search for: varpart

I'm trying to perform a RDA analysis in the vegan package using the "varpart" function. I have a matrix of community structure data in different sites (rows), which I want to explain using 3 matrices of environmental data. The 3 matrices are: water quality parameters; local land use variables; total land use variables. In each matrix, the number of the rows is th...

I am not familiar with the vegan package, so I am just making a guess here. If 'na.action=na.omit' is part of the call to varpart, try removing it from the function call and moving it above as follows: options(na.action="na.omit") RDA_Ger <- varpart(comm, x1, x2, x3, transfo="hellinger", scale = FALSE) Maybe that will help. Regards, Eric On Sat, Sep 16, 2017 at 6:53 PM, Sophi Marmen <sofimarman a...

Dear R-users I applied vegan's varpart function to partition the effects of explanatory matrices. Adj. R square for the unique fraction [a] is 0.25. Does anyone know why the decomposition by hand using rda gives me a different result for [a] (constrained proportion is 0.32)? I used cbind() for the conditional fractions, but it s...

Hi, I did a linear regression with 5 explanatory variables. Now, to see the contribution of each variable, I use varpart from vegan library. But varpart don?t accepts my 5 explanatory variables, it accept only 4. 1- How must I do to use my 5 explanatory variables? 2- Is it the sum of variance fraction of each variable must be equal to 1. Thanks for your help. Komine -- View this message in context: http:/...

I am trying to find the percentage of the parameters explaining the bacterial community composition. I have one data matrix with relative abundance of OTUs and one with environmental parameters. I used varpart in vegan package but the values in the venn diagram is bigger than 100% in total.How is it possible? What might be the reason? Thank you library(vegan) gotud <- decostand(gotu,"hell") G.var <- varpart(gotud,~Depth,~CH4_oxidation,~d13C_DIC+Temperature+Spec.Conductivity+DO+CH4+N2O+p...

The varpart function does not have na.action argument, and all undefined arguments are regarded as explanatory data sets X (they come after ?). Best wishes, Jari Oksnaen

Hello I am using Jari Oksanen's CCA routine from the Vegan package on some estuary data, following a technique applied in (Anderson, M.J. & Gribble, N.A., 1998, Partitioning the variation among spatial, temporal and environmental components in a multivariate data set, Australian Journal of Ecology 23, 158-167). Some steps in the process require that the dependent matrix be constrained by

Hi, I am trying to run the command "forward.sel.par," however I receive the error message: "Error: could not find function 'simpleRDA2'." I have the vegan library loaded. The documentation on "varpart" has not helped me to understand why I cannot call this function. Maybe I am missing something obvious because I am still an 'R' novice. Below is a reproducible example for you. Thank you always for all of your help. Lindsey example: X=matrix(rnorm(30),10,3) Y=matrix(rnorm(50),10,5...

Hi, I am using venn diagram function in AMDA to plot the venn diagram. But it seems in this function, it can only plot 3 or less vectors. Is there a way to plot the venn diagram with more than 3 vectors? Please help. Thanks. Z --------------------------------- [[alternative HTML version deleted]]

Hello, I am a total beginner with ?R? and found a package ?venn? to create a venn diagram. The problem is, I cannot create the vectors required for the diagram. The manual say: "R> venn(accession, libname, main = "All samples") where accession was a vector containing the codes identifying the RNA sequences, and libname was a vector containing the codes identifying the