for all failure branches in `isValidDataset`
-* Renamed `UtilVarComponentOR` to `UtilOrVarCov`
-* Renamed `UtilVarComponentsDBM` to `UtilDBMVarComp`
-* Shorten this log and keep details in a new file, `CodeChangesLog.md`, but this has to be outside this package directory
+* TODO: Shorten this log and keep details in a new file, `CodeChangesLog.md`, but this has to be outside the package directory
 
 
 
@@ -32,6 +32,7 @@ title: "NEWS"
 * Bug fix, Issue 89, see below
 * Fixed entry errors in Excel file (check column names and data type)
 * TODO: `QuickStart`, new chapter on recommended FOMs and those to avoid at all costs
+* TODO: `QuickStart`, explanation of St output
 * Removed SPLIT-PLOT-A and  SPLIT-PLOT-C analyses: no one is using it and I have no dataset or statistician involvement to validate the implementation. It is still available on versions < 2.1.3.
 
 

R/St.R

@@ -68,7 +68,7 @@
 #' @examples
 #' result <- St(dataset02,FOM = "Wilcoxon", method = "DBM") 
 #' result <- St(dataset02,FOM = "Wilcoxon", method = "OR")
-#' result <- St(datasetXModality, FOM = "wAFROC", method = "OR", analysisOption = "ALL")
+#' result <- St(datasetX, FOM = "wAFROC", method = "OR", analysisOption = "ALL")
 #' 
 #' \donttest{
 #' result <- St(dataset05, FOM = "wAFROC")

R/StORAnalysis.R

@@ -153,7 +153,6 @@ StORAnalysis <- function(dataset,
     ANOVA$IndividualTrt <- IndividualTrt
     ANOVA$IndividualRdr <- IndividualRdr
 
-
     trtMeanDiffs <- list()
     trtMeans <- list()
     diffTRName <- list()
@@ -195,7 +194,7 @@ StORAnalysis <- function(dataset,
     if (analysisOption == "RRRC") {
       RRRC <- OR_RRRC(FOMStats, ANOVA, alpha)
       return(list(
-        FOMs = FOMStats[-4],
+        FOMs = FOMStats[-4], # do not show diffTreatmentName
         ANOVA = ANOVA,
         RRRC = RRRC
       ))

R/UtilFigureOfMerit.R

@@ -65,7 +65,7 @@
 #' 
 #' res <- UtilFigureOfMerit(dataset02, FOM = "Wilcoxon") # ROC data
 #' res <- UtilFigureOfMerit(dataset01) # FROC dataset, default wAFROC FOM
-#' res <- UtilFigureOfMerit(datasetXModality, FOM = "wAFROC")
+#' res <- UtilFigureOfMerit(datasetX, FOM = "wAFROC")
 #' 
 #' 
 #'