[R-sig-eco] adonis/vegan

[Diego Fontaneto]

Why does order matter in specifying a model in adonis?

Call:
adonis(formula = presence ~ DO + ph + T + EC, data = presence.env,
permutations = 1000, method = "jaccard") 

                Df SumsOfSqs  MeanSqs  F.Model     R2 Pr(>F)  
DO         1.00000   0.59095  0.59095  1.47514 0.0448  0.035 *
ph         1.00000   0.59785  0.59785  1.49235 0.0453  0.855  
T          1.00000   0.53954  0.53954  1.34681 0.0409  1.000  
EC         1.00000   0.65139  0.65139  1.62601 0.0494  1.000  
Residuals 27.00000  10.81641  0.40061          0.8197         
Total     31.00000  13.19614                   1.0000         

but changing order, both R2 and P change.

Call:
adonis(formula = presence ~ EC + DO + ph + T, data = presence.env,
permutations = 1000, method = "jaccard") 

                Df SumsOfSqs  MeanSqs  F.Model     R2 Pr(>F)   
EC         1.00000   0.69313  0.69313  1.73019 0.0525  0.005 **
DO         1.00000   0.51736  0.51736  1.29143 0.0392  0.958   
ph         1.00000   0.50494  0.50494  1.26043 0.0383  1.000   
T          1.00000   0.66431  0.66431  1.65826 0.0503  1.000   
Residuals 27.00000  10.81641  0.40061          0.8197          
Total     31.00000  13.19614                   1.0000          

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Another question in adonis: is there a way to specify an error term, like
adding "random=~1|locality" to the previous models?

Thanks,
Diego

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Diego Fontaneto
Imperial College London
Silwood Park Campus
Ascot Berkshire SL57PY
United Kingdom