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, log.action)

Arguments

file a connection or a character string giving the name of the file to load.
cols number of columns in dataset.
log.action 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 is a list containing

data a data.frame 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.
processing.log A processing log, 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. requiring that there be exactly 7 columns, whose names in the header are "date", "current across", "current along", "nitrate", "fluorescence", "salinity", and "temperature". If these are not found, read.lobo is likely to fail in some way. Luckily, the code is written in a simple way, so that users should be able to alter it easily if, for example, the names of the current components change to "current to the east", etc.

Author(s)

Dan Kelley

Source

The file was created with the lines given in the example.

References

http://www.satlantic.com/default.asp?mn=1.15.27.139 and http://www.mbari.org/lobo/

See Also

A "lobo" object may be summarized with summary.lobo and plotted with plot.lobo.

Examples

## Not run: 
library(oce)
uri <- paste("http://loboviz.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)
summary(lobo)
## End(Not run)

[Package oce version 0.1-76 Index]