Invalid NONMEM XML file causes error about babelmixr2 HOT 13 CLOSED

Probably pmxTools. Or here if we want to use a non xml method. @kestrel99 mentioned a non xml method that @RikSchoemaker uses

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As I've looked more, it's not an easily-fixable issue either place. The XML file appears to be missing not just some of the closing tags but also some of the needed data. Having it throw an error is likely the best path. We may want to make the error clearer, but otherwise, I think we can leave it for now.

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I'll fix it when I get back. In the meantime can you flag it on the pmxTools GitHub page so I don't forget? (I think a clear error about it being malformed XML is the best.)

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xml reader is used to calculate

• nonmem run time
• nmtran message
• termination message
• covariance information

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The lst reader gives

• termination message
• ofv

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Covariance comes pretty easily from reading the .cov file. I don't know if run time comes easily from another source (though I also don't think it seems to be required...).

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I am writing a .lst parser right now (since most of the ddmore files don't contain .ext files), I can get the run time from that parser. I looked at pmxTools .lst parser and it doesn't get as much as I thought it did.

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PsN has a .lst parser that covers a lot of the potential issues that come up in edge cases. You may want to look at it while you're at it.

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Also, I think that the .cov file has more precision than the .lst file for the covariance matrix (i.e. more significant figures).

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After thinking a bit, all I will extract is the parameter estimates for now. lst parsing is a pain.

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https://github.com/UUPharmacometrics/PsN/blob/18f6d39677506ab568134cf3965c6af7bbda6b99/lib/output/problem/subproblem.pm

if you are looking

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That's about what I remembered.

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Write the parser in nonmem2rx

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