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I am using indicator species analysis using the package labdsv with the indval function

I am new to R and was getting ISA to work previously, but now on my applied data and it is throwing off this error which I cannot seem to resolve. I was wondering if anyone could please help me.

I have a subject x OTU table (26 x 345) The OTUs are in columns and the Rows are the subjects.

My groupings file is also attached containing membership of each subject to 1 (cure) or 2 (relapse)

Subject Groups
    101      1
    102      1
    104      1
    107      1
    108      1
    109      1
    110      1
    112      1
    113      1
    116      1
    122      1
    124      1
    125      1
    126      1
    128      1
    129      1
    134      1
    103      2
    105      2
    114      2
    117      2
    120      2
    130      2
    131      2
    133      2

When I run the indval analysis, I consistently get this error. I cannot seem to understand anything from the message groups from those who got a similar error.

Error in sort.list(y) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a list?

Here is my code and subsequent error

library(labdsv)
family=read.delim("clipboard", row.names=1)
groupings=read.delim("clipboard", row.names=1)
out=indval(family,groupings, numitr=10000)

Error in sort.list(y) : 'x' must be atomic for 'sort.list'
Have you called 'sort' on a list?
vijayantharam
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  • 2
  • It is difficult to provide a clear answer since family and groupings are read from your clipboard. I may suggest that you import your data using read.csv and make sure they look good after import. – essicolo Apr 20 '15 at 02:58
  • Feel free to convey the information to us in any form as suggested in [this post](http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). – Roman Luštrik Apr 20 '15 at 05:12

0 Answers0