removed SPLIT-PLOT A, C; working on X versions of St functions

NAMESPACE

@@ -44,7 +44,6 @@ export(SsPowerTable)
 export(SsSampleSizeKGivenJ)
 export(StSignificanceTesting)
 export(StSignificanceTestingCadVsRad)
-export(StSignificanceTestingCrossedModalities)
 export(Util2Intrinsic)
 export(Util2Physical)
 export(UtilAnalyticalAucsRSM)
@@ -53,6 +52,7 @@ export(UtilAucCBM)
 export(UtilAucPROPROC)
 export(UtilDBM2ORVarCom)
 export(UtilFigureOfMerit)
+export(UtilFigureOfMeritX)
 export(UtilLesDistr)
 export(UtilLesWghtsDS)
 export(UtilLesWghtsLD)
@@ -85,7 +85,6 @@ importFrom(numDeriv,hessian)
 importFrom(numDeriv,jacobian)
 importFrom(stats,approx)
 importFrom(stats,cor)
-importFrom(stats,cov)
 importFrom(stats,dbinom)
 importFrom(stats,dnorm)
 importFrom(stats,integrate)

NEWS.md

@@ -13,6 +13,7 @@ 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
+* 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 previous versions, i.e., versions < 2.1.3.
 
 
 ### Issue 90
@@ -26,7 +27,7 @@ title: "NEWS"
 * Added a sorting step to both worksheets: order by modality, then reader, then case and then rating.
 * Also ALWAYS use `TP_Rating` and `FP_Rating` in these sheets; do not use LL_Rating and/or NL_Rating as this will break the code.
 * Some `goodValues` had to be regenerated. 
-* TODO: Not sure about the split plot codes; these have never been used and I should consider removing them.
+* TODO: Not sure about the split plot codes; these have never been used and I should consider removing them. Done: 8/11/23
 
 
 ### Changes 05/19/2023

R/DfFroc2Roc.R

@@ -29,7 +29,6 @@
 #'
 #' @examples
 #' rocDataSet <- DfFroc2Roc(dataset05)
-#' rocSpDataSet <- DfFroc2Roc(datasetFROCSpC)
 #' 
 #' ## in the following example, because of the smaller number of cases, 
 #' ## it is easy to see the process at work:

R/DfReadDataFile.R

@@ -38,9 +38,7 @@
 #'    treatment and reader IDs (i.e., names). Otherwise, treatment 
 #'    and reader IDs in the original data file will be used.
 #' 
-#' @note WARNING: SPLIT-PLOT-A and SPLIT-PLOT-C have not been tested with real datasets. 
-#'    Contact the maintainer if you desire this funtionality.
-#'    The \code{"MRMC"} format is deprecated. For non-JAFROC formats four file 
+#' @note The \code{"MRMC"} format is deprecated. For non-JAFROC formats four file 
 #'    extensions (\code{.csv}, \code{.txt}, \code{.lrc} and \code{.imrmc}) are possible, 
 #'    all of which are restricted to ROC data. Only the \code{iMRMC} format is actively 
 #'    supported, i.e, files with extension \code{.imrmc}. Other formats (\code{.csv}, 
@@ -181,8 +179,8 @@ preCheck4BadEntries <- function(truthTable) {
 
 
 
-# SPLIT-PLOT-A: Reader nested within test; Hillis 2014 Table VII part (a)
-# SPLIT-PLOT-C: Case nested within reader; Hillis 2014 Table VII part (c)
+
+
 checkTruthTable <- function (truthTable, lrocForcedMark) 
 {
 
@@ -192,7 +190,7 @@ checkTruthTable <- function (truthTable, lrocForcedMark)
   design <- (toupper(truthTable[,6][which(!is.na(truthTable[,6]))]))[2]
   if (design == "CROSSED") design <- "FCTRL"
   if (!(type %in% c("FROC", "ROC", "LROC"))) stop("Unsupported data type: must be ROC, FROC or LROC.\n")
-  if (!(design %in% c("FCTRL", "SPLIT-PLOT-A", "SPLIT-PLOT-C"))) stop("Study design must be FCTRL, SPLIT-PLOT-A or SPLIT-PLOT-C\n")
+  if (!(design %in% c("FCTRL"))) stop("Study design must be FCTRL.\n")
 
   if (type == "LROC") {
     if (is.na(lrocForcedMark)) stop("For LROC dataset one must set the lrocForcedMark flag to a logical") 
@@ -227,64 +225,7 @@ checkTruthTable <- function (truthTable, lrocForcedMark)
   K2 <- length(abnormalCases)
   K <- (K1 + K2)
 
