[adegenet-forum] DaPC vs. BAPS results question

[Thibaut Jombart]

Hello,

the results will be a bit more stable if you increase the number of
starting points for the k-means (see arg. n.start).

It should not really impact the outcome though: here, any K from 2 to 12 is
an equally good solution, at least as judged by the BIC.

Cheers
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR <http://twitter.com/TeebzR>

On 6 December 2016 at 15:17, Felipe Hernández <fhernandeu at uc.cl> wrote:

> Thanks Thibaut,
>
> Here you have the image and values for each estimated K. Any advice is
> more than welcome, thanks!
>
> Best,
> Felipe
>
> > grp
> $Kstat
>      K=1      K=2      K=3      K=4      K=5      K=6      K=7      K=8
> 1494.756 1481.467 1473.864 1472.002 1470.633 1472.970 1470.754 1472.011
>      K=9     K=10     K=11     K=12     K=13     K=14     K=15     K=16
> 1471.813 1473.632 1473.924 1476.759 1476.699 1475.433 1479.546 1481.119
>     K=17     K=18     K=19     K=20     K=21     K=22     K=23     K=24
> 1481.292 1485.865 1488.130 1488.356 1493.552 1494.979 1501.182 1499.258
>     K=25     K=26     K=27     K=28     K=29     K=30     K=31     K=32
> 1500.146 1504.113 1511.598 1511.550 1513.889 1516.275 1522.144 1524.733
>     K=33     K=34     K=35     K=36     K=37     K=38     K=39     K=40
> 1528.089 1530.409 1535.778 1538.049 1541.269 1546.197 1547.656 1552.127
>
> $stat
>      K=5
> 1470.633
>
>
>
> 2016-12-05 10:10 GMT-05:00 Thibaut Jombart <thibautjombart at gmail.com>:
>
>> Dear Felipe,
>>
>> this is always a hard question, as different methods essentially do..
>> different things. The K-means in find.clusters optimizes the variance
>> between groups, while BAPS maximizes a likelihood function under a
>> given population genetics model. So it may be the case that you have
>> ~17 demes roughly at HWE, but that only 4-5 groups are optimum in
>> terms of clearly delineated groups. And this is assuming both methods
>> are 'right'. They may be prone to all sorts of biases. Namely, largely
>> different group variances for the K-means, and deviations from the
>> original model in BAPS.
>>
>> Feel free to post the image (or a link to it) of the BIC for
>> find.clusters if you want a 2-cents advice on the number of K to look
>> at.
>>
>> Best
>> Thibaut
>>
>> --
>> Dr Thibaut Jombart
>> Lecturer, Department of Infectious Disease Epidemiology, Imperial College
>> London
>> Head of RECON: repidemicsconsortium.org
>> sites.google.com/site/thibautjombart/
>> github.com/thibautjombart
>> Twitter: @TeebzR
>>
>>
>> On 5 December 2016 at 14:29, Felipe Hernández <fhernandeu at uc.cl> wrote:
>> > Good morning,
>> >
>> > I wonder if you may guide me with this question (that may be pretty
>> basic
>> > surely). After a run DaPC analysis using adegenet, I'm usually getting K
>> > between 4 and 5 for my dataset (480 hogs, 59 microsats, 39 sampling
>> sites).
>> > Maximum number of clusters tried are 40. Afterwards, I tried to estimate
>> > number of clusters (spatial clustering by individuals) using another
>> > software (BAPS 6.0), but I got an even higher number of estimated
>> cluster
>> > (K=17), after testing different maximum number of K's (i.e., K=5 through
>> > K=20). Any clue about what's the reason of this? Maybe related to the
>> > maximum number of cluster tested? Or, linkage disequilibrium between
>> some
>> > loci? Sorry if the question is really basic, but I would appreciate any
>> > advice.
>> >
>> > Regards,
>> > Felipe
>> >
>> > --
>> > Felipe Hernández
>> > Médico Veterinario (DVM), MSc.
>> > PhD. Candidate
>> > Interdisciplinary Ecology Program
>> > School of Natural Resources and Environment
>> > Wildlife Ecology and Conservation Department
>> > University of Florida
>> >
>> > _______________________________________________
>> > adegenet-forum mailing list
>> > adegenet-forum at lists.r-forge.r-project.org
>> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo
>> /adegenet-forum
>>
>
>
>
> --
> Felipe Hernández
> Médico Veterinario (DVM), MSc.
> PhD. Candidate
> Interdisciplinary Ecology Program
> School of Natural Resources and Environment
> Wildlife Ecology and Conservation Department
> University of Florida
>
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