Take a look at your data.  When I loaded what you attached, there were only
9 species that were in common across the two files:

> dim(s16)
[1] 226  83
> dim(s15)
[1] 96 41
> sum(s15$species %in% s16$species)
[1] 10
> sum(s16$species %in% s15$species)
[1] 10
> length(intersect(s16$species, s15$species))
[1] 9
> length(unique(s16$species))
[1] 173
> length(unique(s15$species))
[1] 90
> x <- merge(s16, s15, by = 'species')
> dim(x)
[1]  12 123
>

so it is not surprising you got the result that you did.



On Thu, Mar 14, 2013 at 6:51 AM, Michael Eisenring <michael.eisenring@gmx.ch
> wrote:

> Dear R-help members
>
> I would be grateful if anyone could help me with the following problem:
>
> I would like to combine two matrices (Schmitt_15 and Schmitt_16, they are
> attached) which have a  species presence/absence x sampling plot structure.
> The aim would be to have in the end only one matrix which shows all
> existing species and their presence/absence on all the different plots.
> To do this I used the "merge" function in R.
> The problem is that my matrix in the end shows only 12 species (but there
> are in total about 100!). I don't know why.
>
> I used the following commands:
>
>
> Schmitt_15
> Schmitt_16
> output<-merge(Schmitt_15,Schmitt_16,by="species")
> write.table(ab,file="output.txt",sep=",")
>
> Can anyone help me?
> Thank you very much!
> Michael
>
>
>
>
> ______________________________________________
> R-help@r-project.org mailing list
> 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.
>
>


-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.

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