你好,这是我在 stackoverflow 或任何类似论坛中的第一个问题,所以如果我错过了什么,请原谅并善待;)
我正在使用R中的vegan包来计算cca分析。因为我的研究是关于物种性状的种内变异,所以我没有“情节 X 物种-矩阵”而是代表“生理-化学-利基”的“个体 X 性状-矩阵”(所以我的物种分数看起来与他们不同习惯了)。所以我的问题是:
- 以这种方式进行分析是否合适?
- 是否可以根据“物种分数”(在我的情况下不是物种分数)来解释 CCA 轴 - 我想获得以下信息:CCA1 与性状 X 最相关。
- 与 premutaion 测试 (anova.cca) 相比,我如何解释双标图箭头的长度 - 因为我得到了许多“长”箭头,但在排列测试中只有少数是显着的?
这是我的摘要(cca)-输出:
Call:
cca(formula = mniche_g ~ cover_total * Richness + altitude + Eastness + lan_TEMP + lan_REACT + lan_NUTRI + lan_MOIST + Condition(glacier/transect/plot/individuum), data = mres_g_sc)
Partitioning of scaled Chi-square:
Inertia Proportion
Total 0.031551 1.00000
Conditioned 0.001716 0.05439
Constrained 0.006907 0.21890
Unconstrained 0.022928 0.72670
Eigenvalues, and their contribution to the scaled Chi-square
after removing the contribution of conditiniong variables
Importance of components:
CCA1 CCA2 CCA3 CA1 CA2 CA3
Eigenvalue 0.00605 0.0005713 0.0002848 0.0167 0.00382 0.002413
Proportion Explained 0.20280 0.0191480 0.0095474 0.5596 0.12805 0.080863
Cumulative Proportion 0.20280 0.2219458 0.2314932 0.7911 0.91914 1.000000
Accumulated constrained eigenvalues
Importance of components:
CCA1 CCA2 CCA3
Eigenvalue 0.00605 0.0005713 0.0002848
Proportion Explained 0.87604 0.0827150 0.0412425
Cumulative Proportion 0.87604 0.9587575 1.0000000
Scaling 2 for species and site scores
* Species are scaled proportional to eigenvalues
* Sites are unscaled: weighted dispersion equal on all dimensions
Species scores
CCA1 CCA2 CCA3 CA1 CA2 CA3
SLA_range_ind 0.43964 -0.002623 -0.0286814 -0.75599 -0.04823 0.003317
SLA_mean_ind 0.01771 -0.042969 0.0246679 -0.01180 0.12732 0.053094
LNC -0.10613 -0.064207 -0.0637272 0.07261 -0.15962 0.198612
LCC -0.01375 0.012131 -0.0005462 0.02573 -0.01539 -0.021314
...
这是我的 anova.cca(cca)-输出:
Permutation test for cca under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999
Model: cca(formula = mniche_g ~ cover_total * Richness + altitude + Eastness + lan_TEMP + lan_REACT + lan_NUTRI + lan_MOIST + Condition(glacier/transect/plot/individuum), data = mres_g_sc)
Df ChiSquare F Pr(>F)
cover_total 1 0.0023710 10.4442 0.002 **
Richness 1 0.0006053 2.6663 0.080 .
altitude 1 0.0022628 9.9676 0.001 ***
Eastness 1 0.0005370 2.3657 0.083 .
lan_TEMP 1 0.0001702 0.7497 0.450
lan_REACT 1 0.0005519 2.4313 0.094 .
lan_NUTRI 1 0.0000883 0.3889 0.683
lan_MOIST 1 0.0001017 0.4479 0.633
cover_total:Richness 1 0.0002184 0.9620 0.351
Residual 101 0.0229283
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
这里是双标图: 在此处输入图像描述
谢谢你们!