[R] PROBLEM: correspondence analysis with vegan

Bert Gunter bgunter.4567 at gmail.com
Wed Oct 26 23:15:28 CEST 2016


1. I appreciate your honesty.

2. What follows is just my opinion. Feel free to ignore.

3. I think you are in a near impossible situation. R is a computer language
for statistics and data analysis:  you need to know both the language and
statistics to use it properly. You know neither.  So from my perspective,
there is a mismatch between your education background and what your
professor seems to expect you to know.

4. There are many good R tutorials on the web, so it shouldn't take more
than a few weeks (or days) to get up and running with R, especially if you
have  prior programming experience.

5. However, the statistics is a different matter.  By your own admission,
your statistical background is minimal; but you are being asked to use a
fairly advanced procedure (corr analysis -- whose utility and validity can
be tricky, by the way).  I do not see how you can proceed without several
semesters of the necessary statistical background -- and that assumes you
have sufficient mathematical training to take those courses!

6. So I would suggest that you sit down with your professor to discuss what
he thinks you know and what you actually know, and what course of action
you need to take to resolve any discrepancy (perhaps even a different

7. If it makes you feel any better, you are far from alone in this regard.
Many students and their professors in a variety of disciplines are misusing
statistics because of inadequate statistical understanding. That is one
reason why we have a so-called "irreproducibility" crisis in Science.

8. Again, just my fallible opinion.

Good luck!


On Oct 26, 2016 7:21 PM, "Julia Lienert via R-help" <r-help at r-project.org>
> Hello All,
> I’m Julia from Germany and I have a problem concerning the vegan package
that I can’t solve on my own (after hours and hours spent searching for a
solution). I was thrown into the topic of working with R by my professor
and wasn’t really aware that this included working with higher statistics
(since I studied pedagogy before and have not much basic statistical
knowledge or knowledge of R).
> I need to do a correspondence analysis on a dataset of vegetation samples
and species as a comma-separated csv file. I have the species names as row
names. The column names indicated zonation + land use and make up the first
row of the matrix. I set the header = TRUE.
> If I tried doing a CA or DCA with this dataset the warning “Error in
rowSums(X): ‘x’ must be numeric” appeared. According to several forums, I
then removed the first column and the CA worked and i could also apply the
envfit function and plot it.
> Now here comes my problem and question:
> when I plotted the arrows { plot(ef, p.max = 0.1) }, I got arrows labeled
with species in my ordination plot. But instead I would need the column
that indicates the zonation/land use (the first column) which I had to
remove in order for the CA/ DCA to work. Is there any way that I can
incorporate the zonation/ land use column as environmental vector after I
did the whole CA/ DCA? Or is there any way for me to do a CA/ DCA without
having to remove the first column?
> I might be missing something but I just started working with R and
haven’t got the time to really work my way in from the basics. I will do
that after this project is done but for now I just hope that you can help
> Greetings,
> Julia
> ______________________________________________
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