Zhiang
I have a new fun question about the calculation of Bruvo distances: Using an infinite alleles model, I can do pieces of the analysis by hand and a few of the numbers are still a bit odd. For example, if I do an infinite alleles bruvo matrix distance (which I think is coded with the flags: add=FALSE, loss=FALSE) on the samples pasted below with two individuals and two microsatellite alleles (one sample diploid and one triploid) it doesn't seem to recognize the shared allele of 190 in the Mar2 locus.
Using band sharing (replen = c(0.00001,0.00001)) the distance given is 1.0, which is not correct (should be 0.83333). I don't think this is a problem with my band sharing trickwith c(2,2) the distance is 0.9739126, which is still too high.
If I add a new size instead of the final 0 (like 2, for instance), I get 0.83333, the expected value. Also, if I replace the 210 with 0, so that both individuals are diploid I get 0.75, as expected. I don't know if this a problem with the way I am formatting things, or if there is something strange going on with the calculations across different ploidy levels.
One possible explanation is that the (add=FALSE, loss=FALSE) is not doing the Infinite alleles model or doing something odd. Interestingly if I type (add=TRUE, loss=FALSE) then I get 0.83333, which is the correct answer with the gene addition model (in this example, both models should give 0.83333). If I replace 203 with 214, then GAM (add=TRUE, loss=FALSE) gives 0.66667 (correct), but Infinite alleles (add=FALSE, loss=FALSE) gives 0.83333 (incorrect).
As I said, most of the numbers are exactly as expected (and the diploid numbers are exactly as I would expect), so overall this doesn't have a huge effect on the analyses, but I would like to figure it out.
Sorry, for the long rambling attempt at explanation here and I would greatly appreciate help. It is likely that there is something I am not understanding.
In addition to this problem most or all mixed ploidy calculations are slightly lower than expected when I do my full analysis with 10 loci, but I haven't figured out exactly how that happens yet. It doesn't seem to happen when I use subsets of two locionly when I use all 10. If I figure it out I will update and let you know to disregard my rambling.
Thanks.
Michael
Ind 

Mar1 


Mar2 


A11H 
1 
242 
236 
228 
214 
190 
210 
A10T 
1 
226 
211 
0 
203 
190 
0 























