From 02bef932d534379e2c5c0e2b3800d3d6e3a034cd Mon Sep 17 00:00:00 2001 From: dpc10ster Date: Sat, 2 Dec 2023 20:11:57 -0500 Subject: [PATCH] edits to NEWS and DfReadDataFile.R --- NEWS.md | 8 +++----- R/DfReadDataFile.R | 39 +++++++++++++++++++++------------------ inst/UpdateHistory.md | 9 +++++---- man/DfReadDataFile.Rd | 36 +++++++++++++++++++----------------- 4 files changed, 48 insertions(+), 44 deletions(-) diff --git a/NEWS.md b/NEWS.md index 525da6b1..550f67f7 100644 --- a/NEWS.md +++ b/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. diff --git a/R/DfReadDataFile.R b/R/DfReadDataFile.R index 0f80cd17..634d76f7 100644 --- a/R/DfReadDataFile.R +++ b/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)) diff --git a/inst/UpdateHistory.md b/inst/UpdateHistory.md index db886f36..37b8e239 100644 --- a/inst/UpdateHistory.md +++ b/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 diff --git a/man/DfReadDataFile.Rd b/man/DfReadDataFile.Rd index 3b654dd3..44c92c47 100644 --- a/man/DfReadDataFile.Rd +++ b/man/DfReadDataFile.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/DfReadDataFile.R \name{DfReadDataFile} \alias{DfReadDataFile} -\title{Read a factorial data file (not split-plot)} +\title{Read a factorial data file (not SPLIT-PLOT)} \usage{ DfReadDataFile( fileName, @@ -15,17 +15,18 @@ DfReadDataFile( } \arguments{ \item{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.} \item{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}.} \item{newExcelFileFormat}{Logical. Must be true to read LROC data. This argument only applies to the \code{"JAFROC"} format. @@ -52,17 +53,18 @@ and reader IDs in the original data file will be used.} A dataset with the structure specified in \code{\link{RJafroc-package}}. } \description{ -Read a disk file and create an ROC, FROC or LROC dataset object - from it. +Read an Excel file and create an ROC, FROC or LROC dataset + object from it. } \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 +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}. This function is used only for factorial datasets. For SPLIT-PLOT