I am trying to find the percentage of the parameters explaining the bacterial community composition. I have one data matrix with relative abundance of OTUs and one with environmental parameters. I used varpart in vegan package but the values in the venn diagram is bigger than 100% in total.How is it possible? What might be the reason? Thank you
library(vegan) gotud <- decostand(gotu,"hell") G.var <- varpart(gotud,~Depth,~CH4_oxidation,~d13C_DIC+Temperature+Spec.Conductivity+DO+CH4+N2O+pH, data=ge) plot(G.var) Sample depth T SpCond DO pH Chl CH4 CH4oxidation N2O TA POC BP SO4 Gi25Feb12 25 24.46 1104 4.42 8.94 1.6 40.00174578 1.1 6.683260809 12.723 41.98069543 0.008282072 150.1168 Gi27.5Fb12 27.5 24.42 1105 4.36 8.93 1.2 68.53538846 1.4 7.431459607 12.711 31.4397919 0.020730967 188.4166 Gi30Fb12 30 23.71 1128 2.62 8.81 1 10.53158545 0.9 8.415644664 12.817 23.06912467 0.007716205 199.9561 Gi32.5Fb12 32.5 23.58 1135 1.63 8.79 1.2 11.77550422 0 7.069811212 12.916 26.80357225 0.00245392 170.9078 Gi35Fb12 35 23.54 1138 1.42 8.78 -0.4 11.57631611 0 6.976269751 12.978 31.80221025 0.006877572 176.4877 Gi37.5Fb12 37.5 23.5 1138 1.37 8.78 0.6 17.19312361 0 7.382521684 12.975 19.67401691 0.007159828 164.5442 OTU matrix Group Otu04518 Otu04569 Otu04598 Otu04636 Otu04671 Otu04672 Otu04795 Otu04821 Otu04891 Otu04930 Otu05062 Otu05118 Otu05148 Otu05440 Otu05520 Otu05555 Otu05690 Otu06033 Otu06037 Otu06194 Otu06354 Gi25Fb12r 0.000567 0 0 0 0.001134 0.000567 0.002834 0.000567 0.000567 0 0 0 0 0.000567 0 0 0 0 0 0 0 Gi275Fb12r 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Gi30Fb12r 0 0 0.003145 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Gi325Fb12r 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0048 0.0208 0 0 0 0 0 Gi35Fb12r 0 0 0 0.001114 0 0 0 0 0 0 0.001114 0 0 0 0 0 0 0 0 0 0 Gi375Fb12r 0 0.001447 0 0 0 0 0 0 0 0 0 0 0.001447 0 0 0 0 0 0 0 0 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
