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LMM output missing something? #237
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I thought lmm 1 is the wald test, 2 is the likelihood ratio test, 3 is the score test, and perhaps 4 is all three tests? |
Yes, you are right
That column of zeroes should not be there :) |
If I run the 4 options with
the result is
you can see logl_H1 differs for lmm 2 and is not computed with lmm 3. It was code introduced in gemma 0.95alpha. See https://github.com/genetics-statistics/GEMMA/blame/84360c191f418bf8682b35e0c8235fcc3bd19a06/src/lmm.cpp. I added the logl_H1 output about 3 years ago with #92 |
I also note the time to compute varies quite a bit for the lmm 1-4 versions. lmm 4 being the worst for doing it all:
|
Anyway, from the code |
Describe the bug
Running -lmm [1-3] gives the following output:
At least one expects lmm3 to show all 3 calculations! Probably a regression on my end.
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