Thank you Stéphane!  That fixed the problem perfectly.





On Mon, Apr 15, 2013 at 12:20 PM, Stéphane Dray <stephane.dray@univ-lyon1.fr
> wrote:

> use row.names = 1 in your read.table. Here, you have an extra-column in
> each data.frame.
>
> Cheers.
>
>
> On 15/04/2013 18:04, daniel hanks wrote:
>
>> Dear All,
>>
>> I am trying to run a fourth corner analysis and I am having trouble. In
>> order to try to work out my problem I have set up dummy data for the
>> species, habitat, and traits as three separate Excel files and imported
>> them into R as below:
>>
>> dumbhab=read.table("dumbhab.**csv", head=T, sep=",")
>> dumbtraits=read.table("**dumbtrait.csv", head=T, sep=",")
>> dumbspecies=read.table("**dumbspecies.csv", head=T, sep=",")
>>
>> They look as such in R:
>>
>>
>>  head(dumbhab)   X   H1    H2    H3
>>>
>> 1 R1  low small  tall
>> 2 R2 high small short
>> 3 R3  low small  tall
>> 4 R4  low small  tall
>> 5 R5 high small short
>> 6 R6 high large short
>>
>>
>>
>>  head(dumbspecies)   X sp1 sp2 sp3 sp4 sp5 sp6 sp7 sp8 sp9 sp10
>>>
>> 1 R1   1   0   0   0   1   1   1   0   0    1
>> 2 R2   0   1   0   1   1   1   0   0   1    1
>> 3 R3   0   1   0   1   0   1   1   0   1    0
>> 4 R4   1   1   1   0   1   1   1   0   0    0
>> 5 R5   0   1   0   1   0   0   0   0   0    0
>> 6 R6   1   1   0   1   0   1   0   1   0
>>
>>
>>
>>  head(dumbtraits)    X TR1 TR2 TR3
>>>
>> 1 Sp1 yes yes yes
>> 2 Sp2  no yes  no
>> 3 Sp3  no yes  no
>> 4 Sp4 yes yes yes
>> 5 Sp5 yes  no yes
>> 6 Sp6 yes  no yes
>>
>>
>> I then have combined them into a single list with:
>>
>> dumb.list=list(species=**dumbspecies,hab=dumbhab,**traits=dumbtraits)
>>
>> The mode of the list is:
>>
>>
>>  mode(dumb.list)[1] "list"
>>>
>>
>> The structure of the list is:
>>
>>
>>  str(dumb.list)List of 3
>>>
>>   $ species:'data.frame':       10 obs. of  11 variables:
>>    ..$ X   : Factor w/ 10 levels "R1","R10","R2",..: 1 3 4 5 6 7 8 9 10 2
>>    ..$ sp1 : int [1:10] 1 0 0 1 0 1 1 0 1 0
>>    ..$ sp2 : int [1:10] 0 1 1 1 1 1 1 0 1 0
>>    ..$ sp3 : int [1:10] 0 0 0 1 0 0 0 0 0 1
>>    ..$ sp4 : int [1:10] 0 1 1 0 1 1 1 1 0 0
>>    ..$ sp5 : int [1:10] 1 1 0 1 0 0 0 1 0 0
>>    ..$ sp6 : int [1:10] 1 1 1 1 0 1 0 1 1 1
>>    ..$ sp7 : int [1:10] 1 0 1 1 0 0 1 1 1 0
>>    ..$ sp8 : int [1:10] 0 0 0 0 0 1 0 1 1 1
>>    ..$ sp9 : int [1:10] 0 1 1 0 0 0 1 1 0 1
>>    ..$ sp10: int [1:10] 1 1 0 0 0 1 1 0 1 0
>>   $ hab    :'data.frame':       10 obs. of  4 variables:
>>    ..$ X : Factor w/ 10 levels "R1","R10","R2",..: 1 3 4 5 6 7 8 9 10 2
>>    ..$ H1: Factor w/ 2 levels "high","low": 2 1 2 2 1 1 2 2 2 1
>>    ..$ H2: Factor w/ 2 levels "large","small": 2 2 2 2 2 1 2 1 2 1
>>    ..$ H3: Factor w/ 2 levels "short","tall": 2 1 2 2 1 1 2 1 2 2
>>   $ traits :'data.frame':       10 obs. of  4 variables:
>>    ..$ X  : Factor w/ 10 levels "Sp1","Sp10","Sp2",..: 1 3 4 5 6 7 8 9 10
>> 2
>>    ..$ TR1: Factor w/ 2 levels "no","yes": 2 1 1 2 2 2 2 2 1 2
>>    ..$ TR2: Factor w/ 2 levels "no","yes": 2 2 2 2 1 1 1 1 2 1
>>    ..$ TR3: Factor w/ 2 levels "no","yes": 2 1 1 2 2 2 2 1 1 2
>>
>>
>> However, when I try to run the analysis I get the error message below.
>>  Can
>> someone please help me out?
>>
>>
>>  dumb.try<-fourthcorner(dumb.**list$hab,dumb.list$species,**
>>> dumb.list$traits,nrepet=99)**Error in if (any(tabL < 0)) stop("negative
>>> values in table L") :
>>>
>>    missing value where TRUE/FALSE neededIn addition: Warning message:In
>>
>> Ops.factor(left, right) : < not meaningful for factors
>>
>>
>>
>> Many Thanks!
>>
>>
>>
>> Daniel
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
> Stéphane DRAY (stephane.dray@univ-lyon1.fr)
> Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
> 43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
> Tel: 33 4 72 43 27 57       Fax: 33 4 72 43 13 88
> http://pbil.univ-lyon1.fr/**members/dray/<http://pbil.univ-lyon1.fr/members/dray/>
>
>
>
>


-- 
Daniel Hanks
President of WVU chapter of The American Fisheries Society
PhD Candidate-Fisheries Biology
West Virginia University
rdhanks@gmail.com
rhanks@mix.wvu.edu
Office:  304.293.0040
Cell:  864.200.8167

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