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 and connect to 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:
- Importing data from your sources
- Uploading into your local MFDB database
- Sampling / grouping this data
- 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.
Besides R, you will also need RPostgres set up to access the database, and PostgreSQL installed if you want to run the database locally too.
Installation of RPostgres will happen automatically, however you need some PostgreSQL libraries before it will work:
apt-get install libpq-dev
Also, you can install the postgresql
package using:
apt-get install postgresql
Some additional instructions are available here: https://wiki.debian.org/PostgreSql
Now, create an mf
database that the user on your computer owns:
$ echo $USER # Check to see who you are, I'm lentinj
lentinj
$ su
# su - postgres
$ psql
postgres=# CREATE USER lentinj;
postgres=# CREATE DATABASE mf OWNER lentinj;
Installation of RPostgres will happen automatically, however you need some PostgreSQL libraries before it will work:
yum install postgresql-devel
Also, you can install the postgresql
package using:
yum install postgresql-server
Some additional instructions are available here: https://fedoraproject.org/wiki/PostgreSQL and some tips when troubleshooting CentOS installations can be found at: http://stackoverflow.com/questions/17633422/psql-fatal-database-user-does-not-exist
Now, create an mf
database that the user on your computer owns:
$ echo $USER # Check to see who you are, I'm lentinj
lentinj
$ su
# su - postgres
$ psql
postgres=# CREATE USER lentinj
postgres=# CREATE DATABASE mf OWNER lentinj;
To install PostgreSQL, download version 9.5 of the database installer from here:
https://www.enterprisedb.com/downloads/postgres-postgresql-downloads
Find the psql shell (SQL shell) in the start menu, and create both an mf
database and user:
postgres=# CREATE USER mf PASSWORD 'mf';
postgres=# CREATE DATABASE mf OWNER mf;
Install using http://postgresapp.com/
Create a database called mf
.
You can install from CRAN:
install.packages('mfdb')
Or use remotes to install this directly:
# install.packages("remotes")
remotes::install_github("gadget-framework/mfdb")
For an introduction to the package, read the package?mfdb
help file in R.
This is also available online.
There are a selection of example scripts in the demo/
folder. The
example-*
scripts show the full process of importing data from specified
sources into the database, then querying this to aggregate into various gadget
model files. The inttest-*
scripts demonstrate other aspects, and also
function as tests to ensure that the library works correctly (thus the ok()
function calls).
Finally, there is documentation on the database schema.
Given the database is setup as above, integration tests and all package
examples can be run with make inttest
.
To run all tests (unit tests, integration, examples and check-as-cran), use
make
.
This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no.613571.