Problem with SimilarityMult for q=1

[fvdperre]

Dear,

I wanted to calculate pairwise similarities for a species x sites matrix using the function SimilarityMult.
Calculating this for q = 1 gave, for some communities, similarity values higher than 1.

On Github, I saw that the package was recently corrected, so I reinstalled it.
The problem is still not solved, and even worse, for some matrices I now get errors when calculating similarities at q1:
Error in rmultinom(1, n[2], p_hat[, 2]) : non-positive probability
In addition: Warning message:
In w * (1 - X/n)^n : longer object length is not a multiple of shorter object length

I tried to google this error, but I can’t seem to find what went wrong.
Again, I did not get this error with the previous version of SpadeR.

Could you please help me solving these two issues?
I included the data I used: q1.txt (gives similarities at q1 bigger than 1) and Error.txt (gives the abovementioned error at q1).

Thank you in advance.
Error.txt
q1.txt

Frederik Van de Perre

[fvdperre]

To add some more details to my previous comment:

1. I get errors when comparing specific sites, in this case site7 and 8:

SimilarityPair(data[,c(1,7)],nboot=200,datatype=datatype)
Error in rmultinom(1, n[2], p_hat[, 2]) : non-positive probability
In addition: Warning message:
In w * (1 - X/n)^n :
longer object length is not a multiple of shorter object length
SimilarityPair(data[,c(1,8)],nboot=200,datatype=datatype)
Error in if (var_ace > 0) { : missing value where TRUE/FALSE needed

2. The similarities higher than 1 at q1 are due to the estimation of the index.
   There must be something wrong with the estimation; even if I compare a site with itself, the estimation gives mistakes:
   Equal-effort:

   Bray-Curtis (observed) 1.0000 0.0651
   Bray-Curtis (estimated) 1.0000 0.0868
   Horn (observed) 1.0000 0.0346
   Horn (estimated) 1.1677 0.0955

3. Because of all the errors, I would like to avoid using SimilarityPair. However, SimilarityMult doesn't have the option to work with incidence data.
   I tried converting incidence data to frequencies, but then I get an error. Obviously, removing the first line, where the number of sampling units is specified, and considering the incidences as abundances gives incorrect values...

I would really like to use your package, but because of all the errors and mistakes, I'm completely stuck. Can you please help me out?