edits to NEWS and DfReadDataFile.R

NEWS.md

@@ -2,24 +2,22 @@
 title: "NEWS"
 ---
 
-## version 2.1.3 (to be posted to CRAN)
+## version 2.1.3
 
 ---
 
 
-### CRAN submission v2.1.3 - postponed until resolved issues
+### CRAN submission v2.1.3 - postponed until Jan 01, 2024
 * Bug fix, Issue 90
 * Bug fix, Issue 89
 * Fixed user data-entry errors in Excel file (check column names and data type)
-* 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.
 * bootstrap and DeLong in `StORAnalysis` disabled for XMod analysis
 * Renamed `StSignificanceTesting` to `St`
 * Renamed `StSignificanceTestingCadVsRad` to `StCadVsRad`
 * Renamed `UtilVarComponentOR` to `UtilOrVarCov`
 * Renamed `UtilVarComponentsDBM` to `UtilDBMVarComp`
-* 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.
 * Removed `UtilOutputReport.R` as `St` output has been updated so this function is no longer needed.
-* Added SPLIT-PLOT analysis back; one function `StSP` Dec 1,23
+* All SPLIT-PLOT analyses is now in one function: `StSP`, implemented Dec 1, 2023
 
 ### Changes 05/19/2023
 * Fixed FROC simulator, easier to read code; both simulators are NOT limited to I = 2.

R/DfReadDataFile.R

@@ -1,20 +1,21 @@
-#' Read a factorial data file (not split-plot) 
+#' Read a factorial data file (not SPLIT-PLOT) 
 #' 
-#' @description Read a disk file and create an ROC, FROC or LROC dataset object 
-#'    from it.
+#' @description Read an Excel file and create an ROC, FROC or LROC dataset 
+#'    object from it.
 #' 
 #' @param fileName A string specifying the name of the file. The file-extension 
-#'    must match the format specified below.
+#'    must match the \code{format} specified below.
 #'    
 #' @param format A string specifying the format of the data file. 
-#'    It can be \code{"JAFROC"}, the default, which requires a \code{.xlsx} Excel file
-#'    (\bold{not \code{.xls}}), \code{"MRMC"} or \code{"iMRMC"}. 
+#'    It can be \code{"JAFROC"}, the default, which requires an \code{.xlsx} 
+#'    Excel file (\bold{not \code{.xls}}), \code{"MRMC"} or \code{"iMRMC"}. 
 #'    For \code{"MRMC"} the format is determined by the data file extension 
 #'    (\code{.csv} or \code{.txt} or \code{.lrc}) 
-#'    as specified in \url{https://perception.lab.uiowa.edu/}. For \code{"iMRMC"} the 
-#'    file extension is \code{.imrmc} and the format is described in 
-#'    \url{https://code.google.com/archive/p/imrmc/}. \bold{See following note for
-#'    important information about deprecation of the \code{"MRMC"} format}.
+#'    as specified in \url{https://perception.lab.uiowa.edu/}. For 
+#'    \code{"iMRMC"} the file extension is \code{.imrmc} and the format is 
+#'    described in \url{https://code.google.com/archive/p/imrmc/}. 
+#'    \bold{See note for important information about deprecation of the 
+#'    \code{"MRMC"} format}.
 #'    
 #'    
 #' @param newExcelFileFormat Logical. Must be true to read LROC data. 
@@ -38,13 +39,14 @@
 #'    modality and reader IDs (i.e., names). Otherwise, modality 
 #'    and reader IDs in the original data file will be used.
 #' 
-#' @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}, 
-#'    \code{.txt}, \code{.lrc}) are deprecated. Such files can still be read by this 
-#'    function and then saved to a JAFROC format file for further analysis within this 
-#'    package. \bold{For non-JAFROC data file formats, the \code{readerID} and 
+#' @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 \code{iMRMC} 
+#'    format is now supported, i.e, files with extension \code{.imrmc}. Other 
+#'    formats (\code{.csv}, \code{.txt}, \code{.lrc}) are deprecated. Such 
+#'    files can still be read by this function and then saved to a JAFROC 
+#'    format file for further analysis within this package. 
+#'    \bold{For non-JAFROC data file formats, the \code{readerID} and 
 #'    \code{modalityID} fields must be unique integers}.
 #' 
 #' @return A dataset with the structure specified in \code{\link{RJafroc-package}}.
@@ -92,7 +94,8 @@ DfReadDataFile <- function (fileName, format = "JAFROC",
     if (!(file_ext(fileName) == "xlsx")) 
       stop("The extension of JAFROC data file must be .xlsx, NOT .xls.\n")
     if (!newExcelFileFormat) { 
-      if (!is.na(lrocForcedMark)) stop("Attempt to read possibly LROC dataset with newExcelFileFormat flag set to FALSE") 
+      if (!is.na(lrocForcedMark)) stop("Attempt to read possibly LROC dataset 
+                                       with newExcelFileFormat flag set to FALSE") 
       return((ReadJAFROCOldFormat(fileName, sequentialNames)))
     } else {
       return(ReadJAFROCNewFormat(fileName, lrocForcedMark, sequentialNames))

inst/UpdateHistory.md

@@ -1,5 +1,5 @@
 ---
-title: "Update History, TODOs and Ideas"
+title: "Update History, TODO's and Ideas"
 ---
 
 ## version 2.1.3
@@ -13,9 +13,10 @@ title: "Update History, TODOs and Ideas"
 * ???DPC??? or !!!DPC!!!
 
 
-### Research Idea(s)
-* `inst/InferredVsReal.R` cross modality analysis
-* Extended Obuchowski's idea - tested with rudimentary FROC simulator; works! Worth a new chapter.
+### Research Idea(s) as of 12/03/2023
+* Reanalyze real vs. inferred Federica datasets using cross modality method; `inst/InferredVsReal.R` cross modality analysis
+* Extended Obuchowski's idea to combining two FROC datasets - tested with rudimentary FROC simulator; works! Worth a new chapter.
+* Extend Obuchowski's idea to SPLIT-PLOT analyses
 
 
 ### TODOs 10/4/23