{"action":"created","issue":{"url":"https://api.github.com/repos/dankelley/oce/issues/881","repository_url":"https://api.github.com/repos/dankelley/oce","labels_url":"https://api.github.com/repos/dankelley/oce/issues/881/labels{/name}","comments_url":"https://api.github.com/repos/dankelley/oce/issues/881/comments","events_url":"https://api.github.com/repos/dankelley/oce/issues/881/events","html_url":"https://github.com/dankelley/oce/issues/881","id":134955443,"number":881,"title":"Bio-Argo (again) ","user":{"login":"CaraWilson","id":10343963,"avatar_url":"https://avatars.githubusercontent.com/u/10343963?v=3","gravatar_id":"","url":"https://api.github.com/users/CaraWilson","html_url":"https://github.com/CaraWilson","followers_url":"https://api.github.com/users/CaraWilson/followers","following_url":"https://api.github.com/users/CaraWilson/following{/other_user}","gists_url":"https://api.github.com/users/CaraWilson/gists{/gist_id}","starred_url":"https://api.github.com/users/CaraWilson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/CaraWilson/subscriptions","organizations_url":"https://api.github.com/users/CaraWilson/orgs","repos_url":"https://api.github.com/users/CaraWilson/repos","events_url":"https://api.github.com/users/CaraWilson/events{/privacy}","received_events_url":"https://api.github.com/users/CaraWilson/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/dankelley/oce/labels/argo","name":"argo","color":"bfd4f2"},{"url":"https://api.github.com/repos/dankelley/oce/labels/graphics","name":"graphics","color":"ededed"},{"url":"https://api.github.com/repos/dankelley/oce/labels/Needs%20Recheck","name":"Needs Recheck","color":"fbca04"},{"url":"https://api.github.com/repos/dankelley/oce/labels/not%20an%20oce%20issue","name":"not an oce issue","color":"f7c6c7"},{"url":"https://api.github.com/repos/dankelley/oce/labels/section","name":"section","color":"207de5"}],"state":"open","locked":false,"assignee":{"login":"dankelley","id":99469,"avatar_url":"https://avatars.githubusercontent.com/u/99469?v=3","gravatar_id":"","url":"https://api.github.com/users/dankelley","html_url":"https://github.com/dankelley","followers_url":"https://api.github.com/users/dankelley/followers","following_url":"https://api.github.com/users/dankelley/following{/other_user}","gists_url":"https://api.github.com/users/dankelley/gists{/gist_id}","starred_url":"https://api.github.com/users/dankelley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dankelley/subscriptions","organizations_url":"https://api.github.com/users/dankelley/orgs","repos_url":"https://api.github.com/users/dankelley/repos","events_url":"https://api.github.com/users/dankelley/events{/privacy}","received_events_url":"https://api.github.com/users/dankelley/received_events","type":"User","site_admin":false},"milestone":null,"comments":7,"created_at":"2016-02-19T19:44:14Z","updated_at":"2016-02-20T16:20:30Z","closed_at":null,"body":"I modified your `read_argo_mbari` code (sent via email) so that it can handle any combination of variable in a file, using the notation suggested by Dan (i.e. `if (\"chlorophyll\" %in% names) {# do something})`, and it now reads all the files in, and I was able to make some of the section plots that I was wanted to make - so thanks to both of you! However there is still some funny error going on that I don’t understand.  I can make nitrate plots for data in files `8514HawaiiQC` and `9274HawaiiQC` but those are the only two of the 11 files of interest which contain nitrate.  For example for `5145HawaiiQC` I can plot temperature or oxygen sections, but not nitrate\r\n```r\r\nsource('read_argo_mbari.R')\r\nfile <- \"5145HawaiiQC.txt\"\r\nd <- read.argo.mbari(file)\r\nds <- as.section(d)\r\n```\r\nThese commands produce plots: \r\n```r\r\nplot(ds, xtype='time', which=\"temperature\",ztype='image',\r\n     ylim=c(0,400),zbreaks=seq(10,30,.2))\r\nplot(ds, xtype='time', which=\"oxygen\",ztype='image',\r\n     ylim=c(0,400),zbreaks=seq(150,250,1))\r\n```\r\nbut\r\n```r\r\nplot(ds, xtype='time', which=\"nitrate\",ztype='image',\r\n     ylim=c(0,400),zbreaks=seq(0,20,1))\r\n```\r\nproduces the following error: \r\n```\r\nError in zz[i, ] <- rev(x@data$station[[stationIndices[i]]]@data[[variable]]) : \r\n  replacement has length zero\r\n```\r\nwhich a `traceback()` call says originates in a call to `plotSubsection`\r\n\r\nAny thoughts or suggestions? \r\n\r\nCara \r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/dankelley/oce/issues/comments/186637793","html_url":"https://github.com/dankelley/oce/issues/881#issuecomment-186637793","issue_url":"https://api.github.com/repos/dankelley/oce/issues/881","id":186637793,"user":{"login":"richardsc","id":233584,"avatar_url":"https://avatars.githubusercontent.com/u/233584?v=3","gravatar_id":"","url":"https://api.github.com/users/richardsc","html_url":"https://github.com/richardsc","followers_url":"https://api.github.com/users/richardsc/followers","following_url":"https://api.github.com/users/richardsc/following{/other_user}","gists_url":"https://api.github.com/users/richardsc/gists{/gist_id}","starred_url":"https://api.github.com/users/richardsc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/richardsc/subscriptions","organizations_url":"https://api.github.com/users/richardsc/orgs","repos_url":"https://api.github.com/users/richardsc/repos","events_url":"https://api.github.com/users/richardsc/events{/privacy}","received_events_url":"https://api.github.com/users/richardsc/received_events","type":"User","site_admin":false},"created_at":"2016-02-20T16:20:30Z","updated_at":"2016-02-20T16:20:30Z","body":"> My talk is first thing Monday morning (8:30) on What insights can satellite data provide about the subsurface? (PP11A-03)\r\n\r\nI'll be there! Look forward to meeting in person, and personally thanking you for your help :) (it really has been help, and not a pain in the ass!)"}}