<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Marcin,<div><br></div><div>You should have a look at the following paper:</div><div><br></div><div>Revell L. J. 2009 Size-correction and principal components for interspecific comparative studies. Evolution 63:3258-3268</div><div><br></div><div>Liam provides code in the paper to run Phylogenetic PCA on species data (not contrasts) in R and Matlab. It works well, I've used it myself.</div><div><br></div><div>Cheers,</div><div><br></div><div>Alejandro</div><div><br></div><div> <br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>__________________________________</div><div><br></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Alejandro Gonzalez Voyer</span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Post-doc</span></font></div><div><br></div><div><font class="Apple-style-span" color="#E01717"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px; "><b>NEW ADDRESS & NEW E-MAIL</b></span></font></font></div><div><br></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Estación Biológica de Doñana (CSIC)</span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Avenida Américo Vespucio s/n</span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">41092 Sevilla </span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Spain</span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br></span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">E-mail: <a href="mailto:alejandro.gonzalez@ebd.csic.es">alejandro.gonzalez@ebd.csic.es</a></span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br></span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Tel: +34- 954 466700, ext 1749</span></font></div><div><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px; "><br></span></font></div></div></div></span></div></span></div></span></div></span></div></span></div></span>Website (From my previous position): <a href="http://www.iee.uu.se/zooekol/default.php?type=personalpage&lang=en&id=146">http://www.iee.uu.se/zooekol/default.php?type=personalpage&lang=en&id=146</a></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
</div>
<br><div><div>On Feb 8, 2010, at 12:43 PM, Marcin Czarnoleski wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi,<br>I would be grateful for an advice how to solve my problem with <br>phyllogenetic analysis pased on PCA (possibly with Mesquite). I use data <br>on some traits of several species. I would like to use PCA to calculate <br>PC scores from these traits, and use these scores to correlate with <br>other characters of the species. But I would like to correct my analysis <br>on a phylogentic signal. So basically, I should calculate <br>phylogenetically corrected PC scores and then correlate them with <br>contrasts of other species characters. But I have a question, should I <br>first run PCA on raw data, and then calculate contrasts of the PC scores <br>obtained from this PCA, and finally use these contrasts in correlattions <br>with contrasts of other characters of species. Or alternativelly, I <br>should run PCA on contrasts of species traits, and then use scores of <br>these PCs to correlate them with contrasts of other charactes of <br>species? If the second approach is recommended then I see two problems. <br>First, to run PCA on contrasts it is adviced to use correlation matrix <br>from contrasts (but correlations are forced through 0 and positivised). <br>If I calculate such matrix and use it as an input file for PCA in an <br>ordinary statistical software, I am unable to calculate PC scores <br>because the information about species (cases) is missing (correlation <br>matrix provides PCA only with correlation coefficients). So withought <br>the scores I cannot proceed further and test correlations between <br>phylogenetically corrected PC scores and contrasts of other traist. <br>Second, even if I was able to obtain phylogenetically corrected PC <br>scores, how should I analyse their correlation with contrasts of other <br>traits. I understand that a normal correlation on contrasts requires <br>prior positivisation and forcing through 0, but I am not sure what <br>should be done in terms of this requirement in the case of scores vs <br>contrasts correlation. I should be grateful for any opinion on my <br>problem and I would be also grateful for the information whether <br>Mesquite can help solve my problem.<br>Marcin Czarnoleski<br>_______________________________________________<br>Mesquitelist mailing list<br><a href="mailto:Mesquitelist@mesquiteproject.org">Mesquitelist@mesquiteproject.org</a><br>http://mesquiteproject.org/mailman/listinfo/mesquitelist<br></div></blockquote></div><br></div></body></html>