[adegenet-forum] xvalDapc confusion

[Nikki Vollmer]

Hi all,



I have used DAPC for my studies a bunch in the past, and am now curious to see how applying xvalDapc to the procedure affects things. I apologize in advance if my confusion is just a result of a brain fart due to the crappy cold weather the northeast US has been having. 



First, is xvalDapc running your DAPC or just validating the parameters (PCAs) to use for running a separate DAPC?



And related to that, what can you do with the results from xvalDapc?  For example do you run xvalDapc, see what number of PCAs give you the highest success, then run a 'regular' DAPC choosing the PCA number from xvalDapc results?  Or do you do the opposite...run DAPC first using what you think is the best number of PCAs, then run xvalDapc to validate the number of PCAs you originally chose?  Or both? (or neither?)



Ultimately I am still wanting to make a scatter plot of my groups for publication. So I supposed I still need to run a single DAPC to do that and can't use the xvalDapc results somehow...right?



Second, in the output for the xvalDapc function what are the numbers under the success column?  I was thinking they were assignment success, but if you do not specify either result="groupMean" or result="overall", which result are you getting?  I have tried it all three ways (not specifying a result, using groupMean, and using overall) and have gotten very different numbers for each (all are close to or above 0.90, but results become more variable when I specify a result argument).  



Thank you in advance for any help you can offer, I really appreciate it!



Nikki
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