[R] PROBLEM: correspondence analysis with vegan

[PIKAL Petr]

Hi Julia

Do not be too much distracted by Bert's comments. I also do not have formal statistical background but R usually keeps me on track as clever people designed its functions and made big effort in providing concise help. Together with this help list it can give you pretty good base for your analysis. However you should not expect to reach mastery overnight.

Beside what have been said, your questions to this help list should include:

- some toy data, preferably obtained by

dput(head(yourdata, 20))

result copied directly to your mail.

- the code you used for your analysis
- some description what you expected and did not obtained

However I agree with Bert that I you do not have any idea how to interpret results from analysis, you are asking for trouble.

Cheers
Petr


> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Julia
> Lienert via R-help
> Sent: Wednesday, October 26, 2016 2:21 PM
> To: r-help at stat.math.ethz.ch
> Subject: [R] PROBLEM: correspondence analysis with vegan
>
> 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 me.
>
> Greetings,
> Julia
>
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