Hello Sir
I am getting problem in plotting in CCA . Could you please help me? I wrote the
below command but I don't know why it is taking only first 5 env data rather
than all 9.
> strain.data <- read.xlsx("Dee rhiz.xlsx", sheetName="strain", header = T,
> row.names = 1)
> env.data <- read.xlsx("Dee rhiz.xlsx", sheetName="env", header = T, row.names
> = 1)
> strain.cca <- cca(strain.data ~ Ph+TotalN+Organicmatter+Ca+K+Na+P+Cu+Mn,
> data=env.data)
> strain.cca
Call: cca(formula = strain.data ~ Ph + TotalN + Organicmatter + Ca + K + Na + P
+ Cu + Mn, data = env.data)
Inertia Proportion Rank
Total 5 1
Constrained 5 1 5
Unconstrained 0 0 0
Inertia is mean squared contingency coefficient
Some constraints were aliased because they were collinear (redundant)
Eigenvalues for constrained axes:
CCA1 CCA2 CCA3 CCA4 CCA5
1 1 1 1 1
> plot(strain.cca)
> summary (strain.cca)
Call:
cca(formula = strain.data ~ Ph + TotalN + Organicmatter + Ca + K + Na + P
+ Cu + Mn, data = env.data)
Partitioning of mean squared contingency coefficient:
Inertia Proportion
Total 5 1
Constrained 5 1
Unconstrained 0 0
Eigenvalues, and their contribution to the mean squared contingency coefficient
Importance of components:
CCA1 CCA2 CCA3 CCA4 CCA5
Eigenvalue 1.0 1.0 1.0 1.0 1.0 0
Proportion Explained 0.2 0.2 0.2 0.2 0.2 0
Cumulative Proportion 0.2 0.4 0.6 0.8 1.0 1
Accumulated constrained eigenvalues
Importance of components:
CCA1 CCA2 CCA3 CCA4 CCA5
Eigenvalue 1.0 1.0 1.0 1.0 1.0
Proportion Explained 0.2 0.2 0.2 0.2 0.2
Cumulative Proportion 0.2 0.4 0.6 0.8 1.0
Biplot scores for constraining variables
CCA1 CCA2 CCA3 CCA4 CCA5
Ph 0.29757 0.85775 -0.3364 0.2242 -0.11088
TotalN -0.01537 -0.67797 0.6132 0.2831 0.28985
Organicmatter 0.14618 0.06462 0.8320 0.3515 0.39827
Ca 0.08310 -0.41940 0.3858 0.8116 0.09834
K 0.37548 0.38360 0.6849 -0.4172 0.26222
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----------------------------------------------------------------------------------
Tshwane University of Technology
----------------------------------------------------------------------------------
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confidential. The full text of the Electronic Mail Disclaimer
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