Mariana, The ‘$’ symbol is used when attempting to extract a component from a list. It is not required in most other circumstances.
If you want to send me your script and data off-line (i.e., not to clutter the list) I am willing to work with you to see what syntax needs to be adjusted. Best, Dean Dr. Dean C. Adams Director of Graduate Education, EEB Program Professor Department of Ecology, Evolution, and Organismal Biology Iowa State University https://www.eeob.iastate.edu/faculty/adams/ phone: 515-294-3834 From: Mariana Díaz Santana Iturrios <[email protected]> Sent: Sunday, February 14, 2021 9:43 AM To: Adams, Dean [EEOB] <[email protected]> Cc: [email protected] Subject: Re: [MORPHMET2] Doubt regarding compare.evol.rates function of Geomorph r package Thank you for your answers, it was helpful to know that I do not have to merge the files to run the analysis. I runned compare.evol.rates and it marks the following error "tree must be of class phylo". If I check the class of my tree: class(tree2), it indicates that it is indeed class phylo. It is worth noting that when I run compare.evol.rates, "phy" is not an option when I use $ symbol on tree2 (tree2 is the name of my phylogenetic tree). I really appreciate your attention and help. El dom, 14 feb 2021 a las 11:24, Adams, Dean [EEOB] (<[email protected]<mailto:[email protected]>>) escribió: Mariana, The phylogeny and data do not be combined into a single file, but do need to be called separately by the function. If you see the help file, the example has: compare.evol.rates(A=Y.gpa$coords, phy=plethspecies$phy, method="simulation",gp=gp.end,iter=999) The ‘A=Y.gpa$coords’ portion is where you specify the data, and the ‘phy=plethspecies$phy’ is where you specify the phylogeny. In the case of this example, both are part of an object ‘plethspecies’. But they do not have to be. It could be: ‘A=mydata’ and ‘phy = myphy’ or whatever else you have called them when you read the data into R from your data files. Hope this helps. Dean Dr. Dean C. Adams Director of Graduate Education, EEB Program Professor Department of Ecology, Evolution, and Organismal Biology Iowa State University https://www.eeob.iastate.edu/faculty/adams/ phone: 515-294-3834 From: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> On Behalf Of Mariana Díaz Santana Iturrios Sent: Saturday, February 13, 2021 12:36 PM To: [email protected]<mailto:[email protected]> Subject: [MORPHMET2] Doubt regarding compare.evol.rates function of Geomorph r package Dear all, I've been trying to use "compare.evol.rates" function of Geomorph r package without success. I account with two separate files: a phylogenetic tree, and a landmark matrix obtained from generalized procrustes analysis. I suspect I somehow have to merge these into a single file although I don't know how to. I appreciate any help on the matter. My best regards, -- Dr. Mariana Díaz-Santana-Iturrios Postdoctoral Position Facultad de Ciencias de La Vida Universidad Andres Bello Santiago, Chile Cell phone number (México)(+52)612-16-144-35 ORCID 0000-0002-5253-5395 -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]<mailto:[email protected]>. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/CAPmxoqRwsw05ox_tL0FPLQEmYOu6uroBSQg7eyXBvr0_yJEbCw%40mail.gmail.com<https://groups.google.com/d/msgid/morphmet2/CAPmxoqRwsw05ox_tL0FPLQEmYOu6uroBSQg7eyXBvr0_yJEbCw%40mail.gmail.com?utm_medium=email&utm_source=footer>. -- Dr. Mariana Díaz-Santana-Iturrios Postdoctoral Position Facultad de Ciencias de La Vida Universidad Andres Bello Santiago, Chile Cell phone number (México)(+52)612-16-144-35 ORCID 0000-0002-5253-5395 -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/CH2PR04MB6617AE893076DF0A5150CBECA2899%40CH2PR04MB6617.namprd04.prod.outlook.com.
