{"id":416,"date":"2019-04-02T11:37:40","date_gmt":"2019-04-02T11:37:40","guid":{"rendered":"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/?p=416"},"modified":"2019-04-02T11:37:40","modified_gmt":"2019-04-02T11:37:40","slug":"update-on-project-4","status":"publish","type":"post","link":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/2019\/04\/02\/update-on-project-4\/","title":{"rendered":"Update on Project #4"},"content":{"rendered":"<p>It appears that <tt>strataG<\/tt> doesn&#8217;t work with the latest version of <tt>R<\/tt> (v 3.5.3). I did, however, realize that it&#8217;s possible to do the analysis using <tt>pegas<\/tt>. You use the same command to read a <tt>FASTA<\/tt> file in as I showed in the notes. Then you run <tt>tajima.test(seqs)<\/tt> on the results (where <tt>seqs<\/tt> is the name of the object you read the DNA sequence information into). I&#8217;ll update the project assignment to show the new syntax later today.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>It appears that strataG doesn&#8217;t work with the latest version of R (v 3.5.3). I did, however, realize that it&#8217;s possible to do the analysis using pegas. You use the same command to read a FASTA file in as I showed in the notes. Then you run tajima.test(seqs) on the results (where seqs is the &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/2019\/04\/02\/update-on-project-4\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Update on Project #4&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-416","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/posts\/416","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/comments?post=416"}],"version-history":[{"count":1,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/posts\/416\/revisions"}],"predecessor-version":[{"id":417,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/posts\/416\/revisions\/417"}],"wp:attachment":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/media?parent=416"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/categories?post=416"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/tags?post=416"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}