Help with RDA analysis, function ''varpart'' in vegan

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Help with RDA analysis, function ''varpart'' in vegan

SophiM
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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Re: 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 <[hidden email]> 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
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.
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Re: Help with RDA analysis, function ''varpart'' in vegan

Bert Gunter-2
Doubt that will make any difference.

My guess is that there is a function in the environment that varpart wants
to use as an object -- i.e. there is a scoping bug in varpart. But that
could be baloney, too.

Please learn about R's debugging tools. Give us the results of traceback()
after the error.

-- Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Sun, Sep 17, 2017 at 1:23 AM, Eric Berger <[hidden email]> wrote:

> 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 <[hidden email]>
> 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
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] 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.
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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and provide commented, minimal, self-contained, reproducible code.
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Re: Help with RDA analysis, function ''varpart'' in vegan

Jari Oksanen
In reply to this post by SophiM
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
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.