tag:blogger.com,1999:blog-8499895524521663926.post6889483893013159891..comments2024-03-27T07:13:39.236-04:00Comments on Phylogenetic Tools for Comparative Biology: force.ultrametric method for ultrametric phylogenies that fail ape::is.ultrametric due to numerical precisionLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-8499895524521663926.post-38336606941777358412018-11-25T15:12:06.442-05:002018-11-25T15:12:06.442-05:00if any of these options works? what should I do?if any of these options works? what should I do?Xochitlhttps://www.blogger.com/profile/08687165991572440067noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-74592919875342790702018-03-26T22:25:01.159-04:002018-03-26T22:25:01.159-04:00We offer you all world famous replica watches, wit...We offer you all world famous <a href="http://www.topreplicareviews.co.uk/" rel="nofollow">replica watches</a>, with same appearance, same quality and same material…you cannot tell which one is a <a href="http://www.topreplicareviews.co.uk/category/replica-rolex/" rel="nofollow">replica-rolex</a> just with your eyes at all!midnhttps://www.blogger.com/profile/14582576902164271268noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-41891029649170909552017-04-02T20:52:49.987-04:002017-04-02T20:52:49.987-04:00Thank you Dave. I hope you are well.Thank you Dave. I hope you are well.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-10385613964225979822017-04-02T20:51:28.521-04:002017-04-02T20:51:28.521-04:00Thanks Emmanuel.Thanks Emmanuel.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-54246816102850916952017-03-29T17:22:20.265-04:002017-03-29T17:22:20.265-04:00For context, I should add that Emmanuel discovered...For context, I should add that Emmanuel discovered this post when I shared it in a bammtools issue discussion regarding recent changes to is.ultrametric in ape, which may be relevant to this discussion:<br /><br />https://github.com/macroevolution/bammtools/issues/45dwbapsthttps://www.blogger.com/profile/17606476387441191531noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-22934542451941404532017-03-29T17:12:14.961-04:002017-03-29T17:12:14.961-04:00Hi Liam,
Great post and nice function! Here'r...Hi Liam,<br /><br />Great post and nice function! Here're a few comments.<br /><br />is.ultrametric() has the option 'option' to choose the method used to test ultrametricity: the default is the scaled range. The other possibility is the variance (option = 2) which used to be the default before ape 4.0.<br /><br />To avoid issues with the number of printed digits in write.tree/nexus, one can use readRDS instead: it makes smaller files that are faster to read/write, and no digits are lost. Of course, you won't be able to open such files with other software than R.<br /><br />A third way to make a tree ultrametric: branching.times() does not test whether the tree is ultrametric, so the values output by this function from an "almost ultrametric" tree can then be input to compute.brtime().<br /><br />Cheers,<br /><br />EmmanuelAnonymoushttps://www.blogger.com/profile/04265340727465812419noreply@blogger.com