[R] Help with RDA analysis, function ''varpart'' in vegan

[Eric Berger]

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 at gmail.com> wrote:

> 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 the same (the sites) and there
> are different column number (measured varibakes).
>
> I use the follow script:
>
> WQ_RDA <- read.csv("F:/Sher_sophi_new3/RDA/WQ_RDA_1.csv", row.names = 1)
> LU2_loc_RDA <- read.csv("F:/Sher_sophi_new3/RDA/LU2_loc_RDA_1.csv",
> row.names = 1)
> LU2_bas_RDA <- read.csv("F:/Sher_sophi_new3/RDA/LU2_basin_RDA_1.csv",
> row.names = 1)
> comm <- read.csv("F:/Sher_sophi_new3/RDA/Final_true_OTUs_97_1.csv",
> row.names = 1)
>
> x1 = as.matrix(WQ_RDA)
> x2 = as.matrix(LU2_loc_RDA)
> x3 = as.matrix(LU2_bas_RDA)
> comm = as.matrix(t(comm))
>
> RDA_Ger = varpart(comm, x1, x2, x3, transfo="hellinger", scale = FALSE,
>                   na.action = na.omit
>
>
> I get this error message:
>
> Error in as.vector(x, mode) :
>   cannot coerce type 'closure' to vector of type 'any'
>
> Can anyone help me figure out what am I doing wrong?
>
> Thanks,
> Sophi
> --
> Sophi Marmen
> Ph.D candidate
> Marine Biology Department
> Leon H. Charney School of Marine Sciences
> University of Haifa, Israel
>
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