# vegan包中RDA proportion of variance的计算

Call: rda(formula = spe.hell ~ pH + SOILDPT, data = env)

Inertia Proportion Rank
Total         0.70476    1.00000
Constrained   0.06250    0.08869    2
Unconstrained 0.64226    0.91131   94
Inertia is variance

Eigenvalues for constrained axes:
RDA1    RDA2
0.04023 0.02227

Eigenvalues for unconstrained axes:
PC1     PC2     PC3     PC4     PC5     PC6     PC7     PC8
0.07321 0.04857 0.04074 0.03144 0.02604 0.02152 0.01917 0.01715
(Showed only 8 of all 94 unconstrained eigenvalues)

The two variables explain 8.9% of variance (the row Constrained and column Proportion in the table above, can be calculated also as the sum of eigenvalues for the contrained axes divided by total variance (inertia): (0.04023+0.02227) /0.70476=0.08868. The first constrained axis (RDA1) explains 0.04023/0.70476=5.7% of variance, while the second (RDA2) explains 0.02227/0.70476=3.2%. Note that the first unconstrained axis (PC1) represents 0.07321/0.70476=10.4% of total variance, which is more than both explanatory variables together; the first two unconstrained explain (0.07321+0.04857)/0.70476=17.3%. This means that the dataset may be structured by some strong environmental variable(s) different from pH and soil depth (we will check this below).

http://blog.sciencenet.cn/blog-1817482-1125943.html

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GMT+8, 2020-7-3 07:35