We don't have enough information to replicate your results, but the warning in the output is suggestive: "Some constraints were aliased because they were collinear (redundant)".
Are some of your columns perfectly correlated with other columns? This could easily happen if there are more columns than rows. ------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Sanjay Kumar Jaiswal Sent: Tuesday, July 18, 2017 4:08 AM To: r-help@r-project.org Subject: [R] Redundancy canonical analysis plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC 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 ________________________________ ---------------------------------------------------------------------------------- Tshwane University of Technology ---------------------------------------------------------------------------------- This email is sent and received in terms of the Electronic Communications Policy of Tshwane University of Technology. In line with this policy, this email is private, privileged and confidential. The full text of the Electronic Mail Disclaimer can be seen on the TUT web site at http://www.tut.ac.za/Other/disclaimer/Pages/default.aspx or obtained by phoning (012) 382-5911 ________________________________ ---------------------------------------------------------------------------------- Tshwane University of Technology ---------------------------------------------------------------------------------- This email is sent and received in terms of the Electronic Communications Policy of Tshwane University of Technology. In line with this policy, this email is private, privileged and confidential. The full text of the Electronic Mail Disclaimer can be seen on the TUT web site at http://www.tut.ac.za/Other/disclaimer/Pages/default.aspx or obtained by phoning (012) 382-5911 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
