{"action":"created","issue":{"url":"https://api.github.com/repos/danlwarren/RWTY/issues/49","labels_url":"https://api.github.com/repos/danlwarren/RWTY/issues/49/labels{/name}","comments_url":"https://api.github.com/repos/danlwarren/RWTY/issues/49/comments","events_url":"https://api.github.com/repos/danlwarren/RWTY/issues/49/events","html_url":"https://github.com/danlwarren/RWTY/issues/49","id":99782231,"number":49,"title":"visualising clades in which multiple chains disagree","user":{"login":"roblanf","id":895251,"avatar_url":"https://avatars.githubusercontent.com/u/895251?v=3","gravatar_id":"","url":"https://api.github.com/users/roblanf","html_url":"https://github.com/roblanf","followers_url":"https://api.github.com/users/roblanf/followers","following_url":"https://api.github.com/users/roblanf/following{/other_user}","gists_url":"https://api.github.com/users/roblanf/gists{/gist_id}","starred_url":"https://api.github.com/users/roblanf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roblanf/subscriptions","organizations_url":"https://api.github.com/users/roblanf/orgs","repos_url":"https://api.github.com/users/roblanf/repos","events_url":"https://api.github.com/users/roblanf/events{/privacy}","received_events_url":"https://api.github.com/users/roblanf/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":10,"created_at":"2015-08-08T08:04:07Z","updated_at":"2015-08-21T02:38:14Z","closed_at":null,"body":"Here's an idea we just came up with over beers. \r\n\r\nOne thing that would be useful to know is, given any summary tree, which splits on that tree are most problematic. Obviously the posterior support is one very useful measure of this. But another really useful measure, if you have analysed >1 replicate chain, would be the standard deviation of split frequencies. \r\n\r\nSo, the obvious idea here is to take a summary tree (the MAP tree would be easy to extract in RWTY), and label each split in that tree with the standard deviation of split frequencies for that split. I can imagine two functions here:\r\n\r\n1. A function that takes any tree, and maps SDSFs onto that tree, and exports it in useful formats (e.g. phylip format with branch labels for the SDSFs).\r\n\r\n2. A function that wraps the function in (1) but does this for the MAP tree. \r\n\r\nWe might also consider attempting to plot the labelled trees for the output, either with numbers on the branches (e.g. we could have numbers with x/y, where x is the posterior support, and y is the SDSFs), and/or colours or branch thickness representing the SDSFs on that branch.\r\n\r\nBack to beers."},"comment":{"url":"https://api.github.com/repos/danlwarren/RWTY/issues/comments/133253635","html_url":"https://github.com/danlwarren/RWTY/issues/49#issuecomment-133253635","issue_url":"https://api.github.com/repos/danlwarren/RWTY/issues/49","id":133253635,"user":{"login":"roblanf","id":895251,"avatar_url":"https://avatars.githubusercontent.com/u/895251?v=3","gravatar_id":"","url":"https://api.github.com/users/roblanf","html_url":"https://github.com/roblanf","followers_url":"https://api.github.com/users/roblanf/followers","following_url":"https://api.github.com/users/roblanf/following{/other_user}","gists_url":"https://api.github.com/users/roblanf/gists{/gist_id}","starred_url":"https://api.github.com/users/roblanf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roblanf/subscriptions","organizations_url":"https://api.github.com/users/roblanf/orgs","repos_url":"https://api.github.com/users/roblanf/repos","events_url":"https://api.github.com/users/roblanf/events{/privacy}","received_events_url":"https://api.github.com/users/roblanf/received_events","type":"User","site_admin":false},"created_at":"2015-08-21T02:38:14Z","updated_at":"2015-08-21T02:38:14Z","body":"Yeah, that answers the question. I think it's kind of a neat approach.\n\nFrom my perspective, I'm not totally sure about plotting things out over\nthe course of a run (I just can't figure out quite what it would tell you),\nbut I can definitely see the benefit of looking at all the taxa in the tree\nrelative to this metric.\n\nEither way, we already have code to do sliding window and cumulative plots\nbased on various metrics, so I don't think it should be a big deal to make\nthe plots. It's just a case of whether we include them in the package.\n\nI'm thinking that we could do something similar to the posterior\nprobability plots, and just plot out the 20 taxa that are most variable, or\nsomething along those lines.\n\nDo you have a function that will calculate the metric on a particular set\nof trees? If you do, and if you're willing to share it here, that would be\na huge help.\n\nOn 21 August 2015 at 11:14, NickCrouch <notifications@github.com> wrote:\n\n> Completely agree with you first comment about plotting means, the code is\n> there to do boxplots I just thought with my data the mean was clearer just\n> to highlight what is going on in general.\n>\n> You can just run it once on all the trees, but you won't see any change\n> over time (if that is informative). The run times would be effectively the\n> same for both running on all at once and in segments, but running both ways\n> would obviously be longer. I think both approaches give the possibility of\n> identifying specific taxa, in general i'm open to suggestions here.\n>\n> In the example you gave for your last question, 'a' would have 3 distinct\n> sister taxa - the middle two rows would count as 1. If a species is sister\n> to a clade of 2 or more species, as long as the species composition remains\n> the same, then the species within that clade can have any topology without\n> counting as a unique pairing. Does that answer your question?\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/danlwarren/RWTY/issues/49#issuecomment-133234738>.\n>\n\n\n\n-- \nRob Lanfear\nSchool of Biological Sciences,\nMacquarie University,\nSydney\n\nphone: +61 (0)2 9850 8204\n\nwww.robertlanfear.com\n"}}