tag:blogger.com,1999:blog-8499895524521663926.post3508083275520149223..comments2024-07-12T21:07:13.125-04:00Comments on Phylogenetic Tools for Comparative Biology: Phylogenetic signal with K and λLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-8499895524521663926.post-23030461552816152512023-01-31T09:28:25.378-05:002023-01-31T09:28:25.378-05:00Hi Lian. Thanks for the post! Could you better exp...Hi Lian. Thanks for the post! Could you better explain the situation in which lambda can be higher than 1 and also what exactly do you mean by "not defined" depending on the tree structure. Thanks! Bruno Vilelahttps://www.blogger.com/profile/07959665828346852858noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-51116381695593979712016-09-30T15:44:17.305-04:002016-09-30T15:44:17.305-04:00Hi
I have problems with consentrait. My tree labe...Hi<br /><br />I have problems with consentrait. My tree labels not match with data table.<br /><br />$tree_not_data<br /><br />Can you help me?<br /><br />Tanks<br />Anonymoushttps://www.blogger.com/profile/12180690475173353991noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-74195424059278731812016-09-01T23:00:06.215-04:002016-09-01T23:00:06.215-04:00There is Anna - you could just use a likelihood ra...There is Anna - you could just use a likelihood ratio test against a Brownian model. If you don't know how to do this, you could email me directly or the R-sig-phylo list. I have trouble keeping up with comments on my blog - particularly on old posts. - LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-78040383724285881572016-07-28T07:24:18.143-04:002016-07-28T07:24:18.143-04:00Hi Liam,
as far as I understand, the p value for...Hi Liam, <br /><br />as far as I understand, the p value for lambda indicates if my value for lambda is significantly different from zero. Is there a way of testing in phytools whether lambda is also significantly different from 1?<br /><br />Cheers, <br />Anna Anonymoushttps://www.blogger.com/profile/06429437943980782297noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-20420489883190173652014-01-18T08:20:17.057-05:002014-01-18T08:20:17.057-05:00Oh, my. That's a big confidence interval.
Tha...Oh, my. That's a big confidence interval.<br /><br />Thanks for clearing this up...<br /><br />JosteinJosteinhttps://www.blogger.com/profile/14533146134202383551noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-51611257433661116482014-01-18T08:00:33.391-05:002014-01-18T08:00:33.391-05:00K & λ are not the same thing. λ measures the s...K & λ are not the same thing. λ measures the similarity of the covariances among species to the covariances expected under Brownian motion; whereas K might be more usefully thought of as a measure of the partitioning of variance. If K>1 then variance tends to be among clades; while if K<1 then variance is within clades (with BM as reference). The variance on K for a given process is quite large. I suspect if you did simulation you might find that K=0.54 (particularly for a relatively small tree) was not different from BM. E.g.:<br /><br />> tree<-pbtree(n=50)<br />> X<-fastBM(tree,nsim=1000)<br />> K<-apply(X,2,phylosig,tree=tree)<br />> quantile(K,c(0.05,0.95))<br /> 5% 95% <br />0.4203233 2.0659019<br /><br />- LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-9492950329594370152014-01-11T10:01:27.885-05:002014-01-11T10:01:27.885-05:00Hi,
I used this function to estimate both lambda...Hi, <br /><br />I used this function to estimate both lambda and K for a data set of 95 species. The estimated K was 0.54 (p=0.013) and lambda was 0.98 (p=0.001). Given how I've understood lambda and Blomberg's own explanation if K:<br /><br />"A K less than one implies that relatives resemble each other less than expected under Brownian motion evolution along the candidate tree. This could be caused by either departure from Brownian motion evolution, such as adaptive evolution that is uncorrelated with the phylogeny (i.e., homoplasy), or ‘‘measurement error’’ in the broad sense."<br /><br />There must be something not quite right here? K tells me there is weak phylogenetic dependence, while lambda returns a value that indicates near perfect phylogentic dependence.<br /><br />Any tips?Josteinhttps://www.blogger.com/profile/14533146134202383551noreply@blogger.com