read.lobo {oce} | R Documentation

## Read a lobo data file

### Description

Read a data file created by a LOBO instrument.

### Usage

    read.lobo(file, cols=7, processingLog)

### Arguments

`file` | a connection or a character string giving the name of the file to load.
`cols` | number of columns in dataset.
`processingLog` | if provided, the action item to be stored in the log. (Typically only provided for internal calls; the default that it provides is better for normal calls by a user.)

### Details

This version of `read.lobo` is really quite crude, having been developed mainly for a “predict the Spring bloom” contest at Dalhousie University. In particular, the function assumes that the data columns are exactly as specified in the Examples section; if you reorder the columns or add new ones, this function is unlikely to work correctly. Furthermore, it should be noted that the file format was inferred simply by downloading files; the supplier makes no claims that the format will be fixed in time.

It is also worth noting that there is no `read.oce` equivalent to `read.lobo`, because the file format has no recognizable header.

### Value

An object of `class` `"lobo"`, which has the following slots:

``data``

: a `list` containing the following vectors:

`time`

  the times of observation

`u`

  one horizontal component of velocity (necessarily eastward) [m/s]

`v`

  an orthogonal component of horizontal velocity [m/s]

`salinity`

  the salinity [PSU]

`temperature`

  the in-situ temperature [degC]

`p`

  the pressure [dbar]

`nitrate`

  the nitrate concentration [unit?]

`fluorescence`

  [unit?]

``metadata`` | : a list containing `header`, the header from the data file.
``processingLog`` | : a processingLog of processing, in the standard `oce` format.

### Note

The `oce` author was unable to find a description of the data format, and so `read.lobo` makes some restrictive assumptions about the data format, e.g. trying to find columns whose names contain the following strings `"date"`, `"current across"`, `"current along"`, `"nitrate"`, `"fluorescence"`, `"salinity"`, `"temperature"` and `"Air temperature"`. The `data` slot in the return value will be filled in with these data, or with vectors with `NA` values, for unfound columns.

### Author(s)

Dan Kelley

### Source

The file was created as given in the example.

### References

http://lobo.satlantic.com and http://www.mbari.org/lobo/

### See Also

The documentation for `lobo-class` explains the structure of LOBO objects, and also outlines the other functions dealing with them.

### Examples

    ## Not run:
    library(oce)
    uri <- paste("http://lobo.satlantic.com/cgi-bin/nph-data.cgi?",
      "min_date=20070220&max_date=20070305",
      "&x=date&",
      "y=current_across1,current_along1,nitrate,fluorescence,salinity,temperature&",
      "data_format=text",sep="")
    lobo <- read.lobo(uri)

    ## End(Not run)

[Package oce version 0.9-18 Index]