[adegenet-forum] dapc technical definitions

valeria montano mirainoshojo at gmail.com
Thu Jun 9 14:50:44 CEST 2011


Many thanks for the answer. Now, I should be able to avoid improper writing

Cheers

Valeria

On 9 June 2011 12:47, Martin Llewellyn <llewellynmartin at hotmail.com> wrote:

>  Dear Thimbaut,
>
> Thanks very much for the new tutorial. Most helpful for preparing figures.
> Is there a full list of allowed colours somewhere ? lightpurple, for
> example, and perhaps for reasons of taste, is not recognised
>
> All the best
>
> M
>
> ------------------------------
> From: t.jombart at imperial.ac.uk
> To: mirainoshojo at gmail.com; adegenet-forum at r-forge.wu-wien.ac.at
> Date: Thu, 9 Jun 2011 09:03:34 +0000
> Subject: Re: [adegenet-forum] dapc technical definitions
>
>
>  Dear Valeria,
>
> discriminant functions are principal components of DA. I use the first
> terminology to prevent ambiguity with PCs of PCA, also used in the method.
>
> Eigenvalues indicate the between/within variance ratio of the corresponding
> discriminant functions. The first eigenvalue is the largest ratio achievable
> using linear combinations of PCs of the PCA. The sum of the eigenvalues is
> merely the sum of these ratio computed for all retained variables. It is an
> indicator of how much between-group variation there is overall in the data,
> but I've never used this information so far.
>
> Cheers
>
> Thibaut
>
>
>    ------------------------------
> *From:* adegenet-forum-bounces at r-forge.wu-wien.ac.at [
> adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of valeria montano
> [mirainoshojo at gmail.com]
> *Sent:* 07 June 2011 18:49
> *To:* adegenet-forum at r-forge.wu-wien.ac.at
> *Subject:* [adegenet-forum] dapc technical definitions
>
>  Dear Thibaut,
>
>  I swear I read the DAPC tutorial, but I couldn't completely clarify
> myself about a couple of stupid things. If I missed them, feel free to
> answer "see page xx" and that's it.
>
>  First, when I refer to the eigenvalues 1, 2 and so on, do I have to say
> discriminant "functions" or can I also use the world component? I didn't use
> this last, but it would be easier to make people absorb them, as it's a new
> method (anyway if it's wrong no probs). Another stupid thing, when referring
> to the highest eigenvalue, I wrote something like: "this is the value which
> shows the highest ratio of among/within group variance"...is that the
> correct definition? (maybe not really elegant).
> Is there any parallel I can do with "the variance explained by this
> component is x"? Does it make sense to calculate the total of the
> eigenvalues of the discriminant functions to assign a % of the
> discrimination ratio they explain?
>
>  well, thanks in advance! (sorry for the chaos!)
>
>  Valeria
>
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