----- Forwarded message from
[email protected] -----
Date: Sun, 25 Nov 2012
16:54:27 -0800
From: [email protected]
Reply-To: [email protected]
Subject: Re: UPGMA:
Euclidean and Procrustes distances
To:
[email protected]
----- Forwarded message from
Carlos Eduardo R D Alencar
Date:
Sat, 24 Nov 2012 11:36:40 -0500
From: Carlos Eduardo R D Alencar
Reply-To: Carlos Eduardo R D Alencar
Subject: Re: UPGMA: Euclidean and Procrustes
distances
To:
[email protected]
Dear Rodrigo,
Good question. That was one of the doubts that I had in mind and were well clarified. My use was to check similarities between groups of crabs in different species and locations.
Well, in a second time you might want to check what the best method of biding grouping (clustering). I would like to leave a tip, according to analyzes already performed by me (in several aspects) morphological, ecological (communities) and etc. ... UPGMA method was not very well. My assessment is based on two coefficients (cophenetic correlation coefficient and aglomeration coefficient). Maybe you want to test them before using the UPGMA.
Cheers
Carlos
--
Carlos Eduardo R. D. Alencar
Biólogo, Msc.
Good question. That was one of the doubts that I had in mind and were well clarified. My use was to check similarities between groups of crabs in different species and locations.
Well, in a second time you might want to check what the best method of biding grouping (clustering). I would like to leave a tip, according to analyzes already performed by me (in several aspects) morphological, ecological (communities) and etc. ... UPGMA method was not very well. My assessment is based on two coefficients (cophenetic correlation coefficient and aglomeration coefficient). Maybe you want to test them before using the UPGMA.
Cheers
Carlos
On Mon, Nov 19, 2012 at
6:41 PM, <[email protected]>
wrote:
Date: Mon, 19 Nov 2012 10:46:37 -0500
----- Forwarded message from Rodrigo Lima -----Subject: RE: UPGMA: Euclidean and Procrustes distances
From: Rodrigo Lima
Reply-To: Rodrigo Lima
To: "[email protected]"Dear Andrea, Oyvind, and Philipp,
Thank you very much for your answers, they totally clarified my doubts.
Best wishes,
Rodrigo
From: [email protected] [[email protected]]
Sent: November 18, 2012 1:40 AM
To: [email protected]
Subject: Re: UPGMA: Euclidean and Procrustes distances
----- Forwarded message from Philipp Mitteröcker -----
Date: Fri, 16 Nov 2012 11:18:49 -0500
From: Philipp Mitteröcker
Reply-To: Philipp Mitteröcker
Subject: Re: UPGMA: Euclidean and Procrustes distances
To: [email protected]
Euclidean distances are equal to Procrustes distances in tangent space, so they are close enough to the original Procrustes distances.
Best,
Philipp
Am 15.11.2012 um 20:32 schrieb [email protected]:
----- Forwarded message from Rodrigo Lima -----
Date: Thu, 15 Nov 2012 12:21:28 -0500
From: Rodrigo Lima
Reply-To: Rodrigo Lima
Subject: UPGMA: Euclidean and Procrustes distances
To: "[email protected]"
Dear morphometricians,
I would greatly appreciate your input on this matter:
The context: I am studying 9 populations of a small rodent species and I wanted to represent morphological relationships between populations using a UPGMA cluster analysis.
The problem: I used the mean population shapes (Procrustes coordinates) to do this analysis in PAST using Euclidean distances and got a nice tree with bootstrap values, but there is no option for using Procrustes distances in this package. I get the same topology using Procrustes distances with R, but I can’t get the bootstrap values on the nodes of the tree.
The questions:1 - Are UPGMA analyses using Euclidean distances and Procrustes distances equivalent?2 - Is there any package in which I could simply enter the Procrustes distances and get a UPGMA tree with bootstrap values?
Thank you in advance,Rodrigo
----- End forwarded message -----
___________________________________
Dr. Philipp Mitteroecker
Department of Theoretical Biology
University of Vienna
Althanstrasse 14
A-1090 Vienna, Austria
Tel: +43 1 4277 56705
Fax: +43 1 4277 9544
email: [email protected]
homepage: http://theoretical.univie.ac.at/people/mitteroecker
----- End forwarded message -----
----- End forwarded message -----
--
Carlos Eduardo R. D. Alencar
Biólogo, Msc.
[email protected]
Bolsista CAPES - Programa de Pós-graduação em Ecologia - PPGE
Grupo de Estudos em Ecologia e Fisiologia de Animais Aquáticos - GEEFAA [www.geefaa.com]
Bolsista CAPES - Programa de Pós-graduação em Ecologia - PPGE
Grupo de Estudos em Ecologia e Fisiologia de Animais Aquáticos - GEEFAA [www.geefaa.com]
Departamento de Botânica, Ecologia e Zoologia - DBEZ
Universidade Federal do Rio Grande do Norte - UFRN
Universidade Federal do Rio Grande do Norte - UFRN
----- End forwarded message -----
----- End forwarded message
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