This vignette serves as a brief introduction to the clivartools package.
The package should be installed from github. You'll need the devtools
package
installed.
devtools::install_github("blongworth/amstools")
To interact with the NOSAMS DB, you'll need the odbc package installed and a working connection to the NOSAMS database via ODBC. An ODBC connection string should be stored in an environment variable called CONSTRING. The package has been tested with the Microsoft MSSQL driver on Windows and Mac OS X, and with the unixODBC and FreeTDS drivers on Linux.
If a Data Source Name (DSN) is set up within your odbc system, a CONSTRING variable in the following format will work:
"DSN=database;UID=username;PWD=password"
This can be done from R with the Sys.setenv
command, but this may or may not
be persistent depending on your environment.
First, load the library.
library(clivartools)
Use getCruises and getStations to find what data to work with.
cruises <- getCruises() cruises[1:5] stations <- getStations(cruises[5]) stations[1:5]
Use getProfile
to get data for a profile. If station
or cruise
are vectors, getProfile
will get data from all cruises/stations requested. If station
is not given, all profiles from a cruise or cruises are returned.
data <- getProfile("A16S", 51) head(data)
plotProfile(data)
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