Sophi Marmen
2017-Sep-16 15:53 UTC
[R] Help with RDA analysis, function ''varpart'' in vegan
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]]
Eric Berger
2017-Sep-17 08:23 UTC
[R] Help with RDA analysis, function ''varpart'' in vegan
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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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]]
Bert Gunter
2017-Sep-17 14:56 UTC
[R] Help with RDA analysis, function ''varpart'' in vegan
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 <ericjberger at 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 <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 > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at 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 at 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]]