{"id":2147,"date":"2012-01-27T12:21:40","date_gmt":"2012-01-27T17:21:40","guid":{"rendered":"http:\/\/blogs.law.harvard.edu\/kotrc\/?p=2147"},"modified":"2012-01-28T11:22:54","modified_gmt":"2012-01-28T16:22:54","slug":"moving-ahead-for-reals-today","status":"publish","type":"post","link":"https:\/\/archive.blogs.harvard.edu\/kotrc\/2012\/01\/27\/moving-ahead-for-reals-today\/","title":{"rendered":"Moving Ahead, For Reals Today"},"content":{"rendered":"

This hiccup has definitely been the biggest motivational hurdle since starting The Big Push at the outset of this year. I think I am doing OK so far. It helped to work on it for a bit last night and feel like I got to some semblance of, if not a resolution, at the very least a tentative way forward.<\/p>\n

I plotted up the PCO ordination based on the new 80%? culling criterion (green symbols) and compared to the previous 50%?nv cull (black tails). The plot shows that, as far as PCO1 and PCO2 are concerned, the points are in pretty much the same place relative to one another (but slightly rotated in space)\u2014this makes sense since PCO can reconstruct relative position but not absolute orientation rotationally.<\/p>\n

\"\"<\/a><\/p>\n

Indeed, if I plot pairwise distances of the two ordinations (based on the two different cull criteria), they are very closely correlated to one another:<\/p>\n

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Tadaa. I think this means I am OK to forge ahead, because choice of culling algorithm does not make a huge difference in where things end up in the PCO1-2 morphospace. Yay. A whole lot of worry for nothing, though it would be really interesting to do the bootstrappy analysis JC suggested and systematically check what happens when you remove characters, randomly as well as stepwise (taking the worst away one by one).<\/p>\n

Forging ahead means, I think, trying to remake Figure 1 with this new selection of characters. This initially proved to be difficult because the new selection of characters, which includes a great deal of characters with mostly “n” states and very few valid states, often led to contingency tables (characters vs. discretized PCO score) with just one column (i.e. all genera fall in the same quarter of the PCO axis regardless of character state). This is a situation for which no association coefficient can be computed, so I had to add an if-else statement to take care of that eventuality. Interestingly, there also seemed to be situations where there was just one row<\/em>\u00a0in the table\u2014now that is much more worrying because it would suggest that there is only one character state for all occurrences, and I thought I had already culled out all such characters beforehand. So, more attention is needed to fix this problem.<\/p>\n","protected":false},"excerpt":{"rendered":"

This hiccup has definitely been the biggest motivational hurdle since starting The Big Push at the outset of this year. I think I am doing OK so far. It helped to work on it for a bit last night and feel like I got to some semblance of, if not a resolution, at the very […]<\/p>\n","protected":false},"author":2222,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[14607,13584],"tags":[16233],"class_list":["post-2147","post","type-post","status-publish","format-standard","hentry","category-research-journal","category-timekeeping","tag-morphospace"],"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/posts\/2147","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/users\/2222"}],"replies":[{"embeddable":true,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/comments?post=2147"}],"version-history":[{"count":6,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/posts\/2147\/revisions"}],"predecessor-version":[{"id":2155,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/posts\/2147\/revisions\/2155"}],"wp:attachment":[{"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/media?parent=2147"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/categories?post=2147"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/archive.blogs.harvard.edu\/kotrc\/wp-json\/wp\/v2\/tags?post=2147"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}