{"action":"closed","issue":{"url":"https://api.github.com/repos/joey711/phyloseq/issues/675","repository_url":"https://api.github.com/repos/joey711/phyloseq","labels_url":"https://api.github.com/repos/joey711/phyloseq/issues/675/labels{/name}","comments_url":"https://api.github.com/repos/joey711/phyloseq/issues/675/comments","events_url":"https://api.github.com/repos/joey711/phyloseq/issues/675/events","html_url":"https://github.com/joey711/phyloseq/issues/675","id":182574170,"number":675,"title":"vegdist and distance not returning the same bray-curtis matrix","user":{"login":"sformel","id":21973147,"avatar_url":"https://avatars.githubusercontent.com/u/21973147?v=3","gravatar_id":"","url":"https://api.github.com/users/sformel","html_url":"https://github.com/sformel","followers_url":"https://api.github.com/users/sformel/followers","following_url":"https://api.github.com/users/sformel/following{/other_user}","gists_url":"https://api.github.com/users/sformel/gists{/gist_id}","starred_url":"https://api.github.com/users/sformel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sformel/subscriptions","organizations_url":"https://api.github.com/users/sformel/orgs","repos_url":"https://api.github.com/users/sformel/repos","events_url":"https://api.github.com/users/sformel/events{/privacy}","received_events_url":"https://api.github.com/users/sformel/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-10-12T16:38:31Z","updated_at":"2016-10-19T17:21:06Z","closed_at":"2016-10-19T17:21:06Z","body":"I'm pretty new to using phyloseq and vegan, so I'm guessing that I am misinterpreting how these commands work.  I was surprised to find the distance function in phyloseq does not return the same matrix as the vegdist function in vegan.  I thought they used the same calculations, so I assumed they would return the same values. Can anyone explain to me where I might be going wrong, or how they are different?\r\n\r\n`data(\"GlobalPatterns\")\r\n\r\np = prune_taxa(taxa_sums(GlobalPatterns) > 0, GlobalPatterns)\r\nGP.chl = subset_taxa(GlobalPatterns, Phylum==\"Chlamydiae\")\r\n\r\nvegdist <- head(vegdist(otu_table(GP.chl), method = \"bray\"))\r\ndistance <- head(distance(otu_table(GP.chl), method = \"bray\")) \r\n\r\nidentical(vegdist,distance)`\r\n\r\n\r\n\r\n\r\nThanks,\r\nSteve"}}
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