[R] Need Help

Petr PIKAL petr.pikal at precheza.cz
Fri Nov 18 09:27:00 CET 2011

> Hi,
> I need to make a subset of my species abundance matrix with only species 

> (columns) that have a total abundance(column sum) greater than 0.5 to do 

> ordination in vegan package. I used following code but it is not 
> Can you please give me a solution.
> gl1<- subset(grassland[,5:44], colSums > 0.05, select=2)

Hm. How did you got this code?



you limit subset to only columns 5:44

function colSums does not know what to sum

by select=2 you are choosing only column 2.

So it is rather weird collection of commands.

grassland[, colSums(grassland) > 0.05]

selects all columns for which their sum is over 0.05. What you want to do 
next is up to you.


> gl1 is my new matrix ,and  grassland[,5:44] is my original matrix.
> thanks,
> Dilshan
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