[R] vegan -varpart is bigger than 100% in total?

Ozgul Inceoglu Ozgul.Inceoglu at ulb.ac.be
Tue Apr 30 15:04:10 CEST 2013


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



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