{"action":"opened","issue":{"url":"https://api.github.com/repos/lmsimp/bioc-pRoloc-hyperLOPIT-workflow/issues/38","repository_url":"https://api.github.com/repos/lmsimp/bioc-pRoloc-hyperLOPIT-workflow","labels_url":"https://api.github.com/repos/lmsimp/bioc-pRoloc-hyperLOPIT-workflow/issues/38/labels{/name}","comments_url":"https://api.github.com/repos/lmsimp/bioc-pRoloc-hyperLOPIT-workflow/issues/38/comments","events_url":"https://api.github.com/repos/lmsimp/bioc-pRoloc-hyperLOPIT-workflow/issues/38/events","html_url":"https://github.com/lmsimp/bioc-pRoloc-hyperLOPIT-workflow/issues/38","id":193180860,"number":38,"title":"Using a seed before svmOptimisation","user":{"login":"lgatto","id":384198,"avatar_url":"https://avatars.githubusercontent.com/u/384198?v=3","gravatar_id":"","url":"https://api.github.com/users/lgatto","html_url":"https://github.com/lgatto","followers_url":"https://api.github.com/users/lgatto/followers","following_url":"https://api.github.com/users/lgatto/following{/other_user}","gists_url":"https://api.github.com/users/lgatto/gists{/gist_id}","starred_url":"https://api.github.com/users/lgatto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lgatto/subscriptions","organizations_url":"https://api.github.com/users/lgatto/orgs","repos_url":"https://api.github.com/users/lgatto/repos","events_url":"https://api.github.com/users/lgatto/events{/privacy}","received_events_url":"https://api.github.com/users/lgatto/received_events","type":"User","site_admin":false},"labels":[{"id":370413602,"url":"https://api.github.com/repos/lmsimp/bioc-pRoloc-hyperLOPIT-workflow/labels/question","name":"question","color":"cc317c","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-02T18:07:53Z","updated_at":"2016-12-02T18:07:53Z","closed_at":null,"body":"@ClaireMulvey asked about using a seed when optimising the parameters. This would be done as shown below. I used `123` as seed (and would take note of it), but any integer can be used (and there's no need to sample that one at random). \r\n\r\n```r\r\nset.seed(123)\r\nparams <- svmOptimisaion(hl, ...)\r\n```\r\n\r\nSaving the `params` saves me for re-running the optimisation routine. If I wanted to re-run it and the same results, I would first set the seed to `123` again.\r\n\r\nBut I don't think that this is necessary, however. The optimisation routine is repeated 100 times (that's the default) and we assume the actual folds don't matter. If they did, i.e. different seeds gave different and incompatible *best* parameters, we would have an issue, and would need to increase the number of iteration and make sure the results converge. We have never observed such an issue. "}}
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