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 <ericjber...@gmail.com> 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 <sofimar...@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 > > > > [[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. > > > > [[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. > [[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.