{"action":"created","issue":{"url":"https://api.github.com/repos/LennonLab/Growth_Curves/issues/11","repository_url":"https://api.github.com/repos/LennonLab/Growth_Curves","labels_url":"https://api.github.com/repos/LennonLab/Growth_Curves/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/LennonLab/Growth_Curves/issues/11/comments","events_url":"https://api.github.com/repos/LennonLab/Growth_Curves/issues/11/events","html_url":"https://github.com/LennonLab/Growth_Curves/issues/11","id":229539088,"number":11,"title":"Negative yield (A)","user":{"login":"jaytlennon","id":4992163,"avatar_url":"https://avatars3.githubusercontent.com/u/4992163?v=3","gravatar_id":"","url":"https://api.github.com/users/jaytlennon","html_url":"https://github.com/jaytlennon","followers_url":"https://api.github.com/users/jaytlennon/followers","following_url":"https://api.github.com/users/jaytlennon/following{/other_user}","gists_url":"https://api.github.com/users/jaytlennon/gists{/gist_id}","starred_url":"https://api.github.com/users/jaytlennon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaytlennon/subscriptions","organizations_url":"https://api.github.com/users/jaytlennon/orgs","repos_url":"https://api.github.com/users/jaytlennon/repos","events_url":"https://api.github.com/users/jaytlennon/events{/privacy}","received_events_url":"https://api.github.com/users/jaytlennon/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-05-18T02:39:07Z","updated_at":"2017-05-21T16:57:14Z","closed_at":null,"body":"Seems that with some data sets (including \"test\") return negative values for yield parameter (A). If positive, the values would seem to be plausible. It is also peculiar that the negative yield parameter which is presumably used to plot predicted values, seems to do a good job of fitting observed data. cc: @mmuscarella @vkuo2 @wrshoemaker "},"comment":{"url":"https://api.github.com/repos/LennonLab/Growth_Curves/issues/comments/302948861","html_url":"https://github.com/LennonLab/Growth_Curves/issues/11#issuecomment-302948861","issue_url":"https://api.github.com/repos/LennonLab/Growth_Curves/issues/11","id":302948861,"user":{"login":"jaytlennon","id":4992163,"avatar_url":"https://avatars3.githubusercontent.com/u/4992163?v=3","gravatar_id":"","url":"https://api.github.com/users/jaytlennon","html_url":"https://github.com/jaytlennon","followers_url":"https://api.github.com/users/jaytlennon/followers","following_url":"https://api.github.com/users/jaytlennon/following{/other_user}","gists_url":"https://api.github.com/users/jaytlennon/gists{/gist_id}","starred_url":"https://api.github.com/users/jaytlennon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaytlennon/subscriptions","organizations_url":"https://api.github.com/users/jaytlennon/orgs","repos_url":"https://api.github.com/users/jaytlennon/repos","events_url":"https://api.github.com/users/jaytlennon/events{/privacy}","received_events_url":"https://api.github.com/users/jaytlennon/received_events","type":"User","site_admin":false},"created_at":"2017-05-21T16:57:14Z","updated_at":"2017-05-21T16:57:14Z","body":"@wrshoemaker @mmuscarella @vkuo2:\r\n\r\nThanks to Will for suggestion. I tried changing the method to `L-BFGS-B`.  I also added the `lower =C...` statement. The output parameters for the `growth.modGomp(\"../data/Pseudo.csv\", \"csv_test\", synergy=F, temp=F, smooth=F)` in test.example.R are identical. \r\n\r\nMake me wonder if the `lower=c(=ymax))` statement is correct/working. We're trying to constrain `A` to positive values, so I tried that as well, and got no differences in parameter output.  \r\n\r\nI don't see other places in `bin` where we would need to make changes to script. Here's what I was playing around with:\r\n\r\n    # Perform grid.mle2 Fits\r\n    fit1<-grid.mle2(minuslogl=s.trim~dnorm(mean=m.gomp(t.trim,c(b0,A,umax,L)),\r\n                    sd=exp(z)),grids=grids1,start=start1,data=tmpdata,\r\n                    method=\"L-BFGS-B\", lower=c(ymax))\r\n\r\nNo pull requests being made"}}
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