Problem with Fourth Corner Analysis

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