tag:blogger.com,1999:blog-8386055846297828307.post7292957528933396013..comments2024-03-28T07:34:49.133+01:00Comments on The Genealogical World of Phylogenetic Networks: Structural data in historical linguisticsUnknownnoreply@blogger.comBlogger2125tag:blogger.com,1999:blog-8386055846297828307.post-17253297608169175442018-09-26T12:46:09.187+02:002018-09-26T12:46:09.187+02:00Thanks a lot for your comments. As your surprise i...Thanks a lot for your comments. As your surprise in the last part shows: the situation is a bit different in linguistics from biology at times, although I think that we are making progress. Our datasets, however, are still very small (a dataset with 200 characters per taxon is already close to being considered as a large one), while on the other hand, parsimony enjoys a bad reputation in our field, so that barely any method that was published in the last 10 years would test it against the Bayesian methods that are generally considered to be more robust. But we'll see what the future brings, especially, if, as I hope, more data of different kinds will be shared publicly in easily accessible formats, so people can play with the data and test its usefulness for phylogenetic reconstruction. Johann-Mattis Listhttps://www.blogger.com/profile/12185355133399020406noreply@blogger.comtag:blogger.com,1999:blog-8386055846297828307.post-21714734516428173812018-09-25T11:47:34.704+02:002018-09-25T11:47:34.704+02:00Since questions are by nature less restricted rega...<i>Since questions are by nature less restricted regarding their content, scholars can easily pick and choose the features in such a way that they confirm the theory they want them to confirm rather than testing it objectively.</i><br /><br />I'm a phylogeneticist in biology. We cannot avoid accidental sampling bias – except by simply making our datasets large enough. As long as we don't end up with redundant characters (i.e. the same character twice in different wordings), this works; there are simulation studies to show that.<br /><br />Total-evidence approach!<br /><br /><i>If features are mixed, phylogenetic methods that work on explicit statistical models (like gain and loss of character states, etc.) may often be inadequate to model the evolution of the characters, especially if the characters are historical.</i><br /><br />Then use parsimony. The behavior of parametric methods (maximum likelihood, Bayesian inference) when given datasets with realistic distributions of missing data is not well understood anyway; it hasn't really been tested.<br /><br />(I have a section discussing that in <a href="https://peerj.com/preprints/1596/" rel="nofollow">this preprint</a>.)<br /><br /><i>Most of the research based on data did not supply the data with the paper, and often authors directly refuse to share the data when asked after publication (see also the post on Sharing supplementary data).</i><br /><br />...Huh. The journals I've published in <b>require</b> authors to publish their data.David Marjanovićnoreply@blogger.com