{"action":"created","issue":{"url":"https://api.github.com/repos/dankelley/oce/issues/812","labels_url":"https://api.github.com/repos/dankelley/oce/issues/812/labels{/name}","comments_url":"https://api.github.com/repos/dankelley/oce/issues/812/comments","events_url":"https://api.github.com/repos/dankelley/oce/issues/812/events","html_url":"https://github.com/dankelley/oce/issues/812","id":124811000,"number":812,"title":"Read BioArgo data","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/I/O","name":"I/O","color":"fbca04"},{"url":"https://api.github.com/repos/dankelley/oce/labels/request","name":"request","color":"bfe5bf"}],"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":32,"created_at":"2016-01-04T18:22:00Z","updated_at":"2016-01-27T03:30:46Z","closed_at":null,"body":"I'd like to use OCE routines with BioArgo data that is available on MBARI's website at http://www.mbari.org/chemsensor/floatviz.htm\r\n\r\nThese files aren't in the standard ARGO format so can't be read by read.drifter.  I've read the data into R (example code below) but am unable to convert it into CTD class (since drifter class doesn’t allow for additional parameters) using as.ctd since the data is only provided as depth, and not pressure as required.  \r\n\r\nThe code below reads in one example file from the MBARI site. It would need to be more flexible to read in all of the available files since different files has different number of parameters depending on which sensors are on the different floats, and the headers are different sizes.\r\n   \r\n```r\r\nBAurl <- url(\"http://www.mbari.org/lobo/Data/FloatVizData/QC/8486HawaiiQC.txt\")\r\n\r\n# Header has repeating variable names (each parameter has a \"QF\", so \r\n# header=T can't be used by read.table).  Additionally each profile has \r\n# a row without any values, so have to use Fill=T with read.table.\r\n# These rows are removed are the file is read in. \r\n\r\ncnames=c(\"Float\",\"Station\",\"Type\",\"Date\",\"Time\",\"Long\",\"Lat\",\"Bdepth\",\"Depth\",\"Depth_QF\",\r\n         \"Temp\",\"Temp_QF\",\"Salinity\",\"Sal_QF\",\"Dens\",\"Dens_QF\",\"Oxygen\",\"Oxygen_QF\",\r\n         \"OxygenSat\",\"OxygenSat_QF\",\"Nitrate\",\"Nitrate_QF\",\"Chlorophyll\",\"Chlorophyll_QF\",\r\n         \"Backscatter\", \"Backscatter_QF\",\"pHinsitu\",\"pHinsitu_QF\",\"pH25C\",\"ph25C_QF\")\r\ncolClasses <- rep(\"numeric\",30)\r\ncolClasses[1:5] <- \"character\"\r\nno_col <- max(count.fields(BAurl, sep = \"\\t\"))\r\n\r\nfloat <- read.table(BAurl,sep=\"\\t\",fill=TRUE,skip=24,col.names=cnames,colClasses=colClasses)\r\nfloat$Date <- paste(float$Date,float$Time)\r\nfloat$Date <- parse_date_time(float$Date, \"%m%d%Y %H%M\")\r\nfloat$Station<-as.numeric(float$Station)\r\n\r\n# Remove rows where Depth = NA \r\n\r\nfloat<-subset(float, !is.na(Depth))\r\n```"},"comment":{"url":"https://api.github.com/repos/dankelley/oce/issues/comments/175371720","html_url":"https://github.com/dankelley/oce/issues/812#issuecomment-175371720","issue_url":"https://api.github.com/repos/dankelley/oce/issues/812","id":175371720,"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},"created_at":"2016-01-27T03:30:46Z","updated_at":"2016-01-27T03:30:46Z","body":"Okay, thanks for the detailed explanation.  \r\n\r\nOn an Argo related note, we also have all of the regular argo data on our ERDDAP. Unfortunately the server we are getting the data from doesn’t retain any of the ARGO id numbers, so there is no way to know which float a profile is from, or to make transects of one float. However if you are interested in getting all profiles from a certain box for a certain timeperiod, which I have wanted to do for some past projects, its much easier getting the data from ERDDAP than sorting through all the different directories on the main ARGO data distribution. \r\n"}}