tag:blogger.com,1999:blog-8499895524521663926.post8682878938996704849..comments2024-02-21T21:35:53.780-05:00Comments on Phylogenetic Tools for Comparative Biology: On the shape of trees with random taxa addition or subtractionLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-8499895524521663926.post-57799738208978212642013-02-28T00:43:23.110-05:002013-02-28T00:43:23.110-05:00David - Yes, this is how the function works; and I...David - Yes, this is how the function works; and I agree that this should result in trees that are not Yule-like. - LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-68866716808147361772013-02-27T02:32:20.427-05:002013-02-27T02:32:20.427-05:00Actually, looking at your code, perhaps I misinter...Actually, looking at your code, perhaps I misinterpreted your previous post about random new tips and cumsum. Now it looks like you're using it to pick an edge at random, with longer edges weighted to have a higher chance of getting chosen relative to their length? That's basically letting edges to go anywhere with uniform probability across the tree, something which would be unexpected under Yule/birth-death.dwbapsthttps://www.blogger.com/profile/17606476387441191531noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-75426043625597386602013-02-27T02:06:03.659-05:002013-02-27T02:06:03.659-05:00I think the basis of what you're doing depends...I think the basis of what you're doing depends on the definition of 'at random'. In a previous post, you describe that you're adding tips as if the probability of an extra tip at any point along any edge increased with time. It isn't exactly clear, but I assume you let the probability increase linearly as branches approach the most terminal tips. This wouldn't be true under any birth/birth-death model; it's much more unlikely for a random tip to be attached further back in time than just a linearly decreasing probability. Just think of the exponential curve of a non-log-scaled LTT...<br /><br />If I remember Nee et al. rightly, the probability of an additional random tip should be the same as the probability of having a branching time of time t, as that's just the probability of having a lineage which survived for duration t.<br /><br />I think if you weighted tip addition in this way, relative to values of the birth and death rates, it would produce trees with no distortion of the estimated gamma parameter.dwbapsthttps://www.blogger.com/profile/17606476387441191531noreply@blogger.com