[R-sig-eco] [vegan]Error in as.vector(x, mode) : , cannot coerce type 'builtin' to vector of type 'any' when perfroming a cca on a dataframe

[Jari Oksanen]

Dear Tim Richter,

Some minimal information is the version of vegan you are using: we have just redesigned the permutation functions in github and R-Forge and it is essential to know where to look at (and we are not too keen to look at the code that will be thrown away in the next release later within a few days).

Secondly, you could give us a traceback() of the error. When you get the error, just type:

traceback()

copy and paste the message and send it to us. This at least tells us where you get the error.

Thirdly, this is a question specific to the vegan package and may not be too exciting for the general public. You may consider contacting the package maintainers directly. 

Cheers, Jari Oksanen
________________________________________
From: r-sig-ecology-bounces at r-project.org <r-sig-ecology-bounces at r-project.org> on behalf of Tim Richter-Heitmann <trichter at uni-bremen.de>
Sent: 13 October 2014 16:49
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] [vegan]Error in as.vector(x, mode) : , cannot coerce type 'builtin' to vector of type 'any' when perfroming a cca on a dataframe

Hi there,

i have three dataframes, which have the same structure (data.frame, 358
observations of 340 variables, every column is "num"eric), and are
basically submatrices of a parental dataset.

I can perform a CCA on all of them (with the explanatory dataset being
"abio")

/cca1_ab <- cca(df1~., data=abio)/

I can also perform an anova on all three cca-derived values

/anova(cca1_ab)/

However, if i do

/sig1_ab<-anova(cca1_ab, by="term", perm=200)/

which i believe gives me confidence values for the fitting of the
explanatory variables, only one of the cca-derived values gives an
unexpected

Error in as.vector(x, mode) : ,  cannot coerce type 'builtin' to vector
of type 'any'

The same is true when i try to perform an ordistep forward selection.
The other two are working fine. Its hard to come up with an explanation,
as the datasets look and behave the same otherwise.

Any idea why this could happen?

I am sorry for not providing data for reproduction, as the data sets are
pretty large.

--
Tim Richter-Heitmann (M.Sc.)
PhD Candidate



International Max-Planck Research School for Marine Microbiology
University of Bremen
Microbial Ecophysiology Group (AG Friedrich)
FB02 - Biologie/Chemie
Leobener Stra�e (NW2 A2130)
D-28359 Bremen
Tel.: 0049(0)421 218-63062
Fax: 0049(0)421 218-63069


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