HELP Index of association --> strange graph!

[Chiara Pedrazzini]

Hi, 

I have a question/problem with the index of association. Indeed, I have 2 species and 2 datasets, stored as genind objects, obj_1i and obj_2i (obj_1i is much bigger than obj_2i).

1.  > obj_1i

/// GENIND OBJECT /////////

 // 413 individuals; 974 loci; 2,870 alleles; size: 5.2 Mb

 // Basic content

   @tab:  413 x 2870 matrix of allele counts

   @loc.n.all: number of alleles per locus (range: 2-3)

   @loc.fac: locus factor for the 2870 columns of @tab

   @all.names: list of allele names for each locus

   @ploidy: ploidy of each individual  (range: 1-1)

   @type:  codom

   @call: .local(x = x, i = i, j = j, loc = ..1, drop = drop)

 // Optional content

   @pop: population of each individual (group size range: 2-21)

   @strata: a data frame with 7 columns ( pop, country, Year, LAT, LON, mat, ... )

2. > obj_2i

/// GENIND OBJECT /////////

 // 241 individuals; 87 loci; 242 alleles; size: 327.3 Kb

 // Basic content

   @tab:  241 x 242 matrix of allele counts

   @loc.n.all: number of alleles per locus (range: 2-3)

   @loc.fac: locus factor for the 242 columns of @tab

   @all.names: list of allele names for each locus

   @ploidy: ploidy of each individual  (range: 1-1)

   @type:  codom

   @call: .local(x = x, i = i, j = j, loc = ..1, drop = drop)

 // Optional content

   @pop: population of each individual (group size range: 1-16)

   @strata: a data frame with 7 columns ( pop, country, Year, LAT, LON, mat, ... )

When I perform analyses of index association I get results for the the second genind object (obj_2i) and strange results for the first.. or well, I get a graph showing the observerved rd, but the is no re-sampled distribution, even with very high permutations. I attached the pictures with the function I used... I don't understand, what does that mean?

Thank you very much in advance for your help!

Chiara