README.md

In sCervino/mfdb: MareFrame DB querying library

MareFrame DB Access package

This package enables automated processing of fisheries data into suitable forms for running ecosystem models against it, e.g. GADGET.

This package contains several distinct sets of functions:

• Create a PostgreSQL database schema (mfdb function)
• Import data into a PostgreSQL database (mfdb_import_* functions)
• Sample / group data from database (other mfdb_* functions)
• Manage GADGET model directories and export data into them (gadget_* functions)

Using this, you can install PostgreSQL locally and have a script automating the process of:

1. Importing data from your sources
2. Uploading into your local MareFrame database
3. Sampling / grouping this data
4. Producing set of GADGET model files ready to be run by GADGET

Also, this libary can be used to connect to a remote database and generate model files from that data.

This work is based on it's predecessor, DST^2.

Prerequisites

Besides R, you also need to have PostgreSQL installed and running on your computer.

Linux (Debian / Ubuntu)

Install the postgresql package using:

apt-get install postgresql

Some additional instructions are available here: https://wiki.debian.org/PostgreSql

If you don't want to use a system-wide database, then investigate https://github.com/mareframe/mfdb-workspace which keeps all the required R dependencies and PostgreSQL database in the local directory.

Otherwise create a database called mf as per the distribution instructions.

Linux (Redhat / Fedora)

Install the postgresql-server package using:

yum install postgresql-server

Some additional instructions are available here: https://fedoraproject.org/wiki/PostgreSQL

If you don't want to use a system-wide database, then investigate https://github.com/mareframe/mfdb-workspace which keeps all the required R dependencies and PostgreSQL database in the local directory.

Otherwise create a database called mf as per the distribution instructions.

Microsoft Windows

Download the latest database installer from here:

http://www.enterprisedb.com/products-services-training/pgdownload#windows

Create a database called mf. http://www.postgresql.org/docs/9.3/static/tutorial-createdb.html

Apple OS X

Install using http://postgresapp.com/

Create a database called mf.

Installing

You can use devtools to install this directly:

# install.packages("devtools")
devtools::install_github("mareframe/mfdb")

Using

Before doing anything, you (or your R script) will need to connect to the database:

> mdb <- mfdb()

See the help entry for the mfdb function for more information.

There are also a selection of example scripts to read through in the demo/ folder.

Acknowledgements

This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no.613571.

sCervino/mfdb documentation built on May 18, 2019, 1:31 p.m.