Does anyone know of a citation for the Odum distance score (available through dist.shared)?
Thanks!
Ugh. I can’t find a reference for that formula referring to “Odum”; however, it is another way of expressing the Bray-Curtis formulation. See:
The conversion is shown in Analysis of Ecological Communities by McCune and Grace
http://home.centurytel.net/~mjm/book.htm
If you look at the example data, they give the same distance values. Also, if you take the 454 SOP data and do the following:
mothur "#summary.shared(shared=final.an.shared, calc=braycurtis-odum)"
You’ll get the following in the output:
label comparison braycurtis odum
0.03 F003D000 F003D002 0.388784 0.388784
0.03 F003D000 F003D004 0.410763 0.410763
0.03 F003D002 F003D004 0.266073 0.266073
0.03 F003D000 F003D006 0.414392 0.414392
0.03 F003D002 F003D006 0.296934 0.296934
0.03 F003D004 F003D006 0.170169 0.170169
0.03 F003D000 F003D008 0.391497 0.391497
0.03 F003D002 F003D008 0.346922 0.346922
0.03 F003D004 F003D008 0.314399 0.314399
0.03 F003D006 F003D008 0.274658 0.274658
0.03 F003D000 F003D142 0.422055 0.422055
0.03 F003D002 F003D142 0.442016 0.442016
0.03 F003D004 F003D142 0.282290 0.282290
0.03 F003D006 F003D142 0.266261 0.266261
0.03 F003D008 F003D142 0.380076 0.380076
0.03 F003D000 F003D144 0.374336 0.374336
0.03 F003D002 F003D144 0.480337 0.480337
0.03 F003D004 F003D144 0.341521 0.341521
0.03 F003D006 F003D144 0.406422 0.406422
0.03 F003D008 F003D144 0.448378 0.448378
0.03 F003D142 F003D144 0.248386 0.248386
0.03 F003D000 F003D146 0.348074 0.348074
0.03 F003D002 F003D146 0.447714 0.447714
0.03 F003D004 F003D146 0.336974 0.336974
0.03 F003D006 F003D146 0.360101 0.360101
0.03 F003D008 F003D146 0.364249 0.364249
0.03 F003D142 F003D146 0.242090 0.242090
0.03 F003D144 F003D146 0.171373 0.171373
0.03 F003D000 F003D148 0.361859 0.361859
0.03 F003D002 F003D148 0.439297 0.439297
0.03 F003D004 F003D148 0.338554 0.338554
0.03 F003D006 F003D148 0.405704 0.405704
0.03 F003D008 F003D148 0.404066 0.404066
0.03 F003D142 F003D148 0.277163 0.277163
0.03 F003D144 F003D148 0.183881 0.183881
0.03 F003D146 F003D148 0.201839 0.201839
0.03 F003D000 F003D150 0.371826 0.371826
0.03 F003D002 F003D150 0.436972 0.436972
0.03 F003D004 F003D150 0.297968 0.297968
0.03 F003D006 F003D150 0.317820 0.317820
0.03 F003D008 F003D150 0.332340 0.332340
0.03 F003D142 F003D150 0.236158 0.236158
0.03 F003D144 F003D150 0.249778 0.249778
0.03 F003D146 F003D150 0.217352 0.217352
0.03 F003D148 F003D150 0.244230 0.244230
Thanks - very helpful!
I’m not adept enough with math to have picked up on these two being equivalent.