tag:blogger.com,1999:blog-8499895524521663926.post41148108004046255..comments2024-03-27T07:13:39.236-04:00Comments on Phylogenetic Tools for Comparative Biology: New version of fastBM() for multiple simulationsLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-8499895524521663926.post-13676030763589121932017-02-14T17:40:02.094-05:002017-02-14T17:40:02.094-05:00Hi Liam,
The output of the internal nodes from fa...Hi Liam,<br /><br />The output of the internal nodes from fastBM looks great, except I cannot figure out the numbering scheme. What is the output tree internal node labeling format?<br /><br />Thank you!Anonymoushttps://www.blogger.com/profile/15638792399195656963noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-63474338590720153122011-03-14T23:03:01.132-04:002011-03-14T23:03:01.132-04:00Great, thanks.Great, thanks.Anonymoushttps://www.blogger.com/profile/01944150859555101169noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-17716151838164187582011-03-14T22:05:22.168-04:002011-03-14T22:05:22.168-04:00It seems like you can only loop rTraitCont(), usin...It seems like you can only loop rTraitCont(), using - for instance - apply(). Thus, computation time increases linearly with the number of simulations. However, rTraitCont() is very fast for a single simulation - so it is still practical to use rTraitCont(), if you want to, unless you are doing a very large number of simulations.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-26341231109900618882011-03-14T16:22:24.017-04:002011-03-14T16:22:24.017-04:00I don't know. That's a good question thou...I don't know. That's a good question though. I will investigate it later and post the results.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-12336502646849056952011-03-14T16:18:09.748-04:002011-03-14T16:18:09.748-04:00By the way, how does rTraitCont from the ape packa...By the way, how does rTraitCont from the ape package compare to sim.char and fastBM? I assume you are limited to looping with rTraitCont for N > 1?Anonymoushttps://www.blogger.com/profile/01944150859555101169noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-45978928581075918272011-03-14T16:10:54.453-04:002011-03-14T16:10:54.453-04:00Works fine, but my 2.4 ghz i5 processor is slower ...Works fine, but my 2.4 ghz i5 processor is slower of course:<br /><br />> tree <- rtree(1000)<br />> system.time(X<-fastBM(tree,nsim=100))<br /> user system elapsed <br /> 0.314 0.019 0.404 <br />> system.time(X<-sim.char(phy=tree,as.matrix(1),nsim=100))<br /> user system elapsed <br /> 25.807 0.100 25.734Anonymoushttps://www.blogger.com/profile/01944150859555101169noreply@blogger.com