RJafroc 2.1.0

TEMP CRAN submission process

Extensive changes to handling of lesDist and relWeights 7/19/22

added Ch19Vig1FrocSampleSize.Rmd 6/7/22

created DfWriteExcelDataFile 3/15/22

fixed wAFROC1_dpc 3/11/22

added example to ChisqrGoodnessOfFit code 3/8/22

argument of St functions 1/24/22

Clarified weights matrix 1/7/22

TBDIF 12-26-21

Changed RSM_yROC to accept physical parameters 12-26-21

Fixed PlotRsmOperatingCharacteristics not working for zeta1 = -Inf

Fixed PlotRsmOperatingCharacteristics returning correct plots but incorrect AUCs

Fixed Issue 73 and deprecated the MRMC file format 10-28-21 - 10-29-21

Added ability to read Excel format LROC datasets 6/11/21 - 6/14/21

Corrected sample size vignettes 4/12/21 and 4/14/21

Intrinsic vs. physical RSM parameters 4/2/21

Moved to RJafrocBook 1/3/21

Added functions RSM_pdfN and RSM_pdfD

CRAN submission process

Simplify handling of lesion distribution and lesion weights

Working on analytical AUCs from RSM

Update StSignificanceTestingCadVsRad()

Modified seed behaviour, no need for SimulateFrocDatasetNoSeed()

Added seed to SimulateFrocDataset()

Fixed errors reading FROC file with no non-diseased cases

NLRating <- as.numeric(NLTable[[4]])
LLRating <- as.numeric(LLTable[[5]])
if (is.na(tt2)) next else { # this is the change
  if (tt2 != 1)  stop("Error in reading LL/TP table") else
  # the is.na() check ensures that an already recorded mark is not overwritten
  if (is.na( LL[i, j, k, el])) LL[i, j, k, el] <- LLRatingCol[l]
}
# if (is.na(tt2)) stop("Error in reading LL/TP table") else {
#   if (tt2 != 1)  stop("Error in reading LL/TP table") else
#     # the is.na() check ensures that an already recorded mark is not overwritten
#     if (is.na( LL[i, j, k, el])) LL[i, j, k, el] <- LLRatingCol[l]
# }

Also replaced

el <- which(unique(truthTableSort$LesionID) == LLLesionIDCol[l]) - 1

with

if (K1 != 0) {
  # this gives 0,1,2,..,max num of lesions
  # which includes zero, hence the minus 1
  el <- which(unique(truthTableSort$LesionID) == LLLesionIDCol[l]) - 1
} else {
  # this gives 1,2,..,max num of lesions
  # which does not include zero, hence no minus 1
  el <- which(unique(truthTableSort$LesionID) == LLLesionIDCol[l])
}

Fixing non-character input error

  readerIDCol <- as.character(truthTable$ReaderID) # bug fix to avoid non-character input error below
  modalityIDCol <- as.character(truthTable$ModalityID) # do:

Simplified plotting routines

Added extensive comments in StORSummaryFRRC.R

Updated package documentation and Ch00 Vignettes

Added stats to ORAnalysisSplitPlotA

Handling of FOMs that depend on single-truth-state cases

Revised UtilPseudoValues 8/7/20

Read real SPLIT-PLOT-A dataset

Update for reading SPLIT-PLOT-A data files

k <- which(unique(truthTableSort$CaseID) == truthTable$CaseID[l])
k <- which(unique(truthTableSort$CaseID) == NLCaseIDCol[l])
k <- which(unique(truthTableSort$CaseID) == LLCaseIDCol[l]) - K1

Tests for UtilOutputReport

Renamed SP datasets 7/9/20

Code for checking for non-sequential lesionIDs in TRUTH 7/8/20

Implemented extensive testing comparing RJafroc to Iowa software

Note on discrepancy vis-a-vis Iowa software

Updated sample size routines

Major reorganization of dataset structure

Major simplifications to all significance testing St functions

Replaced stringsAsFactors = FALSE everywhere data.frame is used except …

After repeated Travis failures

Removed stringsAsFactors arguments in all calls except…

Return transpose for foms member of StSignificanceTesting return object

Moved official good value files to Dropbox

Compared to latest official code

Discovered error

Added seed specification to UtilVarComponentOR

Fixing significance testing with independent calculations in RJafrocBook

Fixed error with msTC

Fixed issue with optim when flipping groups

RJafroc 1.3.2

After work on cran2-update work

Work post acceptance of v1.3.2, as of 3/7/20

After email from Kurt Hornik Kurt.Hornik@r-project.org

Modified UtilPseudoValues.R to work with SPLIT-PLOT data

Created split plot dataset; update all datasets; confirm truthTableStr and DfReadDataFile()

RJafroc 1.3.1

Extended dataset object structure

Extended dataset object structure

Split plot dataset

Error in MS_TC corrected

Extended plotting function to LROC data

Added FROC sample size vignettes and functions

Significance testing functions

CAD and LROC

Variance component input

Other affected functions and new functions:

Needs further testing

Extensions needed

RJafroc 1.2.0

* checking tests ...
 Running ‘testthat.R’ [158s/160s]
 ERROR
 Running the tests in ‘tests/testthat.R’ failed.
 Last 13 lines of output:
   Component "Source": Attributes: < Component "levels": 3 string mismatches >
   List member = 2, Dataset = dataset02, FOM = Wilcoxon, method = DBMH

   ── 2. Failure: SignificanceTestingAllCombinations (@test-significance-te
   CurrentValues[[listMem]] not equal to GoodValues[[listMem]].
   Component "Source": Attributes: < Component "levels": 3 string mismatches >
   List member = 2, Dataset = dataset05, FOM = HrAuc, method = DBMH

RJafroc 1.1.0

RJafroc 1.0.2

RJafroc 1.0.1

RJafroc 1.0.0

RJafroc 0.1.1

RJafroc 0.1.0

RJafroc 0.0.1