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DIDSR / iMRMC

iMRMC: Software to do multi-reader multi-case analysis of reader studies
http://didsr.github.io/iMRMC/
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can't find AUCperReader.csv in R package #161

Closed stevenhurwitt closed 4 years ago

stevenhurwitt commented 4 years ago

Getting an error running the R package on my new machine (using R 4.0.0) using the following:

fake = read.csv("fake88_nurse6_n252_delta15.csv", header = T, sep = ",") result = doIMRMC(fake)

error says:

Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'C:\Users\steve\AppData\Local\Temp\RtmpuY95Mo/imrmcDir/AUCperReader.csv': No such file or directory

Dataset is attached. fake88_nurse6_n252_delta15.zip

Note that running the .jar file works as expected.

brandon-gallas commented 4 years ago

The zip file is empty. Unable to test.

Please download the most recent version of iMRMC = 1.2.2. It has better error reporting.

The most likely reasons are that your Java version is too old or not installed at all.

stevenhurwitt commented 4 years ago

fake88_nurse6_n252_delta15.zip

Non-empty zip file is attached. I'm using iMRMC, 1.2.2 in R, where can I update the java version? I suspect that's the problem. When I download the DIDSR-iMRMC.zip file I can't find the .jar application.

Edit: the version on my machine is iMRMC-v4.0.3

brandon-gallas commented 4 years ago

Look online to update your java version.

The jar file is available as one of the assets of the release:

It is also included in the R package.

You can find it when you install the iMRMC R package. Here it is installed on my computer.

= Test iMRMC-v4.0.2.jar = The data you sent doesn't appear to work "as expected" with iMRMC-v4.0.3.jar.

The problem is that the first column of your file ("ImageNo") is not expected. When I added BEGIN DATA: and removed the "ImageNo" column iMRMC-v4.0.3.jar completed successfully.

= Test in R =

Everything looks fine here.

stevenhurwitt commented 4 years ago

yeah, sorry, i have a different file i use for the java app.

what is your "workDir" defined as? Is there a specific location the java app outputs these files? If so I could probably just point it to there as a workaround.

when i try to just invoke the java app in R i get the following warning:

pkgPath <- path.package("iMRMC", quiet = FALSE) iMRMCjarFullPath <- file.path(pkgPath, "java", iMRMCjar) iMRMCjar <- "iMRMC-v4.0.3.jar" iMRMCjarFullPath <- file.path(pkgPath, "java", iMRMCjar)

system2( "java", args = c("-jar", iMRMCjarFullPath, fileName, file.path(workDir, "imrmcDir")), stdout = FALSE, stderr = TRUE)

warning:

[1] "a total of 0 lines in header" "ERROR: No truth for case " " row = 2 " [4] " readerID = 1 " " caseID = Reader1 " " modalityID = Actual101 " [7] ""

despite the fact that row2 has a truth case right below it:

mrmc_error

a little confused about what could be causing this. it also creates the file 'input.imrmc' in my temp directory but does not make the /imrmcDir, presumably because of this warning. again, java app works fine.

edit: also for what it's worth the issue persists on both my linux and windows machines, yet to test it on mac osx

brandon-gallas commented 4 years ago

Thanks for the feedback.

The problem is with the format of your data. Look closely at the warning you provide. " caseID = Reader1 " That's not right.

When working directly with the file input mode in R, it must adhere to the format expected by the java program. Check the user manual.

When working with a data frame in R, you need a data frame with specific column names: readerID, caseID, modalityID, score. Your column names were different and you had an extra column (ImageNo).

I have added some more error checks and allow the data to include extra columns (when working with a data frame in R). Try the new package iMRMC_1.2.3.tar.gz in the current release.

stevenhurwitt commented 4 years ago

ahhh ok i'll reformat and try it, thanks for your help!

stevenhurwitt commented 4 years ago

ok, now that it's working here is a short tutorial on how to build some additional functionality into the R package (mainly to replicate and extend the Java app). Please let me know if you have any critiques/suggestions, it's a little sparse.

Updated data with correct variable names is attached: fake88_nurse6_n252_delta15.zip

Here is the link to the RPub: https://rpubs.com/stevenhurwitt/610294

brandon-gallas commented 4 years ago

Thanks for this. We will evaluate (@DevinHFD). Assuming AOK, the best place for this might be as a wiki page for others to follow. Happy to give you full credit. We are moving to recode the analysis methods with native R rather than using the java app engine. So maybe there will be an opportunity to build a new related function.

Brandon

DevinHFD commented 4 years ago

Thanks for linking me here (@brandon-gallas ) and also thanks for the tutorial (@stevenhurwitt ). I will go through the package and transfer the java code to R.