get.communitytype output

Commands in mothur
1

I’ve recently runned get.communitytype analysis on my dataset and it outputted …dmm.mix.fit file with a table:

K 	NLE 	logDet 	BIC 	AIC 	Laplace
1 	1029199.17 	23961.2 	1076567.76 	1048693.17 	1023265.99
2 	1040591.29 	62.39 	1135330.9 	1079580.29 	1004794.01
3 	1063994.88 	-21839.64 	1206105.51 	1122478.88 	999331.88
4 	1118626.7 	-53030.58 	1308108.36 	1196605.7 	1020453.54
5 	1129508.97 	-85252.62 	1366361.65 	1226982.97 	997310.09
6 	1188609.82 	-112403.6 	1472833.52 	1305578.82 	1024920.75
7 	1230202.12 	-169400.09 	1561796.84 	1366666.12 	1020100.1
8 	1273052.85 	          -nan 	1652018.59 	1429011.85 	          -nan

Can you please explain the meanings of columns, especially “logDet” one? I haven’t found them neither in manual, nor in Holmes et al., 2012
Can you please also explain what does it mean “-nan”? I see that my Laplace-values haven’t gone to the minimum, oscillating instead. Does “-nan” mean that analysis was closed violently, because 7 is the maximum possible number of classes?
My apologies for asking, this calculation took literally a week on our computer, so I’m trying to understand, what went wrong, before to do a new try)

2

Hi,

The logDet column is the log of the determinant. It’s been a while since I looked, but I think it was outputted in Chris Quince’s original code. What you really care about is K and Laplace and you want Laplace to hit a minimum. get.communitytype will continue on for several iterations after it finds a new minimum.

How many samples do you have? Are these OTUs, phylotypes, or ASVs?

Pat

3

Good morning!

Thank you for a response!

My attention was sticked to that logDet column, cause it first positive and then became negative. I thought maybe there is some meaning in that. But maybe not)

I’m not sure I can securely trust my Laplace minimum, cause instead of finding one minimum, it oscillated and found the second, smaller, minimum, than after 2 more divisions stopped. What if it should oscillate more and reach best minimum e.g. when K=9? Is 7 the maximum possible number of classes?
Do you know what does an abbreviation “-nan” mean?

There are 130 soil samples from 4 horizons of the same soil, some of them are large 250 mg samples, some of them small 10-50 mg. There are OTU’s 97% (~19 000 OTU’s in all dataset).
I thought next time to try to analise large and small samples separately, or to analise only mineral horizons without humus horizon…

Cat

4

Hi Cat,

I’m not sure why you’re getting -nan - there’s no limit on the value of K. My only thought is that your samples are so diverse that it’s hard for the algorithm to find good types. I wouldn’t suggest getting fewer samples, rather you might want more. I think you should probably also try with genus-level phylotypes. I’m not sure what you mean by large and small samples - you want them all to have the same number of sequences (use sub.sample if you aren’t already).

Pat

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