tag:blogger.com,1999:blog-8499895524521663926.post4563027194865142786..comments2024-03-08T04:19:23.697-05:00Comments on Phylogenetic Tools for Comparative Biology: Computing phylogenetic signal across multiple treesLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-8499895524521663926.post-66138998256602246262012-10-16T16:34:19.709-04:002012-10-16T16:34:19.709-04:00Hi James - I just posted about this, here. Thanks ...Hi James - I just posted about this, <a href="http://phytools.blogspot.ca/2012/10/estimating-pagels-for-set-of-traits-in.html" rel="nofollow">here</a>. Thanks for the question. LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-42915328453112188512012-10-16T09:53:17.721-04:002012-10-16T09:53:17.721-04:00Hey Liam,
Thanks for offering all the great R cod...Hey Liam,<br /><br />Thanks for offering all the great R code to do different analyses. One question I had was how to calculate lambda on multiple traits? I have code that gets me close in that it outputs the lambda values but not the log values or p-value. I am not the most savvy R user so any help would be great.<br /><br />Here is what I have so far:<br /><br />Bark_lambda<-numeric(6)<br />for (i in 1:6) Bark_lambda[i] = phylosig(poptree, Bark_for_model[[i]], method = "lambda", test = TRUE)<br /><br /><br />Thanks!<br />jamesj.b.p.https://www.blogger.com/profile/05740976411257750017noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-85856054696049328802011-12-19T04:14:43.782-05:002011-12-19T04:14:43.782-05:00Thanks Liam for the details. I realized that my pr...Thanks Liam for the details. I realized that my problem was that I had some terminal branches with zero lengths. So I was able to obtain the K values after transforming those zero lenghts to 0.1<br />I hope this is a valid trick<br />Best,<br />JulissaAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-91017908777750514042011-12-13T21:45:50.135-05:002011-12-13T21:45:50.135-05:00BTW, I meant to say that we would normally read in...BTW, I meant to say that we would normally read in our set of trees using read.tree or read.nexus; or we would estimate them using the phangorn library. The random trees in this analysis are included merely for illustrative purposes.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.com