[adegenet-forum] DAPC

[Carly Graham]

Hello,

I have been looking at the population structure of whitefish in a small lake area. I used xvalDapc to determine the optimal number of PCs to retain for the dapc analysis. When I look at the output from this xval command I see that the following:

$`Median and Confidence Interval for Random Chance`
      2.5%        50%      97.5% 
0.08354526 0.12267036 0.17258877 

$`Mean Successful Assignment by Number of PCs of PCA`
       20        40        60        80       100       120       140       160       180 
0.1319444 0.1694444 0.1680556 0.1875000 0.2013889 0.1291667 0.1666667 0.1250000 0.1125000 

$`Number of PCs Achieving Highest Mean Success`
[1] "100"

$`Root Mean Squared Error by Number of PCs of PCA`
       20        40        60        80       100       120       140       160       180 
0.8704578 0.8361065 0.8360719 0.8177360 0.8051124 0.8730468 0.8389395 0.8772458 0.8905042 

$`Number of PCs Achieving Lowest MSE`
[1] "100"


From this I have interpreted that I should use 100 PCs. From there when I run the dapc with 100 PCs and then look at output from summary(dapc) I have an assignment probability of 0.8701923. Where I am confused is how to interpret the “Mean Successful Assignment” from the above output. Does this also correspond to the assignment to populations? If so, is it more accurate to assume that the assignment probability is 0.2013889?

Thanks,


Carly Graham
PhD Candidate
University of Regina





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