Hi Thibaut! <br>I'm remembering what you say "<i>you can read anything into R, with more or less pain</i>"... I'm experiencing some pain with dists again... Here is the thing. I have a bootstraped file with 1000 dist matrices from AFLPsurv... but they are square matrices... grrr.... I cannot use the <span style="font-family: courier new,monospace;">as.dist</span> function directly to transform them to triangular matrices. How can I do it? Do I need a loop? And then, if I manage it, how can I export them? I tried to export a single triangle matrix (using <span style="font-family: courier new,monospace;">write.table</span>) and it says "<span style="font-family: courier new,monospace;">cannot coerce class "dist" into a data.frame</span>"... Tricky...<br>
My last question (hopefully) is related to this an to my previous monmonier question. Can I use this bootstraped file (if I manage to convert it) as the dist object for the monmonier function? <br>Thank you very much!!!<br>
<br>Consuelo<br><br clear="all">-------------<br>Consuelo Hermosilla<br>PhD student<br>Departamento de Ecología y Biología Animal<br>Departamento de Bioquímica, Genética e Inmunología, Área de Genética<br>Facultad de Ciencias del Mar<br>
Campus de As Lagoas-Marcosende<br>Universidad de Vigo<br>36310 Vigo<br>SPAIN<br>Mobile: +34 692 633 298<br><br>oooO<br>( ) Oooo<br> ( ( )<br> _) ) /<br> (_/<br><br>Stop Gaza Massacre<br>
<br><br><div class="gmail_quote">On Thu, Apr 15, 2010 at 5:21 PM, Jombart, Thibaut <span dir="ltr"><<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Consuelo,<br>
<br>
good question about searching in the archives... I don't know (shame on me). My best guess for now is googling a question preceeded by 'adegenet-forum'. For instance, if you google:<br>
"adegenet-forum seppop"<br>
then you find an appropriate discussion in the archives as first answer. Lucky enough, 'adegenet-forum horse riding' does not point to anything in the archives...<br>
Thanks for pointing this out, I will mention that on the website.<br>
<br>
As for your other question: you could read a triangular matrix into R (you can read anything into R, with more or less pain), but a more straightforward way is using 'as.dist' on your rectangular matrix.<br>
<br>
M <- matrix(1:9, ncol=3)<br>
M <- M + t(M)<br>
diag(M) <- 0<br>
M # M is a symmetric matrix<br>
[,1] [,2] [,3]<br>
[1,] 0 6 10<br>
[2,] 6 0 14<br>
[3,] 10 14 0<br>
<br>
<br>
foo=as.dist(M)<br>
foo # lower triangular matrix<br>
1 2<br>
2 6<br>
3 10 14<br>
<br>
<br>
Best regards<br>
<br>
Thibaut<br>
<br>
________________________________________<br>
From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] On Behalf Of Consuelo Hermosilla [<a href="mailto:cheluna@gmail.com">cheluna@gmail.com</a>]<br>
Sent: 15 April 2010 14:48<br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: [adegenet-forum] distribution<br>
<div><div></div><div class="h5"><br>
Hello Thibaut,<br>
<br>
I'd like to know, how can I import a triangular matrix into R? For example, for amova analysis in pegas, the input distance matrix must be triangular. The thing is I have calculated the Fsts in Structure and I wanted to import them to run the Amova in pegas. But I don't know how to convert my square Fst matrix into a triangular one. I could save it as a triangular matrix, but R does not read triangular matrix, does it? Do you know how can I do it?<br>
<br>
The other thing, is there a way to search in the past threads of the forum? I mean, instead of search in each month manually?<br>
<br>
Thanks!!<br>
<br>
Consuelo<br>
<br>
-------------<br>
Consuelo Hermosilla<br>
PhD student<br>
Departamento de Ecología y Biología Animal<br>
Departamento de Bioquímica, Genética e Inmunología, Área de Genética<br>
Facultad de Ciencias del Mar<br>
Campus de As Lagoas-Marcosende<br>
Universidad de Vigo<br>
36310 Vigo<br>
SPAIN<br>
Mobile: +34 692 633 298<br>
<br>
oooO<br>
( ) Oooo<br>
( ( )<br>
_) ) /<br>
(_/<br>
<br>
Stop Gaza Massacre<br>
</div></div></blockquote></div><br>