-  if (design == "SPLIT-PLOT-A") {
-
-   # for this design the length is twice what it needs to be
-    caseIDCol <- as.integer(truthTable$CaseID)[1:(L/2)]
-    # lesionIDCol <- as.integer(truthTable$LesionID)[1:(L/2)]
-    weightsCol <- truthTable$Weight[1:(L/2)]
-    # preserve the strings; DO NOT convert to integers
-    J <-  0 # find max number of readers, given that his data has 3 readers in one group and 4 in the other group
-    for (el in 1:length(readerIDCol)) {
-      if (length(strsplit(readerIDCol[el], split = ",")[[1]]) > J) J <- length(strsplit(readerIDCol[el], split = ",")[[1]])
-    }
-    rdrArr <- array(dim = c(L,J))
-    for (l in 1:L) {
-      val <- strsplit(readerIDCol[l], split = ",|\\s")[[1]]
-      val <- val[val != ""]
-      for (i in 1:length(val)) {
-        rdrArr[l,i] <- val[i]
-      }
-    }
-    # preserve the strings; DO NOT convert to integers
-    I <- length(strsplit(modalityIDCol[1], split = ",")[[1]])
-    trtArr <- array(dim = c(L,I))
-    for (l in 1:L) {
-      if (grep("^\\(.\\)", modalityIDCol[l]) == 1) { # match found to something like (1), i.e., one nested factor
-        val <- grep("^\\(.\\)", modalityIDCol[l], value = T)
-        val <- strsplit(val, split = "\\(|\\)")[[1]]
-        val <- val[val != ""]
-        for (i in 1:length(val)) {
-          trtArr[l] <- val[i]
-        }
-      } else stop("Was expecting nested notation, using () brackets ...")
-    }
-  } else if (design == "SPLIT-PLOT-C") {
-
-    # preserve the strings; DO NOT convert to integers
-    J <- length(strsplit(readerIDCol[1], split = ",")[[1]])
-    rdrArr <- array(dim = c(L,J))
-    for (l in 1:L) {
-      if (grep("^\\(.\\)", readerIDCol[l]) == 1) { # match found to something like (1), i.e., one nested factor
-        val <- grep("^\\(.\\)", readerIDCol[l], value = T)
-        val <- strsplit(val, split = "\\(|\\)")[[1]]
-        val <- val[val != ""]
-        for (i in 1:length(val)) {
-          rdrArr[l] <- val[i]
-        }
-      } else stop("Was expecting nested notation, using () brackets ...")
-      # preserve the strings; DO NOT convert to integers
-      I <- length(strsplit(modalityIDCol[1], split = ",")[[1]])
-      trtArr <- array(dim = c(L,I))
-      for (l in 1:L) {
-        val <- strsplit(modalityIDCol[l], split = ",|\\s")[[1]]
-        val <- val[val != ""]
-        for (i in 1:length(val)) {
-          trtArr[l,i] <- val[i]
-        }
-      }
-    }
-  } else if (design == "FCTRL") {
+  if (design == "FCTRL") {
     # preserve the strings; DO NOT convert to integers
     J <- length(strsplit(readerIDCol[1], split = ",")[[1]]) # bug non-character input error for HUGE dataset
     rdrArr <- array(dim = c(L,J))
@@ -307,13 +248,8 @@ checkTruthTable <- function (truthTable, lrocForcedMark)
     }
   } else stop("incorrect design value")
 
-  if (design == "SPLIT-PLOT-A") {
-    rdrArr1D <- t(unique(rdrArr)) # rdrArr is 2-dimensional; rdrArr1D is a one-dimensional array of all the readers in the study
-    rdrArr1D <- rdrArr1D[!is.na(rdrArr1D)] # this modification is needed for HYK dataset with 3 readers in one group and 4 in the other
-  } else {
     if (any(is.na(rdrArr))) stop("Illegal value in ReaderID column in Truth sheet")
     rdrArr1D <- as.vector(unique(rdrArr)) # rdrArr is 2-dimensional; rdrArr1D is a one-dimensional array of all the readers in the study
-  }
   if (any(is.na(trtArr))) stop("Illegal value in ModalityID column in Truth sheet")
   trtArr1D <- as.vector(unique(trtArr))
 
@@ -324,18 +260,7 @@ checkTruthTable <- function (truthTable, lrocForcedMark)
   for (l in 1:L) {
     k <- which(unique(truthTableSort$CaseID) == truthTable$CaseID[l])
     el <- lesionIDCol[l] + 1
-    if (design == "SPLIT-PLOT-A") {
-      i <- which(unique(trtArr) == trtArr[l])
-      for (j1 in 1:length(rdrArr[l,])) {
-        j <- which(rdrArr1D == rdrArr[l,j1])
-        truthTableStr[i, j, k, el] <- 1
-      }
-    }
-    else if (design == "SPLIT-PLOT-C") {
-      i <- which(unique(trtArr) == trtArr[l,])
-      j <- which(rdrArr1D == rdrArr[l])
-      truthTableStr[i, j, k, el] <- 1
-    } else if (design == "FCTRL") {
+    if (design == "FCTRL") {
       i <- which(unique(trtArr) == trtArr[l,])
       j <- which(rdrArr1D == rdrArr[l,])
       truthTableStr[i, j, k, el] <- 1

R/ORAnalysisFactorial.R

@@ -94,7 +94,6 @@ ORAnalysisFactorial <- function(dataset, FOM, FPFValue, alpha = 0.05, covEstMeth
 } 
 
 
-# 5/30/20 returning zeroes instead of NAs; simplifies handling of SPLIT-PLOT-C dataseets
 FOMijk2VarCov <- function(resampleFOMijk, varInflFactor) {
 
   I <- dim(resampleFOMijk)[1]
@@ -119,8 +118,6 @@ FOMijk2VarCov <- function(resampleFOMijk, varInflFactor) {
 
   Var <- 0
   count <- 0
-  I <- dim(covariances)[1]
-  J <- dim(covariances)[3]
   for (i in 1:I) {
     for (j in 1:J) {
       Var <- Var + covariances[i, i, j, j]
@@ -179,8 +176,7 @@ FOMijk2VarCov <- function(resampleFOMijk, varInflFactor) {
     Var = Var,
     Cov1 = Cov1,
     Cov2 = Cov2,
-    Cov3 = Cov3,
-    CovMatrix = covariances
+    Cov3 = Cov3
   ))
 
 }