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Mouse-Imaging-Centre / RMINC

Statistics for MINC volumes: A library to integrate voxel-based statistics for MINC volumes into the R environment. Supports getting and writing of MINC volumes, running voxel-wise linear models, correlations, etc.; correcting for multiple comparisons using the False Discovery Rate, and more. With contributions from Jason Lerch, Chris Hammill, Jim Nikelski and Matthijs van Eede. Some additional information can be found here:
https://mouse-imaging-centre.github.io/RMINC
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consistency: hanat* models use "." instead of "-" to prefix predictor names #243

Closed gdevenyi closed 5 years ago

gdevenyi commented 5 years ago

A anatLmer model has columns such as "tvalue-age", an equivalent hanatLmer model has "tvalue.age" instead. Took us a while to figure this out as #242 didn't give us the most useful error.

jasonlerch commented 5 years ago

For historical reasons. The - causes problems with data.tree, the underlying library we use for hierarchical trees. So we could have either changed all the other, older bits of code with the potential failure in scripts that would cause, to do what we did here and have some inconsistency. Happy to change everything to ‘.’ If the breakage is worth the consistency.

Jason

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gdevenyi commented 5 years ago

A foolish consistency is the hobgoblin of little minds.

I'd be happy with a better way to find the column names in the hanat* model object. I found that I couldn't inspect the object in rstudio unlike some other RMINC objects, and printing it resulted in the tree, rather than the model columns being displayed. Eventually found that names worked.

Of course #242 caused pain as well, since I didn't know I was misnaming the column to begin with.

cfhammill commented 5 years ago

I think I'll close this for now. If anyone feels strongly that we should change the naming convention we can reopen.