ANOSIM: R values >>1

mothur bugs
1

Hi Pat and Sarah,

I’m running the following command:
anosim(phylip=SC_GP60_allelelength.dist, design=GP60.design, iters=100000)

with the following input files:
SC_GP60_allelelength.dist

10
Goat13
H34 81
Goat2 225 36
C1 576 225 81
C189 729 324 144 9
C245 900 441 225 36 9
C99 1089 576 324 81 36 9
L12 1296 729 441 144 81 36 9
L6 1521 900 576 225 144 81 36 9
C28 2304 1521 1089 576 441 324 225 144 81

the following design file specifies 2 groups:
GP60.design

Goat13 2
H34 2
Goat2 2
C1 1
C189 1
C245 1
C99 1
L12 1
L6 1
C28 1

I get the following results:

comparison R-value P-value
1-2 11235.5 0.00807*

which seems weird since I understand that R ranges from 0-1. When I run other dist and design files, the results make sense but in the above case, I can’t figure out what’s causing the high R value.

thanks,

Giovanni

2

I suspect the problem is that your distances are greater than 1 and our implementation of anosim assumes they are between 0 and 1.

pat