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@dpc10ster dpc10ster released this 14 Aug 15:58
v2.1.0
448d059

CRAN accepted 7/24/22

  • Version 2.1.0
  • On cran210 branch.
  • Steps to reduce file size to less than 5 Mb:
    • Removed RoiData.xlsx.
  • Otherwise identical to developer and master as of 07/7/22.

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

  • Removed unnecessary dimension on lesDist, it is now always 1D
  • Affected files are UtilLesDistrVector.R and UtilLesionWeightsMatrix.R
  • lesDistr and relWeight must have same lengths and sum to unity
  • relWeight = 0 imposes equal weights
  • can remove a lesion by setting the corresponding lesDist entry to zero
  • need further testing on above capability

added Ch19Vig1FrocSampleSize.Rmd 6/7/22

  • Added added Ch19Vig2FrocSampleSize.Rmd and Ch19Vig2FrocSampleSize.Rmd
  • These vignettes got accidentally removed, perhaps because it was failing tests
  • R CMD CHK works
  • Found lots of instances of four backticks, instead of 3; this is probably why some vignettes were not loading on website

created DfWriteExcelDataFile 3/15/22

  • needed to write Nico simulated FROC data to JAFROC format excel file
  • removed JAFROC format writes capability from DfSaveDataFile; it is now in DfWriteExcelDataFile

fixed wAFROC1_dpc 3/11/22

  • needed to divide final value by (K * K2)
  • cpp code unaffected; this only affected R version used to debug
  • checked R code vs cpp; see JT_R_Py_Foms.xlsx in PyJafrocscraps directory

added example to ChisqrGoodnessOfFit code 3/8/22

argument of St functions 1/24/22

  • analysisOption must be DBM or OR
  • Not "ORH"

Clarified weights matrix 1/7/22

  • See test-RSM-formulae.R
  • Search in code for rsm-pred-wafroc-curve: rsmFormulae.R and UtilAnalyticalAucsRSM.R
  • See RJafrocFrocBook, search for rsm-pred-wafroc-curve
  • Push to developer and master

TBDIF 12-26-21

  • TBDIF: To be done in future
  • Created much confusion in RJafrocFrocBook, chapter on 3-fits
  • RsmFormulae.R: This file is a mess.
  • Remove AUCs in PlotRsmOperatingCharacteristics? - these are done in UtilAnalyticalAucsRsm
  • Add to tests?
  • Replace error function with Phi functions?
  • Remove redundant column in weights matrix
  • change lambdaP to lambda and lambda to lambdaI and corresponding changes in book

Changed RSM_yROC to accept physical parameters 12-26-21

  • So as to be consistent with RSM_xROC
  • Created much confusion in RJafrocFrocBook, chapter on 3-fits
  • Added checks for valid RSM parameters in RsmFormulae.R .
  • Changed all such functions in RsmFormulae.R to accept physical parameters.

Fixed PlotRsmOperatingCharacteristics not working for zeta1 = -Inf

  • Global search string "bug fix 12/7/21" to locate all changes.
  • Starting value of for-loop cannot be -Inf; detect it and set to -3

Fixed PlotRsmOperatingCharacteristics returning correct plots but incorrect AUCs

  • Global search string "bug fix 11/24/21" to locate all changes.
  • Basic issue was that I was using zeta1 = -20 instead of the supplied value.

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

  • Global search string "T1-RRRC for ROC data #73"" to locate all changes.
  • Basic issue was missing truthTableStr in any file *.imrc when read by DfReadDataFile.
  • See under tests: StSignificanceTestingCadVsRad: Issue T1-RRRC for ROC data #73 for recreation of this issue.
  • Updated R and RStudio.
  • File DfExtracDataset.R was also affected: the change fixes an error that did not get caught before.
  • Updated documentation and links in StSignificanceTestingCadVsRad.R.
  • Note that For non-JAFROC data file formats, the readerID and modalityID fields must be unique integers, as indicated in documentation of DfReadDataFile().
  • Giving thought to removing support for all non-JAFROC formatted files; otherwise I need to maintain support for four file extensions (*.lrc, *.txt, *.csv and *.imrmc) for the simplest data structure (one rating for each modality-reader-case). This is unnecessarily complicating the code. Final resolution: I will support only *.imrmc. Other formats can still be read by DfReadDataFile() and then saved to a JAFROC format file for analysis within the RJafroc package.

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

  • Extended DfReadDataFile to accommodate LROC data; added flag lrocForcedMark
  • Must use newExcelFileFormat = T for this capability
  • Added toy LROC files: see inst/extdata/toyFiles/LROC/lroc*.xlsx
  • See ReadJAFROCNewFormat.R, just before final return, for added code
  • Added tests in test-DfReadDataFile().

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

  • Ch19Vig1FrocSampleSize.Rmd and Ch19Vig2FrocSampleSize.Rmd
  • Fixed SsFrocNhRsmModel.R to not return lesion distribution and weights
  • Fixed vignettes that were using the old structure returned by sig. testing function
  • Fixed 2 FROC SS vignettes; fixed SsFrocNhRsmModel.R to do binning internal to the function
  • Added a test for SsFrocNhRsmModel().
  • Updated Rcpp to 1.0.6. NOTE: version 1.0.6.6 created horrendous errors - R aborts.

Intrinsic vs. physical RSM parameters 4/2/21

  • All C++ functions take physical parameters
  • Rest take intrinsic parameters (2 exceptions, like RSM_xROC and RSM_pdfN)
  • Cleanup:
    • PlotRsmOperatingCharacteristics.R,
    • UtilAnallyticalAucsRSM.R,
    • rsmFormulae.R
    • affected related test files: test-RSM-formulae.R and test-model-aucs.R
    • Used goodValues to check that nothing has changed

Moved to RJafrocBook 1/3/21

  • Vignette Ch10Vig1QuickStart
  • Vignette Ch10Vig2QuickStart
  • Function Compare3ProperRocFits.R
  • Associated files in inst: MRMCRuns and ANALYZED

Added functions RSM_pdfN and RSM_pdfD

  • Needed for Swets predictions in book; but of general utility.
  • Other new functions added of type RSM_*()
  • Need to vectorize all Cpp functions; no need to carry both scalar and vector types.
  • Add tests for new functions RSM_*()
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