tag:blogger.com,1999:blog-8499895524521663926.post946446776486509713..comments2024-05-17T16:18:49.298-04:00Comments on Phylogenetic Tools for Comparative Biology: Using make.simmap() with brownie.lite()Liam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-8499895524521663926.post-40627992250804461982012-01-25T17:02:15.340-05:002012-01-25T17:02:15.340-05:00thanks a lot Liam, and congratulations for this ve...thanks a lot Liam, and congratulations for this very interesting blog!<br /><br />Joan.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-67938850571788999242012-01-24T16:59:20.610-05:002012-01-24T16:59:20.610-05:00Hi Joan.
I simple function that pulls out the sta...Hi Joan.<br /><br />I simple function that pulls out the states at the internal (& terminal nodes of the tree is as follows:<br /><br />getNodes<-function(tree){<br /> X<-matrix(NA,nrow(tree$edge),ncol(tree$edge))<br /> for(i in 1:nrow(tree$edge)) <br /> X[i,]<-names(tree$maps[[i]])[c(1,length(tree$maps[[i]]))]<br /> return(X)<br />}<br /><br />The function returns a matrix where the elements correspond to the nodes in matrix tree$edge. Getting, say, the frequencies of nodes in each state across a set of mapped trees is only a little bit more complicated. I will try to write a function & post for this as soon as I get a chance.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-3871137843099257812012-01-20T12:22:22.238-05:002012-01-20T12:22:22.238-05:00Hi Liam,
regarding the function make.simmap, I ca...Hi Liam,<br /><br />regarding the function make.simmap, I can see in the output you get how your states are distributed across the branches of your tree (with $mapped.edge). How difficult could be to visualize exactly the same but for your nodes? I mean, how your states are distributed across the nodes of your tree and with what probability.<br /><br />I am new in R and I would appreciate any possible help with this.<br /><br />thanks a lot!<br /><br />Joan.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-50314858065553848632011-06-24T00:18:46.215-04:002011-06-24T00:18:46.215-04:00Direct link to new version of brownie.lite() is he...Direct link to new version of brownie.lite() is <a href="http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/brownie.lite/v0.2/brownie.lite.R" rel="nofollow">here</a>.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.com